Mercurial > repos > galaxy-australia > cactus_cactus
diff test-data/evolverMammals.maf @ 0:85f68b344286 draft
"planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8f8363625623f2ff3f04d12d227673ac134eba24"
| author | galaxy-australia |
|---|---|
| date | Mon, 04 Apr 2022 06:27:44 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/evolverMammals.maf Mon Apr 04 06:27:44 2022 +0000 @@ -0,0 +1,238809 @@ +##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 +