Mercurial > repos > galaxy-australia > cactus_export
changeset 6:aaa0d6a8b808 draft
planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
| author | galaxy-australia |
|---|---|
| date | Thu, 12 Jan 2023 02:00:10 +0000 |
| parents | 764845535798 |
| children | 5abf2c2249aa |
| files | cactus_export.xml macros.xml test-data/evolverMammals_noroot.maf |
| diffstat | 3 files changed, 18889 insertions(+), 1279 deletions(-) [+] |
line wrap: on
line diff
--- a/cactus_export.xml Mon Nov 14 06:02:47 2022 +0000 +++ b/cactus_export.xml Thu Jan 12 02:00:10 2023 +0000 @@ -1,5 +1,5 @@ <tool id="cactus_export" name="Cactus: export" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> - <description>whole-genome multiple sequence alignment to other formats.</description> + <description>whole-genome multiple sequence alignment to other formats</description> <macros> <import>macros.xml</import> </macros>
--- a/macros.xml Mon Nov 14 06:02:47 2022 +0000 +++ b/macros.xml Thu Jan 12 02:00:10 2023 +0000 @@ -1,13 +1,12 @@ <macros> - <token name="@TOOL_VERSION@">2.2.4</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">2.4.0</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">20.09</token> - <token name="@DIGEST@">b22eb2ef1d8c6f152d12d0e4300ac68affea5aafb2f7022f9078e8e72e41654d</token> <xml name="requirements"> <requirements> <!-- Cactus is not in bioconda --> <!-- Devoper provides a Docker container --> - <container type="docker">quay.io/comparative-genomics-toolkit/cactus@sha256:@DIGEST@</container> + <container type="docker">quay.io/comparative-genomics-toolkit/cactus:v@TOOL_VERSION@</container> </requirements> </xml> <xml name="citations">
--- a/test-data/evolverMammals_noroot.maf Mon Nov 14 06:02:47 2022 +0000 +++ b/test-data/evolverMammals_noroot.maf Thu Jan 12 02:00:10 2023 +0000 @@ -3422,6 +3422,70 @@ s simRat_chr6.simRat.chr6 11039 11 + 647215 ACAATCTCTTA a +s simMouse_chr6.simMouse.chr6 11603 5 + 636262 ATCCC +s Anc0.Anc0refChr2 6528 5 + 17989 ATCCC +s Anc1.Anc1refChr6 34612 5 + 197743 ATCCC +s Anc2.Anc2refChr17 28482 5 + 28526 ATACA +s mr.mrrefChr0 10664 5 + 130230 ATCCC +s mr.mrrefChr0 119688 5 - 130230 ATCCC +s mr.mrrefChr5 220265 5 + 294540 ATCTC +s simCow_chr6.simCow.chr6 346008 5 + 602619 GCACT +s simDog_chr6.simDog.chr6 336875 5 + 593897 ATACA +s simMouse_chr6.simMouse.chr6 373650 5 + 636262 ATCTC +s simMouse_chr6.simMouse.chr6 624781 5 - 636262 ATCCC +s simRat_chr6.simRat.chr6 365749 5 + 647215 ATCTC +s simRat_chr6.simRat.chr6 636287 5 - 647215 CTCCC +s simRat_chr6.simRat.chr6 11050 5 + 647215 ACCCC + +a +s simMouse_chr6.simMouse.chr6 11608 1 + 636262 A +s Anc0.Anc0refChr2 6533 1 + 17989 A +s Anc1.Anc1refChr6 34617 1 + 197743 A +s Anc2.Anc2refChr17 28491 1 + 28526 A +s mr.mrrefChr0 10669 1 + 130230 A +s mr.mrrefChr0 119693 1 - 130230 A +s mr.mrrefChr5 220270 1 + 294540 A +s simCow_chr6.simCow.chr6 346017 1 + 602619 A +s simDog_chr6.simDog.chr6 336884 1 + 593897 A +s simMouse_chr6.simMouse.chr6 373655 1 + 636262 A +s simMouse_chr6.simMouse.chr6 624786 1 - 636262 A +s simRat_chr6.simRat.chr6 365754 1 + 647215 A +s simRat_chr6.simRat.chr6 636292 1 - 647215 A +s simRat_chr6.simRat.chr6 11055 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 11609 3 + 636262 ACC +s Anc0.Anc0refChr2 6534 3 + 17989 AGC +s Anc1.Anc1refChr6 34618 3 + 197743 AGC +s Anc2.Anc2refChr17 28492 3 + 28526 AGA +s mr.mrrefChr0 10670 3 + 130230 ACC +s mr.mrrefChr0 119694 3 - 130230 GGT +s mr.mrrefChr5 220271 3 + 294540 AGC +s simCow_chr6.simCow.chr6 346018 3 + 602619 AGA +s simDog_chr6.simDog.chr6 336885 3 + 593897 AGA +s simMouse_chr6.simMouse.chr6 373656 3 + 636262 AGC +s simMouse_chr6.simMouse.chr6 624787 3 - 636262 GGT +s simRat_chr6.simRat.chr6 365755 3 + 647215 AGA +s simRat_chr6.simRat.chr6 636293 3 - 647215 GGC +s simRat_chr6.simRat.chr6 11058 3 + 647215 ATC + +a +s simMouse_chr6.simMouse.chr6 11612 3 + 636262 TCA +s Anc0.Anc0refChr2 6537 3 + 17989 TCA +s Anc1.Anc1refChr6 34621 3 + 197743 TCA +s Anc2.Anc2refChr17 28495 3 + 28526 TCA +s mr.mrrefChr0 10673 3 + 130230 TCA +s mr.mrrefChr0 119697 3 - 130230 TCA +s mr.mrrefChr5 220274 3 + 294540 CCA +s simCow_chr6.simCow.chr6 346021 3 + 602619 TAA +s simDog_chr6.simDog.chr6 336888 3 + 593897 TCA +s simMouse_chr6.simMouse.chr6 373659 3 + 636262 CCA +s simMouse_chr6.simMouse.chr6 624790 3 - 636262 TCA +s simRat_chr6.simRat.chr6 365758 3 + 647215 CTA +s simRat_chr6.simRat.chr6 636296 3 - 647215 TCA +s simRat_chr6.simRat.chr6 11067 3 + 647215 TCA + +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 @@ -3483,7 +3547,22 @@ s simRat_chr6.simRat.chr6 11078 4 + 647215 AAGG a -s simMouse_chr6.simMouse.chr6 11631 1 + 636262 T +s simMouse_chr6.simMouse.chr6 11627 7 + 636262 ATACTTT +s Anc0.Anc0refChr2 6551 6 + 17989 ACAG-GG +s Anc1.Anc1refChr2 113615 6 - 144309 ACAG-GG +s Anc1.Anc1refChr6 34635 6 + 197743 ATAC-GT +s Anc2.Anc2refChr0 51606 6 + 56053 ACAG-GG +s mr.mrrefChr0 10688 6 + 130230 ATAC-TT +s mr.mrrefChr0 119700 6 - 130230 ATAC-GC +s mr.mrrefChr5 220294 6 + 294540 AGGG-GT +s simCow_chr6.simCow.chr6 55081 6 + 602619 ACAG-GG +s simDog_chr6.simDog.chr6 48656 6 + 593897 ACAG-GG +s simHuman_chr6.simHuman.chr6 551636 6 - 601863 ACAG-AG +s simMouse_chr6.simMouse.chr6 373679 6 + 636262 AGGG-GT +s simMouse_chr6.simMouse.chr6 624793 6 - 636262 ATAC-GC +s simRat_chr6.simRat.chr6 365778 6 + 647215 AGAG-AT +s simRat_chr6.simRat.chr6 636299 6 - 647215 ACAC-GC +s simRat_chr6.simRat.chr6 11082 6 + 647215 ATAC-TT a s simMouse_chr6.simMouse.chr6 11634 3 + 636262 TCA @@ -3501,6 +3580,114 @@ s simRat_chr6.simRat.chr6 11088 3 + 647215 TCA a +s simMouse_chr6.simMouse.chr6 11637 9 + 636262 GTATTAGCA +s Anc0.Anc0refChr2 6560 9 + 17989 GTGTTAAGA +s Anc1.Anc1refChr2 113624 9 - 144309 GTGTTAAGA +s Anc1.Anc1refChr6 34644 9 + 197743 GTATTATCA +s Anc2.Anc2refChr0 51615 9 + 56053 GTGTTAAGA +s mr.mrrefChr0 10697 9 + 130230 GTATTAGCA +s mr.mrrefChr0 119706 9 - 130230 GTATTAACA +s mr.mrrefChr5 220303 9 + 294540 GTATTATCA +s simCow_chr6.simCow.chr6 55090 9 + 602619 GTGTTAAGA +s simDog_chr6.simDog.chr6 48665 9 + 593897 GTGTTAAGA +s simHuman_chr6.simHuman.chr6 551645 9 - 601863 ATGTAAAGA +s simMouse_chr6.simMouse.chr6 373688 9 + 636262 GTATTATCA +s simMouse_chr6.simMouse.chr6 624799 9 - 636262 GTATTAACA +s simRat_chr6.simRat.chr6 365787 9 + 647215 ATATGAACA +s simRat_chr6.simRat.chr6 636335 9 - 647215 GTATTAACA +s simRat_chr6.simRat.chr6 11091 9 + 647215 GTATTAGTA + +a +s simMouse_chr6.simMouse.chr6 11646 2 + 636262 TG +s Anc0.Anc0refChr2 6569 2 + 17989 TG +s Anc1.Anc1refChr2 113633 2 - 144309 TG +s Anc1.Anc1refChr6 34653 2 + 197743 TG +s Anc2.Anc2refChr0 51624 2 + 56053 TG +s mr.mrrefChr0 10706 2 + 130230 TG +s mr.mrrefChr0 119715 2 - 130230 TG +s mr.mrrefChr5 220312 2 + 294540 TG +s simCow_chr6.simCow.chr6 55099 2 + 602619 TG +s simDog_chr6.simDog.chr6 48674 2 + 593897 TG +s simHuman_chr6.simHuman.chr6 551654 2 - 601863 TG +s