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view test-data/evolverMammals_both.maf @ 8:9baa871cb1d1 draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8368f7c3190075a0708b9f2d045b35702117eede
author galaxy-australia
date Wed, 15 Feb 2023 05:08:07 +0000
parents 85f68b344286
children
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##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