simMouse_chr6.simMouse.chr6 373697 2 + 636262 TG +s simMouse_chr6.simMouse.chr6 624808 2 - 636262 TG +s simRat_chr6.simRat.chr6 365796 2 + 647215 TG +s simRat_chr6.simRat.chr6 636346 2 - 647215 TG +s simRat_chr6.simRat.chr6 11100 2 + 647215 TG + +a +s simMouse_chr6.simMouse.chr6 11648 9 + 636262 AATGCTAAA +s Anc0.Anc0refChr2 6571 9 + 17989 AAATGTTAA +s Anc1.Anc1refChr2 113635 9 - 144309 AAATGTTAA +s Anc1.Anc1refChr6 34655 9 + 197743 GAATGTTGA +s Anc2.Anc2refChr0 51626 9 + 56053 AAATGTTAA +s mr.mrrefChr0 10708 9 + 130230 AATGCTAAA +s mr.mrrefChr0 119717 9 - 130230 GAAAGTTGT +s mr.mrrefChr5 220314 9 + 294540 GAATGTTGA +s simCow_chr6.simCow.chr6 55101 8 + 602619 AAATGTTA- +s simDog_chr6.simDog.chr6 48676 9 + 593897 AGATGATAA +s simHuman_chr6.simHuman.chr6 551656 9 - 601863 AAATGTTAA +s simMouse_chr6.simMouse.chr6 373699 9 + 636262 GAATGTTGA +s simMouse_chr6.simMouse.chr6 624810 9 - 636262 GAAAGTTGT +s simRat_chr6.simRat.chr6 365798 9 + 647215 GAGTGCTGA +s simRat_chr6.simRat.chr6 636348 9 - 647215 GAATGTTGA +s simRat_chr6.simRat.chr6 11157 9 + 647215 AATTATACA + +a +s simMouse_chr6.simMouse.chr6 11657 31 + 636262 CTCAGTCTTGGACCAATTCTGATTGTCTAGG +s Anc0.Anc0refChr2 6580 31 + 17989 TTCAGTCTTAGAAAGATTTTGATTATCTGGG +s Anc1.Anc1refChr2 113644 31 - 144309 TTCAGTCTTAGAAAGATTTTGATTATCTGGG +s Anc1.Anc1refChr6 34664 31 + 197743 CTCAGTCTTGAACAGATCTTTATTATCTGGG +s Anc2.Anc2refChr0 51635 31 + 56053 TTCAGTCTTAGAAAGATTTTGATTATCTGGG +s mr.mrrefChr0 10717 31 + 130230 CTCAGTCTTGGACCAATTCTGATTGTCTAGG +s mr.mrrefChr0 119726 31 - 130230 CTCAGTCTTGAACAGACCTTTATTATCTGGG +s mr.mrrefChr5 220323 31 + 294540 CCGAGTCTTGAACAGATCTTTATTATCTGGG +s simCow_chr6.simCow.chr6 55109 15 + 602619 -----------AAAGATTTTCATT-----TG +s simDog_chr6.simDog.chr6 48685 31 + 593897 TTCAGTCTTAGATATATTTTGATTATCTGGG +s simHuman_chr6.simHuman.chr6 551665 31 - 601863 CTCAGCCTTGGAAAGCTTTTGATTGTCCAGG +s simMouse_chr6.simMouse.chr6 373708 31 + 636262 CCGAGTCTTGAACAGATCTTTATTATCTGGG +s simMouse_chr6.simMouse.chr6 624819 31 - 636262 CTCAGTCTTGAACAGACCTTTATTATCTGGG +s simRat_chr6.simRat.chr6 365807 31 + 647215 CTGTATCTTGAACAGATCTTTATTATCTGGG +s simRat_chr6.simRat.chr6 636357 31 - 647215 TTAAGTCTTGAACAGACCTTTATTATCTGGG +s simRat_chr6.simRat.chr6 234007 31 - 647215 CTCAGTCTTGGACAGATTTTGATTGTCTAGG + +a +s simMouse_chr6.simMouse.chr6 11688 11 + 636262 AATTTTCCTTT +s Anc0.Anc0refChr2 6612 11 + 17989 AATGTTCTTTC +s Anc1.Anc1refChr2 113676 11 - 144309 AATGTTCTTTC +s Anc1.Anc1refChr6 34695 11 + 197743 AATGTTCCTTC +s Anc2.Anc2refChr0 51667 11 + 56053 AATGTTCTTTC +s mr.mrrefChr0 10748 11 + 130230 AATTTTCCTTT +s mr.mrrefChr0 119757 11 - 130230 AATGTTCCTTC +s mr.mrrefChr5 220354 11 + 294540 AATGTTCTTTC +s simCow_chr6.simCow.chr6 55125 11 + 602619 AATGTTCTTTT +s simDog_chr6.simDog.chr6 48717 11 + 593897 AGTGTTCCTTC +s simHuman_chr6.simHuman.chr6 551697 11 - 601863 AAAGACGTTTC +s simMouse_chr6.simMouse.chr6 373739 11 + 636262 AATGTTCTTTC +s simMouse_chr6.simMouse.chr6 624850 11 - 636262 AATGTTCCTTC +s simRat_chr6.simRat.chr6 365838 11 + 647215 AATGTTCTCTC +s simRat_chr6.simRat.chr6 636388 11 - 647215 AATGTTCTTTC +s simRat_chr6.simRat.chr6 234038 11 - 647215 AATATGCCTTT + +a +s simMouse_chr6.simMouse.chr6 11699 6 + 636262 TGGTGA +s Anc0.Anc0refChr2 6623 6 + 17989 TTGTAA +s Anc1.Anc1refChr2 113687 6 - 144309 TTGTAA +s Anc1.Anc1refChr6 34706 6 + 197743 TAGTGA +s Anc2.Anc2refChr0 51678 6 + 56053 TTGTAA +s mr.mrrefChr0 10759 6 + 130230 TGGTGA +s mr.mrrefChr0 119768 6 - 130230 TAGTGA +s mr.mrrefChr5 220365 6 + 294540 TAGTGA +s simCow_chr6.simCow.chr6 55136 6 + 602619 TGGTAA +s simDog_chr6.simDog.chr6 48756 6 + 593897 GTCTGA +s simHuman_chr6.simHuman.chr6 551708 6 - 601863 TTGTAA +s simMouse_chr6.simMouse.chr6 373750 6 + 636262 TAGTGA +s simMouse_chr6.simMouse.chr6 624861 6 - 636262 TAGTGA +s simRat_chr6.simRat.chr6 365849 6 + 647215 TAGTGA +s simRat_chr6.simRat.chr6 636399 6 - 647215 TAGTGA +s simRat_chr6.simRat.chr6 234049 6 - 647215 TGGTGA + +a s simMouse_chr6.simMouse.chr6 11705 6 + 636262 CCTGTT s Anc0.Anc0refChr2 6629 6 + 17989 CCTGTT s Anc1.Anc1refChr2 113693 6 - 144309 CCTGTT @@ -3516,6 +3703,96 @@ s simRat_chr6.simRat.chr6 234055 6 - 647215 CCTGTT a +s simMouse_chr6.simMouse.chr6 11711 12 + 636262 GGACAGGGCCAT +s Anc0.Anc0refChr2 6635 12 + 17989 AGGCAGGCCTAT +s Anc1.Anc1refChr2 113699 12 - 144309 AGGCAGGCCTAT +s Anc1.Anc1refChr6 34718 12 + 197743 AGACAGGGCCAT +s Anc2.Anc2refChr0 51690 12 + 56053 AGGCAGGCCTAT +s mr.mrrefChr0 10771 12 + 130230 GGACAGGGCCAT +s mr.mrrefChr0 119774 12 - 130230 AGACAGGGTCAT +s mr.mrrefChr5 220377 12 + 294540 AGGCAGGGCCCT +s simCow_chr6.simCow.chr6 55148 4 + 602619 AGTT-------- +s simDog_chr6.simDog.chr6 48768 12 + 593897 AGGCAGGCCTAT +s simHuman_chr6.simHuman.chr6 551720 12 - 601863 GGGCAGGGCTCT +s simMouse_chr6.simMouse.chr6 373762 12 + 636262 AGGCAGGGCCCT +s simMouse_chr6.simMouse.chr6 624873 12 - 636262 AGACAGGGTCAT +s simRat_chr6.simRat.chr6 365861 12 + 647215 AGGCAGTGCCAT +s simRat_chr6.simRat.chr6 636405 12 - 647215 AGGCAGAGCCAT +s simRat_chr6.simRat.chr6 234061 12 - 647215 GGACAGGGCCAT + +a +s simMouse_chr6.simMouse.chr6 11723 16 + 636262 TCGCTCATATTCATTT +s Anc0.Anc0refChr2 6654 16 + 17989 TCATTTAAGTCTAGTT +s Anc1.Anc1refChr2 113718 16 - 144309 TCATTTAAGTCTAGTT +s Anc1.Anc1refChr6 34730 16 + 197743 TTGCTCAATACCATTT +s Anc2.Anc2refChr0 51709 16 + 56053 TCATTTAAGTCTAGTT +s mr.mrrefChr0 10783 16 + 130230 TCGCTCATATTCATTT +s mr.mrrefChr0 119786 16 - 130230 TTGCTCAATACCATTT +s mr.mrrefChr5 220389 16 + 294540 TTGCTCAATACCATTT +s simCow_chr6.simCow.chr6 55152 8 + 602619 --------GTTGAGTT +s simDog_chr6.simDog.chr6 48787 16 + 593897 TCATTTAAGTCTAGTT +s simHuman_chr6.simHuman.chr6 551739 16 - 601863 TTGCTCAAAACCAGTG +s simMouse_chr6.simMouse.chr6 373774 16 + 636262 TTGCTCAATACCATTT +s simMouse_chr6.simMouse.chr6 624885 16 - 636262 TTGCTCAATACCATTT +s simRat_chr6.simRat.chr6 365873 16 + 647215 TTGCTCAGTTCCATTT +s simRat_chr6.simRat.chr6 636417 16 - 647215 TTGCTCAATACCATTT +s simRat_chr6.simRat.chr6 234073 16 - 647215 TTGCTCATATTCATTT + +a +s simMouse_chr6.simMouse.chr6 11739 3 + 636262 TCA +s Anc0.Anc0refChr2 6680 3 + 17989 TCA +s Anc1.Anc1refChr2 113744 3 - 144309 TCA +s Anc1.Anc1refChr6 34746 3 + 197743 TCA +s Anc2.Anc2refChr0 51735 3 + 56053 TCA +s mr.mrrefChr0 10799 3 + 130230 TCA +s mr.mrrefChr0 119802 3 - 130230 TCA +s mr.mrrefChr5 220405 3 + 294540 TCA +s simCow_chr6.simCow.chr6 55170 3 + 602619 TGA +s simDog_chr6.simDog.chr6 48813 3 + 593897 TCA +s simHuman_chr6.simHuman.chr6 551768 3 - 601863 TCA +s simMouse_chr6.simMouse.chr6 373790 3 + 636262 TCA +s simMouse_chr6.simMouse.chr6 624901 3 - 636262 TCA +s simRat_chr6.simRat.chr6 365889 3 + 647215 TCA +s simRat_chr6.simRat.chr6 636433 3 - 647215 TCA +s simRat_chr6.simRat.chr6 234089 3 - 647215 TCA + +a +s simMouse_chr6.simMouse.chr6 11742 16 + 636262 TGGTGAAGACGTTTGT +s Anc0.Anc0refChr2 6685 16 + 17989 TAGTGAACACCCGAGT +s Anc1.Anc1refChr2 113749 16 - 144309 TAGTGAACACCCGAGT +s Anc1.Anc1refChr6 34749 16 + 197743 TGGTGAAGACCTTTGT +s Anc2.Anc2refChr0 51740 16 + 56053 TAGTGAACACCCGAGT +s mr.mrrefChr0 10802 16 + 130230 TGGTGAAGACGTTTGT +s mr.mrrefChr0 119805 16 - 130230 TGGTAAAAACCTTCGT +s mr.mrrefChr5 220408 16 + 294540 TGGTGAAGATTTATGT +s simCow_chr6.simCow.chr6 55175 16 + 602619 TGGTGAGCACCCGCGT +s simDog_chr6.simDog.chr6 48818 16 + 593897 TAGTGAAGGCTTGAGG +s simHuman_chr6.simHuman.chr6 551773 16 - 601863 TAGTGAACACCCTTGT +s simMouse_chr6.simMouse.chr6 373793 16 + 636262 TGGTGAAGATTTATGT +s simMouse_chr6.simMouse.chr6 624904 16 - 636262 TGGTAAAAACCTTCGT +s simRat_chr6.simRat.chr6 365892 16 + 647215 TGTTGAAGACCTTCGC +s simRat_chr6.simRat.chr6 636436 16 - 647215 TGGTGAGGGCCTTTGT +s simRat_chr6.simRat.chr6 234092 16 - 647215 TGGTGAAGACTTTTGT + +a +s simMouse_chr6.simMouse.chr6 11758 3 + 636262 TGG +s Anc0.Anc0refChr2 6701 3 + 17989 TGG +s Anc1.Anc1refChr2 113765 3 - 144309 TGG +s Anc1.Anc1refChr6 34765 3 + 197743 TGG +s Anc2.Anc2refChr0 51756 3 + 56053 TGG +s mr.mrrefChr0 10818 3 + 130230 TGG +s mr.mrrefChr0 119821 3 - 130230 GAG +s mr.mrrefChr5 220424 3 + 294540 TGG +s simCow_chr6.simCow.chr6 55191 3 + 602619 TGG +s simDog_chr6.simDog.chr6 48834 3 + 593897 TGG +s simHuman_chr6.simHuman.chr6 551789 3 - 601863 TGG +s simMouse_chr6.simMouse.chr6 373809 3 + 636262 TGG +s simMouse_chr6.simMouse.chr6 624920 3 - 636262 GAG +s simRat_chr6.simRat.chr6 365908 3 + 647215 CAG +s simRat_chr6.simRat.chr6 636470 3 - 647215 AGG +s simRat_chr6.simRat.chr6 234108 3 - 647215 TGG + +a s simMouse_chr6.simMouse.chr6 11761 18 + 636262 TCTATTCACTGGTTAGAA s Anc0.Anc0refChr2 6704 18 + 17989 CATGTTTGCTAATAGGGG s Anc1.Anc1refChr2 113768 18 - 144309 CATGTTTGCTAATAGGGG @@ -3531,10 +3808,75 @@ 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 +s simMouse_chr6.simMouse.chr6 11779 16 + 636262 AGAGCTACCTGAATAT +s Anc0.Anc0refChr2 6722 14 + 17989 CA--CTCCCTGAGCAC +s Anc1.Anc1refChr2 113786 14 - 144309 CA--CTCCCTGAGCAC +s Anc1.Anc1refChr6 34786 14 + 197743 CA--CTACCTGAATAT +s Anc2.Anc2refChr0 51777 14 + 56053 CA--CTCCCTGAGCAC +s mr.mrrefChr0 10839 14 + 130230 AG--CTACCTGAATAT +s mr.mrrefChr0 119824 14 - 130230 CA--CTGCCTGAATAC +s mr.mrrefChr5 220445 14 + 294540 CA--CTACCTGAATAT +s simCow_chr6.simCow.chr6 55212 14 + 602619 CA--CTACCTGAGCAC +s simDog_chr6.simDog.chr6 48855 14 + 593897 CA--CTCACTGAGCAC +s simHuman_chr6.simHuman.chr6 551810 14 - 601863 CA--CTCCATGAGCAC +s simMouse_chr6.simMouse.chr6 373830 14 + 636262 CA--CTACCTGAATAT +s simMouse_chr6.simMouse.chr6 624923 14 - 636262 CA--CTGCCTGAATAC +s simRat_chr6.simRat.chr6 365929 14 + 647215 CA--ATACCTGAATAT +s simRat_chr6.simRat.chr6 636473 14 - 647215 CA--CTACCTGAATAC +s simRat_chr6.simRat.chr6 234129 14 - 647215 TG--CTACCCGAATAC + +a +s simMouse_chr6.simMouse.chr6 11795 30 + 636262 AGTACTCCTGTAGTGGCACATACTTTGTAG +s Anc0.Anc0refChr2 6740 27 + 17989 AGCACTCCTGTGGC---ACATTCCGTGCGG +s Anc1.Anc1refChr2 113804 27 - 144309 AGCACTCCTGTGGC---ACATTCCGTGCGG +s Anc1.Anc1refChr6 34800 30 + 197743 AGTACTCCTGTGGTTGAACATTCTTTGTAG +s Anc2.Anc2refChr0 51795 27 + 56053 AGCACTCCTGTGGC---ACATTCCGTGCGG +s mr.mrrefChr0 10853 30 + 130230 AGTACTCCTGTAGTGGCACATACTTTGTAG +s mr.mrrefChr0 119838 30 - 130230 AGTACTCCTGTGGTTGAATGTTCTTTGTAG +s mr.mrrefChr5 220459 30 + 294540 AGTACTCCTGTGGTTGAGCATTCTTTGCAG +s simCow_chr6.simCow.chr6 55230 27 + 602619 AGCACTCCTGTGGC---ACATTCCGTGCGG +s simDog_chr6.simDog.chr6 48873 3 + 593897 AGC--------------------------- +s simHuman_chr6.simHuman.chr6 551828 27 - 601863 AGCCCTCGTGTGGC---ACATTACTTGTAG +s simMouse_chr6.simMouse.chr6 373844 30 + 636262 AGTACTCCTGTGGTTGAGCATTCTTTGCAG +s simMouse_chr6.simMouse.chr6 624937 30 - 636262 AGTACTCCTGTGGTTGAATGTTCTTTGTAG +s simRat_chr6.simRat.chr6 365943 30 + 647215 AGGACTCCTGTGGTTGAACATTCTTTACGG +s simRat_chr6.simRat.chr6 636487 30 - 647215 AGTACTCCTGTGGTTGAACATTCTTTATAG +s simRat_chr6.simRat.chr6 234143 30 - 647215 AGTACTCCTGTAGTGGAACATTCTTTGTAT + +a +s simMouse_chr6.simMouse.chr6 11825 11 + 636262 TGTCTGTATTG +s Anc0.Anc0refChr2 6767 6 + 17989 AATGTG----- +s Anc1.Anc1refChr2 113831 6 - 144309 AATGTG----- +s Anc1.Anc1refChr6 34830 11 + 197743 TGTCTGTATTG +s Anc2.Anc2refChr0 51822 6 + 56053 AATGTG----- +s mr.mrrefChr0 10883 11 + 130230 TGTCTGTATTG +s mr.mrrefChr0 119868 11 - 130230 TGTCTGTATTG +s mr.mrrefChr5 220489 11 + 294540 CACCTGTTTTG +s simCow_chr6.simCow.chr6 55258 6 + 602619 AATGTG----- +s simHuman_chr6.simHuman.chr6 551855 6 - 601863 AGTGTA----- +s simMouse_chr6.simMouse.chr6 373876 11 + 636262 CACCTGTTTTG +s simMouse_chr6.simMouse.chr6 624967 11 - 636262 TGTCTGTATTG +s simRat_chr6.simRat.chr6 365973 11 + 647215 CGCCTGTTTTG +s simRat_chr6.simRat.chr6 636517 11 - 647215 TGTCTGTATTG +s simRat_chr6.simRat.chr6 234173 11 - 647215 TGTCTGTATTA + +a +s simMouse_chr6.simMouse.chr6 11836 10 + 636262 GATATTGCAG +s Anc1.Anc1refChr6 34841 10 + 197743 GATATTGCAG +s mr.mrrefChr0 10894 10 + 130230 GATATTGCAG +s mr.mrrefChr0 119879 10 - 130230 GGTGTTACAG +s simMouse_chr6.simMouse.chr6 624978 10 - 636262 GGTGTTACAG +s simRat_chr6.simRat.chr6 636528 10 - 647215 GATATTGCAG +s simRat_chr6.simRat.chr6 234184 10 - 647215 GATATTGCAA + +a +s simMouse_chr6.simMouse.chr6 11846 5 + 636262 GGTCA +s Anc1.Anc1refChr6 34851 4 + 197743 GG-CT +s mr.mrrefChr0 10904 4 + 130230 GG-CA +s mr.mrrefChr0 123476 4 - 130230 AT-TT +s simMouse_chr6.simMouse.chr6 629203 4 - 636262 AT-TT +s simRat_chr6.simRat.chr6 640640 4 - 647215 AT-CT +s simRat_chr6.simRat.chr6 234194 4 - 647215 GA-CA a s simMouse_chr6.simMouse.chr6 11851 49 + 636262 GGTTAAGTACACATTTAAGGTATAGTACTTCTTGCAATTTATGATGATC @@ -10000,17 +10342,18 @@ 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 +s simMouse_chr6.simMouse.chr6 27949 31 + 636262 CTATCATTCATTTAGCCATACTCTTTACTGG +s Anc0.Anc0refChr9 6081 31 + 35212 TTAATATTCATTTAACCATGATCTTTACTGG +s Anc1.Anc1refChr2 129843 31 - 144309 TTAATATTCATTTAACCATGATCTTTACTGG +s Anc2.Anc2refChr0 25088 31 - 56053 TTAATATTAATTTAACCAAGATCTTTACTGA +s mr.mrrefChr0 26427 31 + 130230 CTATCATTCATTTAGCCATACTCTTTACTGG +s mr.mrrefChr0 26225 31 + 130230 TTTACATTCATTTAGCCATACTCTTTACTGG +s simCow_chr6.simCow.chr6 566396 31 - 602619 TTAATATCAATGTAACCACGATCTTTGCCGA +s simDog_chr6.simDog.chr6 561915 31 - 593897 TTAATGTTAGTTTTAACAAAATCTTCACTGA +s simHuman_chr6.simHuman.chr6 569281 31 - 601863 TTAATATTTAGTTAACCATGATCTTTACTGC +s simMouse_chr6.simMouse.chr6 27753 30 + 636262 TTTACATTCATTTAGCCATACTCTTTACTG- +s simRat_chr6.simRat.chr6 19854 31 + 647215 TTTAGATTCATTTAGCCATACTCTTTACTGG +s simRat_chr6.simRat.chr6 20049 31 + 647215 CTATCATTCTTTTAGCCATACTCTTTACTGG a s simMouse_chr6.simMouse.chr6 27980 1 + 636262 C @@ -10026,41 +10369,99 @@ 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 +s simMouse_chr6.simMouse.chr6 27981 6 + 636262 CTCCCA +s Anc0.Anc0refChr9 6130 6 + 35212 CTCCCA +s Anc1.Anc1refChr2 129892 6 - 144309 CTCCCA +s Anc2.Anc2refChr0 25137 6 - 56053 CTCGCA +s mr.mrrefChr0 26459 6 + 130230 CTCCCA +s mr.mrrefChr0 26259 6 + 130230 CTCCCA +s simCow_chr6.simCow.chr6 566445 6 - 602619 CCCACA +s simDog_chr6.simDog.chr6 561964 6 - 593897 CTTGCA +s simHuman_chr6.simHuman.chr6 569330 6 - 601863 CTCCCA +s simMouse_chr6.simMouse.chr6 27785 6 + 636262 CTCCCA +s simRat_chr6.simRat.chr6 20081 6 + 647215 CTCCCA + +a +s simMouse_chr6.simMouse.chr6 27987 20 + 636262 ATCATCCTACTGCAATGTGT +s Anc0.Anc0refChr9 6136 20 + 35212 ATTATCTTACTGAGATGTGT +s Anc1.Anc1refChr2 129898 20 - 144309 ATTATCTTACTGAGATGTGT +s Anc2.Anc2refChr0 25143 20 - 56053 ATTATCTCACTGAGATGTGT +s mr.mrrefChr0 26465 20 + 130230 ATCATCCTACTGCAATGTGT +s mr.mrrefChr0 26265 20 + 130230 ATCATCCTACTGCAATGTGT +s simCow_chr6.simCow.chr6 566451 20 - 602619 ATTGTCTCACTGAGCTGTGT +s simDog_chr6.simDog.chr6 561970 17 - 593897 ATTATCTCACTGGGATG--- +s simHuman_chr6.simHuman.chr6 569336 20 - 601863 ATTATCTTACTTAGATGTGT +s simMouse_chr6.simMouse.chr6 27791 17 + 636262 ATCATCCTGCTGCAATG--- +s simRat_chr6.simRat.chr6 19886 20 + 647215 ATCACCCTACTGCAATGTGT +s simRat_chr6.simRat.chr6 20087 20 + 647215 ATCATCCTACTGCAATGTGT + +a +s simMouse_chr6.simMouse.chr6 28007 19 + 636262 TGGGATCAGGTGTGGACAG +s Anc0.Anc0refChr9 6156 19 + 35212 TGGGATCAGATGTAGATAG +s Anc1.Anc1refChr2 129918 19 - 144309 TGGGATCAGATGTAGATAG +s Anc2.Anc2refChr0 25163 19 - 56053 TGGGATCAGATGTAGATCG +s mr.mrrefChr0 26485 19 + 130230 TGGGATCAGGTGTGGACAG +s mr.mrrefChr0 26285 19 + 130230 TGGGATTAGATGTTGACAG +s simCow_chr6.simCow.chr6 566471 19 - 602619 TGGGATCAGATGTTGCTGG +s simDog_chr6.simDog.chr6 561987 11 - 593897 --------GATGTAGATCG +s simHuman_chr6.simHuman.chr6 569356 19 - 601863 TGGGTTCATATGTAGATAC +s simMouse_chr6.simMouse.chr6 27808 17 + 636262 --GGATTAGATGTTGACAG +s simRat_chr6.simRat.chr6 19906 19 + 647215 TGGGATGAGATGTGGACAG +s simRat_chr6.simRat.chr6 20116 19 + 647215 TGGGGTCAGATGTGGACAG + +a +s simMouse_chr6.simMouse.chr6 28026 6 + 636262 CTTACT +s Anc0.Anc0refChr9 6175 6 + 35212 ATCATT +s Anc1.Anc1refChr2 129937 6 - 144309 ATCATT +s Anc2.Anc2refChr0 25182 6 - 56053 ATCATT +s mr.mrrefChr0 26504 6 + 130230 CTTACT +s mr.mrrefChr0 26304 6 + 130230 ATCATT +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 27825 6 + 636262 ATCATG +s simRat_chr6.simRat.chr6 19925 6 + 647215 ATTACT +s simRat_chr6.simRat.chr6 20137 6 + 647215 TTTATT + +a +s simMouse_chr6.simMouse.chr6 28032 39 + 636262 TTGAAGAGCCCTCAAGGGCTCCTCAGCCCAAATAAAACA +s Anc0.Anc0refChr9 6181 31 + 35212 TTGAAGAGCCCTCAGG--------AGAGCAAATAGCACA +s Anc1.Anc1refChr2 129943 39 - 144309 TTGAAGAGCCCTCAGGGGCTCAGCAGAGCAAATAGCACA +s Anc2.Anc2refChr0 25188 31 - 56053 TTGAAGAGGCCTCAGG--------AGAGTAAATAGCACA +s mr.mrrefChr0 26516 39 + 130230 TTGAAGAGCCCGCAAGGGCCTCGCAGCCCAAATAAAACA +s mr.mrrefChr0 26310 39 + 130230 TTGAAGAGCCCTCAAGGGCTCTGCATCTCAAATAGAACT +s simCow_chr6.simCow.chr6 566496 31 - 602619 TTGAAGAGGCCTTAGG--------AGAGTAAATAGCACA +s simDog_chr6.simDog.chr6 562004 31 - 593897 CAGAAGAGGCCTCAGG--------AGGGTAAATAGCACA +s simHuman_chr6.simHuman.chr6 569381 39 - 601863 TTGAAGAGCCCTCAGGGCCTCAGGATAACAAATGGCACC +s simMouse_chr6.simMouse.chr6 27831 38 + 636262 TTGAAGAGCC-TCAAGGGCTCTGCAGCTCAGATAAAACT +s simRat_chr6.simRat.chr6 19931 39 + 647215 TTGAAGAGCCCTCAAGGGCTTTGCATCCCAAAAAGAACA +s simRat_chr6.simRat.chr6 20168 39 + 647215 TTGAAGAGCCCGCAAGGGCCTGGCAGCCCAAATAAAACA + +a +s simMouse_chr6.simMouse.chr6 28071 6 + 636262 ACTATA +s Anc0.Anc0refChr9 6282 6 + 35212 ACTAAA +s Anc1.Anc1refChr2 130052 6 - 144309 ACTAAA +s Anc2.Anc2refChr0 25289 6 - 56053 AATCAA +s mr.mrrefChr0 26555 6 + 130230 ACTAAA +s mr.mrrefChr0 26349 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 27869 6 + 636262 ACTAAA +s simRat_chr6.simRat.chr6 19970 6 + 647215 ACTAAA +s simRat_chr6.simRat.chr6 20207 6 + 647215 ACTAAA + +a +s simMouse_chr6.simMouse.chr6 28077 5 + 636262 GTGGT +s Anc0.Anc0refChr9 6288 5 + 35212 GTAGT +s Anc1.Anc1refChr2 130058 5 - 144309 GTAGT +s Anc2.Anc2refChr0 25310 5 - 56053 GTAAT +s mr.mrrefChr0 26561 5 + 130230 GTAGT +s mr.mrrefChr0 26355 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 27875 5 + 636262 GTAGT +s simRat_chr6.simRat.chr6 19976 5 + 647215 GTAGT +s simRat_chr6.simRat.chr6 20213 5 + 647215 GTAGT a s simMouse_chr6.simMouse.chr6 28082 1 + 636262 A @@ -10073,6 +10474,48 @@ s simRat_chr6.simRat.chr6 20218 1 + 647215 A a +s simMouse_chr6.simMouse.chr6 28083 2 + 636262 AG +s Anc0.Anc0refChr9 6294 2 + 35212 AA +s Anc1.Anc1refChr2 130064 2 - 144309 AA +s Anc2.Anc2refChr0 25316 2 - 56053 AA +s mr.mrrefChr0 26567 2 + 130230 AG +s mr.mrrefChr0 26360 2 + 130230 AA +s simCow_chr6.simCow.chr6 566615 2 - 602619 TA +s simDog_chr6.simDog.chr6 562132 2 - 593897 AA +s simHuman_chr6.simHuman.chr6 569499 1 - 601863 -A +s simMouse_chr6.simMouse.chr6 27880 2 + 636262 AA +s simRat_chr6.simRat.chr6 19981 2 + 647215 AC +s simRat_chr6.simRat.chr6 20219 2 + 647215 AG + +a +s simMouse_chr6.simMouse.chr6 28085 7 + 636262 CTTAGGC +s Anc0.Anc0refChr9 6296 7 + 35212 CTTAGGC +s Anc1.Anc1refChr2 130066 7 - 144309 CTTAGGC +s Anc2.Anc2refChr0 25318 7 - 56053 CTTATGA +s mr.mrrefChr0 26569 7 + 130230 CTTAGGC +s mr.mrrefChr0 26362 7 + 130230 CATAGGC +s simCow_chr6.simCow.chr6 566617 6 - 602619 CTTATG- +s simDog_chr6.simDog.chr6 562134 7 - 593897 CTTATGA +s simHuman_chr6.simHuman.chr6 569500 7 - 601863 CCAAGGC +s simMouse_chr6.simMouse.chr6 27883 7 + 636262 CATAGGC +s simRat_chr6.simRat.chr6 19983 7 + 647215 CTTAGGC +s simRat_chr6.simRat.chr6 20221 7 + 647215 CTTAGGG + +a +s simMouse_chr6.simMouse.chr6 28092 17 + 636262 TTATTATGAACATGTTA +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 26576 17 + 130230 TTATTATGAACATGTTA +s mr.mrrefChr0 26369 17 + 130230 CTATTATGAACATGTTA +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 27890 17 + 636262 CTATTATGAACATGTTA +s simRat_chr6.simRat.chr6 19990 17 + 647215 CTATTATGAACCTGTTA +s simRat_chr6.simRat.chr6 20228 17 + 647215 TCATTATGAATATGTTA + +a s simMouse_chr6.simMouse.chr6 28109 1 + 636262 T s Anc0.Anc0refChr9 6314 1 + 35212 T s Anc1.Anc1refChr2 130090 1 - 144309 T @@ -10084,7 +10527,46 @@ s simRat_chr6.simRat.chr6 20245 1 + 647215 T a -s simMouse_chr6.simMouse.chr6 28116 1 + 636262 C +s simMouse_chr6.simMouse.chr6 28110 35 + 636262 GTGCACCACAGAATAATATTTAGTTTGCTAGTAGT +s Anc0.Anc0refChr9 6315 30 + 35212 GTGGAC-ACAG----TTATTTGGTCTAGTGCCAGT +s Anc1.Anc1refChr2 130091 34 - 144309 GTGGAC-ACAGAATATTATTTGGTCTAGTGCCAGT +s Anc2.Anc2refChr0 25337 30 - 56053 GTGGAC-ACAG----TTGTTTGGCCTAGTGCCCTT +s mr.mrrefChr0 26594 34 + 130230 GTGCAC-ACAGAATAATATTTAGTTTGCTAGCAGT +s mr.mrrefChr0 26386 34 + 130230 GTGTAC-ATAGGATAATAGATAGTGCTCTAGCAGT +s simCow_chr6.simCow.chr6 566635 30 - 602619 ACGGAC-ACAG----TTGTTTGGCCTAATGCGATT +s simDog_chr6.simDog.chr6 562154 30 - 593897 GTGGAC-TCAG----TTGTATGGCCTTGTACCCTT +s simHuman_chr6.simHuman.chr6 569525 30 - 601863 GTGGAC-ACAG----TTATTTGGACTAGTGCCGAT +s simMouse_chr6.simMouse.chr6 27907 34 + 636262 GTGTAC-ATAGGATAATAGATAGTGCTCTAGCAGT +s simRat_chr6.simRat.chr6 20008 34 + 647215 GTGTAT-ATGGAATAATAATTAGTTCTATAGTGGC +s simRat_chr6.simRat.chr6 20246 34 + 647215 GTGCAC-ATAGGATAATAATTAGCTCTCTAGCAGT + +a +s simMouse_chr6.simMouse.chr6 28145 3 + 636262 TAA +s Anc0.Anc0refChr9 6347 3 + 35212 TAT +s Anc1.Anc1refChr2 130127 3 - 144309 TAT +s Anc2.Anc2refChr0 25369 3 - 56053 TAT +s mr.mrrefChr0 26630 3 + 130230 TAA +s mr.mrrefChr0 26422 3 + 130230 TAA +s simCow_chr6.simCow.chr6 566667 3 - 602619 TAT +s simDog_chr6.simDog.chr6 562186 3 - 593897 TAT +s simHuman_chr6.simHuman.chr6 569557 3 - 601863 TAT +s simMouse_chr6.simMouse.chr6 27943 3 + 636262 TAA +s simRat_chr6.simRat.chr6 20044 3 + 647215 TAA +s simRat_chr6.simRat.chr6 20282 3 + 647215 TAA + +a +s simMouse_chr6.simMouse.chr6 28148 2 + 636262 GA +s Anc0.Anc0refChr9 6350 1 + 35212 -A +s Anc1.Anc1refChr2 130130 2 - 144309 AA +s Anc2.Anc2refChr0 25372 1 - 56053 -A +s mr.mrrefChr0 26633 2 + 130230 GA +s mr.mrrefChr0 26425 2 + 130230 GA +s simCow_chr6.simCow.chr6 566670 1 - 602619 -A +s simDog_chr6.simDog.chr6 562189 1 - 593897 -A +s simHuman_chr6.simHuman.chr6 569560 1 - 601863 A- +s simMouse_chr6.simMouse.chr6 27947 2 + 636262 GA +s simRat_chr6.simRat.chr6 20047 2 + 647215 GA +s simRat_chr6.simRat.chr6 20285 2 + 647215 GA a s simMouse_chr6.simMouse.chr6 28150 14 + 636262 CTATCACCAGCACA @@ -11250,6 +11732,76 @@ s simRat_chr6.simRat.chr6 22239 6 + 647215 CCTAGA a +s simMouse_chr6.simMouse.chr6 29996 2 + 636262 GA +s Anc0.Anc0refChr9 7627 2 + 35212 GG +s Anc1.Anc1refChr2 131448 2 - 144309 GG +s Anc2.Anc2refChr0 26719 2 - 56053 GG +s mr.mrrefChr0 28453 2 + 130230 GA +s mr.mrrefChr0 28020 2 + 130230 GG +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 29552 2 + 636262 GG +s simRat_chr6.simRat.chr6 21673 2 + 647215 GG +s simRat_chr6.simRat.chr6 22245 2 + 647215 GA + +a +s simMouse_chr6.simMouse.chr6 29998 13 + 636262 TTGTTATAAATAG +s Anc0.Anc0refChr9 7629 13 + 35212 TTGTTAGGACTAG +s Anc1.Anc1refChr2 131450 13 - 144309 TTGTTAGGACTAG +s Anc2.Anc2refChr0 26721 13 - 56053 TTGGTAGGCCATG +s mr.mrrefChr0 28455 13 + 130230 TTGTTATAAATAG +s mr.mrrefChr0 28022 13 + 130230 GTGTTAAGAATAG +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 29554 13 + 636262 GTCTTAAGAATAG +s simRat_chr6.simRat.chr6 21675 13 + 647215 TTGTTAAGAATAG +s simRat_chr6.simRat.chr6 22255 13 + 647215 TGATTCCAAAGAA + +a +s simMouse_chr6.simMouse.chr6 30011 1 + 636262 G +s Anc0.Anc0refChr9 7642 1 + 35212 G +s Anc1.Anc1refChr2 131463 1 - 144309 G +s Anc2.Anc2refChr0 26734 1 - 56053 G +s mr.mrrefChr0 28468 1 + 130230 G +s mr.mrrefChr0 28035 1 + 130230 G +s simCow_chr6.simCow.chr6 568588 1 - 602619 G +s simDog_chr6.simDog.chr6 563725 1 - 593897 G +s simHuman_chr6.simHuman.chr6 570808 1 - 601863 G +s simMouse_chr6.simMouse.chr6 29567 1 + 636262 G +s simRat_chr6.simRat.chr6 21688 1 + 647215 T +s simRat_chr6.simRat.chr6 22275 1 + 647215 G + +a +s simMouse_chr6.simMouse.chr6 30012 3 + 636262 ATG +s Anc0.Anc0refChr9 7643 3 + 35212 ATG +s Anc1.Anc1refChr2 131464 3 - 144309 ATG +s Anc2.Anc2refChr0 26735 3 - 56053 GAG +s mr.mrrefChr0 28469 3 + 130230 ATG +s mr.mrrefChr0 28036 3 + 130230 ATG +s simCow_chr6.simCow.chr6 568589 3 - 602619 GAA +s simDog_chr6.simDog.chr6 563726 3 - 593897 GAG +s simHuman_chr6.simHuman.chr6 570809 3 - 601863 ATG +s simMouse_chr6.simMouse.chr6 29569 3 + 636262 ATG +s simRat_chr6.simRat.chr6 21689 3 + 647215 ATG +s simRat_chr6.simRat.chr6 22276 3 + 647215 ATG + +a +s simMouse_chr6.simMouse.chr6 30015 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 28472 4 + 130230 TTGG +s mr.mrrefChr0 28039 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 29572 4 + 636262 TTGG +s simRat_chr6.simRat.chr6 21807 4 + 647215 TTGG +s simRat_chr6.simRat.chr6 22279 4 + 647215 TTGG + +a s simMouse_chr6.simMouse.chr6 30019 4 + 636262 GTGT s Anc0.Anc0refChr9 7650 4 + 35212 GTGT s Anc1.Anc1refChr2 131471 4 - 144309 GTGT @@ -11261,6 +11813,34 @@ s simRat_chr6.simRat.chr6 22283 4 + 647215 GTAT a +s simMouse_chr6.simMouse.chr6 30023 20 + 636262 TTATCTGTTAAATGTGAACA +s Anc0.Anc0refChr9 7654 20 + 35212 TTGTCTATTAGATGTAAACA +s Anc1.Anc1refChr2 131475 20 - 144309 TTGTCTATTAGATGTAAACA +s Anc2.Anc2refChr0 26746 20 - 56053 TTGTCTATTAGGTGTAAACA +s mr.mrrefChr0 28480 20 + 130230 TTATCTGTTAAATGTGAACA +s mr.mrrefChr0 28043 20 + 130230 GTGTTTATCTAATGTGAACA +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 29576 20 + 636262 GTGTTCATGTAATGTGAACA +s simRat_chr6.simRat.chr6 21811 20 + 647215 GTGTTTATCTAATGAGAACA +s simRat_chr6.simRat.chr6 22287 20 + 647215 TTATCTGTTAGATGTGAACA + +a +s simMouse_chr6.simMouse.chr6 30043 10 + 636262 GGGTTGCATT +s Anc0.Anc0refChr9 7677 10 + 35212 GGGCTGTCTG +s Anc1.Anc1refChr2 131498 10 - 144309 GGGCTGTCTG +s Anc2.Anc2refChr0 26769 10 - 56053 GGGCTGTCCG +s mr.mrrefChr0 28500 10 + 130230 GGGTTGCATT +s mr.mrrefChr0 28067 10 + 130230 AGACTGTCTG +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 29600 10 + 636262 AGACTGTCTG +s simRat_chr6.simRat.chr6 21835 10 + 647215 AGACTGTACA +s simRat_chr6.simRat.chr6 22307 10 + 647215 GGGTTGTAAT + +a s simMouse_chr6.simMouse.chr6 30053 6 + 636262 ATGTGC s Anc0.Anc0refChr9 7687 6 + 35212 ATGTGC s Anc1.Anc1refChr2 131508 6 - 144309 ATGTGC @@ -11272,6 +11852,20 @@ s simRat_chr6.simRat.chr6 22317 6 + 647215 ATGTGC a +s simMouse_chr6.simMouse.chr6 30059 13 + 636262 TTTGTCTTTACTC +s Anc0.Anc0refChr9 7693 13 + 35212 TCTGTCTTTTCTC +s Anc1.Anc1refChr2 131514 13 - 144309 TCTGTCTTTTCTC +s Anc2.Anc2refChr0 26785 13 - 56053 CCTGTCTTTTCTC +s mr.mrrefChr0 28516 13 + 130230 TTTGTCTTTACTC +s mr.mrrefChr0 28077 13 + 130230 TTGGTCTTTGGCC +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 29610 13 + 636262 TTGGTCTTTGGCC +s simRat_chr6.simRat.chr6 21845 13 + 647215 TTTTCCTTTGACC +s simRat_chr6.simRat.chr6 22323 13 + 647215 TTTCTCTTTAGTC + +a s simMouse_chr6.simMouse.chr6 30072 3 + 636262 CTG s Anc0.Anc0refChr9 7706 3 + 35212 TTG s Anc1.Anc1refChr2 131527 3 - 144309 TTG @@ -11283,11 +11877,188 @@ s simRat_chr6.simRat.chr6 22336 3 + 647215 TCA a +s simMouse_chr6.simMouse.chr6 30075 12 + 636262 CTACTGGGGCCT +s Anc0.Anc0refChr9 7709 12 + 35212 CCACTGGGGCTT +s Anc1.Anc1refChr2 131530 12 - 144309 CCACTGGGGCTT +s Anc2.Anc2refChr0 26801 12 - 56053 ACACTGGGGCTT +s mr.mrrefChr0 28532 12 + 130230 CTACTGGGGCCT +s mr.mrrefChr0 28090 12 + 130230 TTACTGGGGCAT +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 29623 12 + 636262 TTACTGGGGCAT +s simRat_chr6.simRat.chr6 21858 12 + 647215 TTACTGTAGCAC +s simRat_chr6.simRat.chr6 22339 12 + 647215 CTACTGGGGCCT + +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 30088 12 + 636262 AGGACTAGGTCT +s Anc0.Anc0refChr9 7721 11 + 35212 -GGACTGGGTCT +s Anc1.Anc1refChr2 131542 12 - 144309 AGGACTGGGTCT +s Anc2.Anc2refChr0 26813 11 - 56053 -GGCCTGGGCCT +s mr.mrrefChr0 28545 12 + 130230 AGGACTAGGTCT +s mr.mrrefChr0 28102 12 + 130230 AAGACTGGATCT +s simCow_chr6.simCow.chr6 568667 11 - 602619 -GGCTTAGGTCT +s simDog_chr6.simDog.chr6 563793 11 - 593897 -GGCCTGGGCCT +s simMouse_chr6.simMouse.chr6 29635 12 + 636262 AAGACTGGATCT +s simRat_chr6.simRat.chr6 21870 12 + 647215 AAGGCTGGGGCT +s simRat_chr6.simRat.chr6 22352 12 + 647215 AGGACTAGGTCT + +a +s simMouse_chr6.simMouse.chr6 30100 7 + 636262 GACTCTT +s Anc0.Anc0refChr9 7732 7 + 35212 CACTCTT +s Anc1.Anc1refChr2 131554 7 - 144309 CACTCTT +s Anc2.Anc2refChr0 26824 7 - 56053 CACCCTT +s mr.mrrefChr0 28557 7 + 130230 GACTCTT +s mr.mrrefChr0 28114 7 + 130230 CTTTTTT +s simCow_chr6.simCow.chr6 568678 7 - 602619 TACTCAT +s simDog_chr6.simDog.chr6 563804 7 - 593897 CACCCTT +s simMouse_chr6.simMouse.chr6 29647 7 + 636262 CTTTTTT +s simRat_chr6.simRat.chr6 21882 7 + 647215 CTTTTTT +s simRat_chr6.simRat.chr6 22380 7 + 647215 GACTCTC + +a +s simMouse_chr6.simMouse.chr6 30107 20 + 636262 CATACACAGGTGGCCAAAGT +s Anc0.Anc0refChr9 7739 20 + 35212 GATTAATTGGTAGCCAAAGT +s Anc1.Anc1refChr2 131561 20 - 144309 GATTAATTGGTAGCCAAAGT +s Anc2.Anc2refChr0 26835 20 - 56053 GATTAATTGGTAGCTCATGC +s mr.mrrefChr0 28564 20 + 130230 CATACACAGGTGGCCAAAGT +s mr.mrrefChr0 28121 20 + 130230 GATTTATTGGTAGCCAAAGT +s simCow_chr6.simCow.chr6 568689 20 - 602619 AACTGATTCATAGCCCAAGC +s simDog_chr6.simDog.chr6 563815 20 - 593897 GATTAATTGGTAGCTCATGC +s simMouse_chr6.simMouse.chr6 29654 20 + 636262 GATTTATTGGTAGCCAAAGT +s simRat_chr6.simRat.chr6 21889 20 + 647215 GAGTCATTGGTAGCCAAAGT +s simRat_chr6.simRat.chr6 22387 20 + 647215 CATACATGGGTGGCCAACGT + +a +s simMouse_chr6.simMouse.chr6 30127 8 + 636262 GGCAGCAA +s Anc0.Anc0refChr9 7759 8 + 35212 GGCAGAGT +s Anc1.Anc1refChr2 131581 8 - 144309 GGCAGAGT +s Anc2.Anc2refChr0 26855 8 - 56053 AGCAGAGT +s mr.mrrefChr0 28584 8 + 130230 GGCAGCAA +s mr.mrrefChr0 28141 8 + 130230 GGCAGAGG +s simCow_chr6.simCow.chr6 568709 8 - 602619 AGTAAAGT +s simDog_chr6.simDog.chr6 563835 8 - 593897 AGCAGAGT +s simMouse_chr6.simMouse.chr6 29674 8 + 636262 GGCAGAGG +s simRat_chr6.simRat.chr6 21933 8 + 647215 GGTAAAGA +s simRat_chr6.simRat.chr6 22407 8 + 647215 GGCAGCAG + +a +s simMouse_chr6.simMouse.chr6 30135 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 28592 13 + 130230 TTCTTTTTGGACA +s mr.mrrefChr0 28149 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 29682 13 + 636262 TTCTTTTTGGACA +s simRat_chr6.simRat.chr6 21941 13 + 647215 ATCTTTTTGGACA +s simRat_chr6.simRat.chr6 22415 13 + 647215 TTCTTTTCAGACA + +a +s simMouse_chr6.simMouse.chr6 30148 27 + 636262 AAACCAAGGAAAAAACTGAAGAAAGTA +s Anc0.Anc0refChr9 7780 27 + 35212 AAACCAGAGAAAAAGCTGAGAAAAGTA +s Anc1.Anc1refChr2 131602 27 - 144309 AAACCAGAGAAAAAGCTGAGAAAAGTA +s Anc2.Anc2refChr0 26877 27 - 56053 AAACAAGAGAAAAAGCAGTGAAAACTA +s mr.mrrefChr0 28605 27 + 130230 AAACCAAGGAAAAAACTGAAGAAAGTA +s mr.mrrefChr0 28162 27 + 130230 AAACCAAAGAAAAAACTGAAAAAAGTA +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 29695 27 + 636262 AAACCAAAGAAAAAACTGAACAAAGTA +s simRat_chr6.simRat.chr6 21954 27 + 647215 AAACCAAAGAAAAAAATGAAAAAAGTA +s simRat_chr6.simRat.chr6 22428 27 + 647215 AAACAAAGGGAAAAACTGAAGAAAGTA + +a +s simMouse_chr6.simMouse.chr6 30175 13 + 636262 AAATTGTGTCCTT +s Anc0.Anc0refChr9 7807 13 + 35212 AAGTCATGCCCCT +s Anc1.Anc1refChr2 131629 13 - 144309 AAGTCATGCCCCT +s Anc2.Anc2refChr0 26904 13 - 56053 AAGTCATGCCCCT +s mr.mrrefChr0 28632 13 + 130230 AAATTGTGTCCTT +s mr.mrrefChr0 28189 13 + 130230 AAATCAGGTCCCT +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 29722 13 + 636262 AAATCAGGTCCCT +s simRat_chr6.simRat.chr6 21981 13 + 647215 AACTCAGGTCCCT +s simRat_chr6.simRat.chr6 22455 13 + 647215 AGATCGTGTCCTT + +a +s simMouse_chr6.simMouse.chr6 30188 24 + 636262 TGCAGAATATTAGACCCAGTTAGT +s Anc0.Anc0refChr9 7837 19 + 35212 TCCACAATTTTAGACCCAG----- +s Anc1.Anc1refChr2 131659 24 - 144309 TCCACAATTTTAGACCCAGTTAGT +s Anc2.Anc2refChr0 26943 19 - 56053 TACACAATTTTAGACCCTA----- +s mr.mrrefChr0 28645 24 + 130230 TGCAGAATATTAGACCCAGTTAGT +s mr.mrrefChr0 28202 24 + 130230 TCCAGAATTTTAGACCCGGTTGGT +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 29735 24 + 636262 TCCAGAATTTTAGACCCGGTTGGT +s simRat_chr6.simRat.chr6 21994 24 + 647215 TCCAGAATTTTAGACTGGGTTGGT +s simRat_chr6.simRat.chr6 22468 24 + 647215 TTCAGAATTTTAGACCCAGCTAGT + +a +s simMouse_chr6.simMouse.chr6 30212 13 + 636262 TAGTCACTAGGCT +s Anc0.Anc0refChr9 7856 13 + 35212 TTTTCACTAGGCT +s Anc1.Anc1refChr2 131683 13 - 144309 TTTTCACTAGGCT +s Anc2.Anc2refChr0 26962 13 - 56053 TCTTTCCTAGGCT +s mr.mrrefChr0 28669 13 + 130230 TAGTCACTAGGCT +s mr.mrrefChr0 28226 13 + 130230 TTGTCACTAGGCT +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 29759 13 + 636262 TTGTCACTAGGCT +s simRat_chr6.simRat.chr6 22018 13 + 647215 TTGTCACTAGGCT +s simRat_chr6.simRat.chr6 22492 13 + 647215 TAGTAACTAGGCT + +a +s simMouse_chr6.simMouse.chr6 30225 5 + 636262 CAAAA +s Anc0.Anc0refChr9 7878 5 + 35212 CAAAA +s Anc1.Anc1refChr2 131705 5 - 144309 CAAAA +s Anc2.Anc2refChr0 26984 5 - 56053 CAAAA +s mr.mrrefChr0 28682 5 + 130230 CAAAA +s mr.mrrefChr0 28239 5 + 130230 TGAAA +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 29772 5 + 636262 TGAAA +s simRat_chr6.simRat.chr6 22031 5 + 647215 TGAAA +s simRat_chr6.simRat.chr6 22505 5 + 647215 TGAAA + +a +s simMouse_chr6.simMouse.chr6 30230 13 + 636262 ACAGCTATAAGTG +s Anc0.Anc0refChr9 7883 13 + 35212 GCAGGTATAAATG +s Anc1.Anc1refChr2 131710 13 - 144309 GCAGGTATAAATG +s Anc2.Anc2refChr0 26989 13 - 56053 TCAGGTATAAATG +s mr.mrrefChr0 28687 13 + 130230 ACAGCTATAAGTG +s mr.mrrefChr0 28244 13 + 130230 GTAGGTCTAAGTG +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 29777 13 + 636262 GTAGGTCTAAGTG +s simRat_chr6.simRat.chr6 22036 13 + 647215 ATACGTCTACGTG +s simRat_chr6.simRat.chr6 22510 13 + 647215 ACAGGTATAAGTG + +a +s simMouse_chr6.simMouse.chr6 30243 1 + 636262 G +s Anc0.Anc0refChr9 7896 1 + 35212 G +s Anc1.Anc1refChr2 131723 1 - 144309 G +s Anc2.Anc2refChr0 27002 1 - 56053 G +s mr.mrrefChr0 28700 1 + 130230 G +s mr.mrrefChr0 28257 1 + 130230 A +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 29790 1 + 636262 A +s simRat_chr6.simRat.chr6 22049 1 + 647215 G +s simRat_chr6.simRat.chr6 22523 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 @@ -11298,7 +12069,115 @@ s simRat_chr6.simRat.chr6 22524 2 + 647215 AC a -s simMouse_chr6.simMouse.chr6 30263 120 + 636262 TTCAGATCAACTAGCAGGGTGCTTGTGGTTAAGGCACTACTTGATTTGAGAAGTCCCGCCACTAAGTTCCGACTTAATTTTTACTAGACAGAATTTAGTGGACCTTCTTGCAGCTATGAA +s simMouse_chr6.simMouse.chr6 30246 3 + 636262 CTT +s Anc0.Anc0refChr9 7899 3 + 35212 CTC +s Anc1.Anc1refChr2 131726 3 - 144309 CTC +s Anc2.Anc2refChr0 27005 3 - 56053 TTC +s mr.mrrefChr0 28703 3 + 130230 CTT +s mr.mrrefChr0 28258 3 + 130230 CTC +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 29791 3 + 636262 CTC +s simRat_chr6.simRat.chr6 22050 3 + 647215 CTC +s simRat_chr6.simRat.chr6 22526 3 + 647215 CTC + +a +s simMouse_chr6.simMouse.chr6 30249 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 28706 3 + 130230 CTT +s mr.mrrefChr0 28261 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 29794 3 + 636262 CTT +s simRat_chr6.simRat.chr6 22053 3 + 647215 CTT +s simRat_chr6.simRat.chr6 22529 3 + 647215 CTG + +a +s simMouse_chr6.simMouse.chr6 30252 134 + 636262 GCATCTATGAATTCAGATCAACTAGCAGGGTGCTTGTGGTTAAGGCACTACTTGATTTGAGAAGTCCCGCCACTAAGTTCCGACTTAATTTTTACTAGACAGAATTTAGTGGACCTTCTTGCAGCTATGAAATC +s Anc0.Anc0refChr9 7905 14 + 35212 GCATCTAAGAA------------------------------------------------------------------------------------------------------------------------ATC +s Anc1.Anc1refChr2 131732 14 - 144309 GCATCTAAGAA------------------------------------------------------------------------------------------------------------------------ATC +s Anc2.Anc2refChr0 27034 14 - 56053 GCATCTAAGAA------------------------------------------------------------------------------------------------------------------------ATC +s mr.mrrefChr0 28709 14 + 130230 GCATCTATGAA------------------------------------------------------------------------------------------------------------------------ATC +s mr.mrrefChr0 28264 14 + 130230 GCATCTAAGAA------------------------------------------------------------------------------------------------------------------------GTC +s simCow_chr6.simCow.chr6 568890 14 - 602619 GCAGCTAAGTA------------------------------------------------------------------------------------------------------------------------ATC +s simDog_chr6.simDog.chr6 564063 14 - 593897 GCATCTAAGAA------------------------------------------------------------------------------------------------------------------------ATC +s simHuman_chr6.simHuman.chr6 571008 14 - 601863 CTGTGTGTCAA------------------------------------------------------------------------------------------------------------------------ATC +s simMouse_chr6.simMouse.chr6 29797 14 + 636262 GCATCTAAGAA------------------------------------------------------------------------------------------------------------------------GTC +s simRat_chr6.simRat.chr6 22056 14 + 647215 ACATCTAAGAG------------------------------------------------------------------------------------------------------------------------GTC +s simRat_chr6.simRat.chr6 22532 14 + 647215 GCATCTATGCA------------------------------------------------------------------------------------------------------------------------ATC + +a +s simMouse_chr6.simMouse.chr6 30386 44 + 636262 AGATCAAGTAGCATGGTGCTTGTGGTTAAGGCACTACTTGATTT +s Anc0.Anc0refChr9 7919 44 + 35212 AGATGAAGAACCATAGTGCTTGGGGCTAAGGCACCACTTGATTT +s Anc1.Anc1refChr2 131746 44 - 144309 AGATGAAGAACCATAGTGCTTGGGGCTAAGGCACCACTTGATTT +s Anc2.Anc2refChr0 27048 44 - 56053 AGATAAGGAACCATAGTGCTTGGGGCTAAGGCACCAATTGATGT +s mr.mrrefChr0 28723 44 + 130230 AGATCAAGTAGCATGGTGCTTGTGGTTAAGGCACTACTTGATTT +s mr.mrrefChr0 28278 44 + 130230 AGATGAAGAACCACAGTGCTTGTGATTAAGGCACCACCTGATTT +s simCow_chr6.simCow.chr6 568904 43 - 602619 AGACAATGAACCATGGTGCTTAGAGCTAAGGCACCACTTGA-GT +s simDog_chr6.simDog.chr6 564077 44 - 593897 AGATAAGGAACCATAATGCTTGGGGCTAGGGCACCAATTGATGT +s simHuman_chr6.simHuman.chr6 571029 39 - 601863 AGATGAAGAACCATAGTCCATGGGACTAAGGGACCAC-----AT +s simMouse_chr6.simMouse.chr6 29811 44 + 636262 AGATGAAGAACCACAGTGCTTGTGATTAAGGCACCACCTGATTT +s simRat_chr6.simRat.chr6 22070 44 + 647215 AGATGAAGAACCACAATGCTTGTGATTAAGGCACCACCTGATTT +s simRat_chr6.simRat.chr6 22546 44 + 647215 AGATCAAGTAGCATTGTGCTTAAGATTAAGGCACAACTTGATCT + +a +s simMouse_chr6.simMouse.chr6 30430 18 + 636262 GAGAAGTCCCACCACTAA +s Anc0.Anc0refChr9 7963 18 + 35212 GAGAAGGCCAGTTACTGG +s Anc1.Anc1refChr2 131790 18 - 144309 GAGAAGGCCAGTTACTGG +s Anc2.Anc2refChr0 27092 18 - 56053 GAGAAGGCCAGTTACTGG +s mr.mrrefChr0 28767 18 + 130230 GAGAAGTCCCACCACTAA +s mr.mrrefChr0 28322 18 + 130230 GGGAAGGCCCATTACTGA +s simCow_chr6.simCow.chr6 568947 18 - 602619 GAGCAGTCCAATTACTGG +s simDog_chr6.simDog.chr6 564121 18 - 593897 GAGAGGGCCAGCTACTGG +s simHuman_chr6.simHuman.chr6 571068 18 - 601863 GAGAAGGGCAGTTTCTGG +s simMouse_chr6.simMouse.chr6 29856 18 + 636262 GGGAAGGCCCAGTACAGA +s simRat_chr6.simRat.chr6 22114 18 + 647215 GGGAAGCCCCATTACTGA +s simRat_chr6.simRat.chr6 22590 18 + 647215 GAGAAATCCCACCACTAA + +a +s simMouse_chr6.simMouse.chr6 30448 10 + 636262 GTTCCCACTT +s Anc0.Anc0refChr9 7981 9 + 35212 G-CCTCACTT +s Anc1.Anc1refChr2 131808 10 - 144309 GTCCTCACTT +s Anc2.Anc2refChr0 27110 9 - 56053 G-CCTATCTT +s mr.mrrefChr0 28785 10 + 130230 GTTCCCACTT +s mr.mrrefChr0 28340 10 + 130230 GTCCCCACCT +s simCow_chr6.simCow.chr6 568965 9 - 602619 A-ACTCTCTT +s simDog_chr6.simDog.chr6 564139 9 - 593897 G-CCCATCTG +s simHuman_chr6.simHuman.chr6 571086 9 - 601863 G-TCTTACCT +s simMouse_chr6.simMouse.chr6 29878 10 + 636262 GTTCCCACCT +s simRat_chr6.simRat.chr6 22132 10 + 647215 GTCCCCACCT +s simRat_chr6.simRat.chr6 22608 10 + 647215 ATTCCCACTT + +a +s simMouse_chr6.simMouse.chr6 30458 7 + 636262 AATTTTT +s Anc0.Anc0refChr9 7990 7 + 35212 AATTTTT +s Anc1.Anc1refChr2 131818 7 - 144309 AATTTTT +s Anc2.Anc2refChr0 27119 7 - 56053 AACTTTT +s mr.mrrefChr0 28795 7 + 130230 AATTTTT +s mr.mrrefChr0 28361 7 + 130230 ACTTTTT +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 29904 7 + 636262 ACTTTTT +s simRat_chr6.simRat.chr6 22153 7 + 647215 ACTTTAA +s simRat_chr6.simRat.chr6 22618 7 + 647215 AATTTTT + +a +s simMouse_chr6.simMouse.chr6 30465 9 + 636262 ACTAGACAG +s Anc0.Anc0refChr9 7997 3 + 35212 ACT------ +s Anc1.Anc1refChr2 131825 9 - 144309 ACTAGGCAG +s Anc2.Anc2refChr0 27126 3 - 56053 AGT------ +s mr.mrrefChr0 28802 9 + 130230 ACTAGACAG +s mr.mrrefChr0 28368 9 + 130230 ACCAGGCTG +s simCow_chr6.simCow.chr6 568990 3 - 602619 AGT------ +s simDog_chr6.simDog.chr6 564155 3 - 593897 AGT------ +s simMouse_chr6.simMouse.chr6 29911 9 + 636262 ACCAGGCTG +s simRat_chr6.simRat.chr6 22160 9 + 647215 ACCAAGCTG +s simRat_chr6.simRat.chr6 22625 9 + 647215 ACTAGACAG a s simMouse_chr6.simMouse.chr6 30474 3 + 636262 GAT @@ -11306,7 +12185,115 @@ s simRat_chr6.simRat.chr6 22634 3 + 647215 AAT a -s simMouse_chr6.simMouse.chr6 30519 1 + 636262 G +s simMouse_chr6.simMouse.chr6 30477 5 + 636262 TTCAC +s Anc0.Anc0refChr9 8000 5 + 35212 CTTGC +s Anc1.Anc1refChr2 131834 5 - 144309 CTTGC +s Anc2.Anc2refChr0 27129 5 - 56053 CCTGT +s mr.mrrefChr0 28814 5 + 130230 TTCAC +s mr.mrrefChr0 28377 5 + 130230 CTTGC +s simCow_chr6.simCow.chr6 568993 5 - 602619 CCTGT +s simDog_chr6.simDog.chr6 564158 5 - 593897 CCTGT +s simMouse_chr6.simMouse.chr6 29920 5 + 636262 CTTGC +s simRat_chr6.simRat.chr6 22169 5 + 647215 ATTGC +s simRat_chr6.simRat.chr6 22637 5 + 647215 TTCAC + +a +s simMouse_chr6.simMouse.chr6 30482 13 + 636262 CTTGGGAAAGTAT +s Anc0.Anc0refChr9 8005 13 + 35212 TTTTGGAGAGTAC +s Anc1.Anc1refChr2 131839 13 - 144309 TTTTGGAGAGTAC +s Anc2.Anc2refChr0 27134 13 - 56053 TTTTGATGAGTAC +s mr.mrrefChr0 28819 13 + 130230 CTTGGGAAAGTAT +s mr.mrrefChr0 28382 13 + 130230 TTTAGGAGAGTAC +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 29925 13 + 636262 TTTAGGAGAGTAC +s simRat_chr6.simRat.chr6 22174 13 + 647215 TTTAGGAGAGGAC +s simRat_chr6.simRat.chr6 22644 13 + 647215 CTTAGGTAAGTAT + +a +s simMouse_chr6.simMouse.chr6 30495 19 + 636262 TCACAAATTTGAGGCTTCC +s Anc0.Anc0refChr9 8020 19 + 35212 CCAAAAACTTGGGGCTTCT +s Anc1.Anc1refChr2 131854 19 - 144309 CCAAAAACTTGGGGCTTCT +s Anc2.Anc2refChr0 27149 19 - 56053 CCAAAAACTTGGGGCTTCT +s mr.mrrefChr0 28832 19 + 130230 TCACAAATTTGAGGCTTCC +s mr.mrrefChr0 28395 19 + 130230 CTATAAACTTGGTGCTTCC +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 29938 19 + 636262 CTATAAACTAGGGGCTTCC +s simRat_chr6.simRat.chr6 22187 19 + 647215 CTACGAACTTAGTGCTTCC +s simRat_chr6.simRat.chr6 22657 19 + 647215 CCACAAACATGGGGCTCCC + +a +s simMouse_chr6.simMouse.chr6 30514 4 + 636262 CTGT +s Anc0.Anc0refChr9 8039 4 + 35212 CTGT +s Anc1.Anc1refChr2 131873 4 - 144309 CTGT +s Anc2.Anc2refChr0 27168 4 - 56053 TTGT +s mr.mrrefChr0 28851 4 + 130230 CTGT +s mr.mrrefChr0 28414 4 + 130230 CCAT +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 29957 4 + 636262 CCAT +s simRat_chr6.simRat.chr6 22206 4 + 647215 TCAT +s simRat_chr6.simRat.chr6 22676 4 + 647215 TTGT + +a +s simMouse_chr6.simMouse.chr6 30518 7 + 636262 GGTAAGT +s Anc0.Anc0refChr9 8044 6 + 35212 G-TAAGT +s Anc1.Anc1refChr2 131878 6 - 144309 G-TAAGT +s Anc2.Anc2refChr0 27173 6 - 56053 G-TAAGT +s mr.mrrefChr0 28855 6 + 130230 G-TAAGT +s mr.mrrefChr0 28419 6 + 130230 G-TAAGT +s simCow_chr6.simCow.chr6 569037 6 - 602619 G-TAAGT +s simDog_chr6.simDog.chr6 564203 6 - 593897 G-TAGGT +s simHuman_chr6.simHuman.chr6 571139 6 - 601863 G-TGAGT +s simMouse_chr6.simMouse.chr6 29962 6 + 636262 G-TAAGT +s simRat_chr6.simRat.chr6 22211 6 + 647215 G-TAAGT +s simRat_chr6.simRat.chr6 22680 6 + 647215 G-TAAGT + +a +s simMouse_chr6.simMouse.chr6 30525 10 + 636262 CTGTATGCTA +s Anc0.Anc0refChr9 8050 10 + 35212 TTGTATGATC +s Anc1.Anc1refChr2 131884 10 - 144309 TTGTATGATC +s Anc2.Anc2refChr0 27179 10 - 56053 TTGTATGATC +s mr.mrrefChr0 28861 10 + 130230 ATGTATGTGA +s mr.mrrefChr0 28425 10 + 130230 TTGTATGATA +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 29968 10 + 636262 TTATATGATA +s simRat_chr6.simRat.chr6 22217 10 + 647215 CTGTAGAATA +s simRat_chr6.simRat.chr6 22686 10 + 647215 ATGTATGTGG + +a +s simMouse_chr6.simMouse.chr6 30535 7 + 636262 GCCATCA +s Anc0.Anc0refChr9 8075 7 + 35212 GTCATCA +s Anc1.Anc1refChr2 131909 7 - 144309 GTCATCA +s Anc2.Anc2refChr0 27204 7 - 56053 GTCATCA +s mr.mrrefChr0 28871 7 + 130230 GCCATCA +s mr.mrrefChr0 28435 7 + 130230 GTCATCA +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 29978 7 + 636262 GTCATCA +s simRat_chr6.simRat.chr6 22227 7 + 647215 GTCATCA +s simRat_chr6.simRat.chr6 22696 7 + 647215 GCCACCA + +a +s simMouse_chr6.simMouse.chr6 30542 6 + 636262 ATCAGC +s Anc0.Anc0refChr9 8082 6 + 35212 ATTGGC +s Anc1.Anc1refChr2 131916 6 - 144309 ATTGGC +s Anc2.Anc2refChr0 27211 6 - 56053 ATTGGC +s mr.mrrefChr0 28878 6 + 130230 ATCAGC +s mr.mrrefChr0 28447 6 + 130230 ACTAGA +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 29990 6 + 636262 ACTAGA +s simRat_chr6.simRat.chr6 22239 6 + 647215 CCTAGA +s simRat_chr6.simRat.chr6 22703 6 + 647215 ATCAGC a s simMouse_chr6.simMouse.chr6 30548 7 + 636262 AGTATTT @@ -20072,62 +21059,134 @@ 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 +s simMouse_chr6.simMouse.chr6 54576 5 + 636262 AGGGC +s Anc0.Anc0refChr4 2375 5 - 45765 AGTGC +s Anc1.Anc1refChr2 33077 5 + 144309 AGTGC +s Anc2.Anc2refChr0 55400 5 + 56053 AGTGC +s mr.mrrefChr0 52014 5 + 130230 AGGGC +s simCow_chr6.simCow.chr6 59008 5 + 602619 AGTGC +s simDog_chr6.simDog.chr6 52951 5 + 593897 AGAGC +s simHuman_chr6.simHuman.chr6 53251 5 + 601863 AGTGC +s simMouse_chr6.simMouse.chr6 54384 3 + 636262 --GGC +s simRat_chr6.simRat.chr6 47504 5 + 647215 AGGGC + +a +s simMouse_chr6.simMouse.chr6 54581 51 + 636262 AACGAAACATACTTAGTGTCCCAAGAGTTTTGTTTACATCCCTCTTTTTGG +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 54387 51 + 636262 AATAAAAAGTGCTTAGGGTCCCAAGGGTTTGGTTTAAATCCTTCTTTTTGA +s simRat_chr6.simRat.chr6 47509 51 + 647215 AATGAGAAATGCTTCGGGTCCCAAGGGTTTGGTTTACATCCTTCTTTTGGG + +a +s simMouse_chr6.simMouse.chr6 54632 7 + 636262 GGTTGAA +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 54438 7 + 636262 GGTTTAA +s simRat_chr6.simRat.chr6 47560 6 + 647215 GGAGTA- + +a +s simMouse_chr6.simMouse.chr6 54639 8 + 636262 AAGGAATG +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 54445 8 + 636262 AAGGACTG + +a +s simMouse_chr6.simMouse.chr6 54647 25 + 636262 CTGACATCTTTAAACATATTGTTGG +s Anc0.Anc0refChr4 2451 24 - 45765 CTGACATCCT-AAACATATTGTTGG +s Anc1.Anc1refChr2 33153 24 + 144309 CTGACATCCT-AAACATATTGTTGG +s Anc2.Anc2refChr0 55480 24 + 56053 CTAACATCCT-AAACATATTGTTGG +s mr.mrrefChr0 52085 24 + 130230 CTGACATCCT-AAACATATTGTTGG +s simCow_chr6.simCow.chr6 59088 21 + 602619 ---ACATCGT-TAACATATTGTGGA +s simDog_chr6.simDog.chr6 53055 24 + 593897 CTAACACCCT-AAGCATACTGTTGG +s simHuman_chr6.simHuman.chr6 53307 24 + 601863 CTGACATCCT-AAACAAATTGTTGG +s simMouse_chr6.simMouse.chr6 54453 23 + 636262 CTGACATCCT-AAAC-TATTGTTGG +s simRat_chr6.simRat.chr6 47566 18 + 647215 ------TCCT-GAACATATTATTGT + +a +s simMouse_chr6.simMouse.chr6 54672 12 + 636262 AGATATGAGATG +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 54476 12 + 636262 AGATATGAGGTG +s simRat_chr6.simRat.chr6 47584 12 + 647215 AGATATGAGATG + +a +s simMouse_chr6.simMouse.chr6 54684 8 + 636262 CTGTTCCT +s Anc0.Anc0refChr4 2487 7 - 45765 GTGTT-CC +s Anc1.Anc1refChr2 33189 8 + 144309 GTGTTCCC +s Anc2.Anc2refChr0 55516 7 + 56053 GTGCT-CC +s mr.mrrefChr0 52121 8 + 130230 CTGTTCCT +s simCow_chr6.simCow.chr6 59140 7 + 602619 ATGCA-CC +s simDog_chr6.simDog.chr6 53091 7 + 593897 GTGCT-CC +s simHuman_chr6.simHuman.chr6 53343 8 + 601863 GTGTTCCC +s simMouse_chr6.simMouse.chr6 54488 7 + 636262 CTGT-CCT +s simRat_chr6.simRat.chr6 47596 8 + 647215 CTGTTCCT + +a +s simMouse_chr6.simMouse.chr6 54692 12 + 636262 AAAGAATATCCT +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 54495 12 + 636262 AAAGACTTTCCT +s simRat_chr6.simRat.chr6 47604 12 + 647215 AAAGACTTTCCT + +a +s simMouse_chr6.simMouse.chr6 54704 3 + 636262 CTA +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 54507 3 + 636262 CGA +s simRat_chr6.simRat.chr6 47616 3 + 647215 CTA + +a +s simMouse_chr6.simMouse.chr6 54707 61 + 636262 GGTAACCATTATGTTGTTTGCTTTGCATGTACCATACTGGACCAAGGCACAGTTTGATTAG +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 54510 61 + 636262 GGTAACAGTTATGTTGTTTGCTTTGCCCATATCATACTGGACCTAGGCACAGTTTGATTAT +s simRat_chr6.simRat.chr6 47619 60 + 647215 GGTAACCGTTATGTTGTTTGCTTTGCCCATGCTATACTGGACTAAGGCACAGTTTGATAA- + +a +s simMouse_chr6.simMouse.chr6 54768 79 + 636262 TGATAGAATATGTGATAGGTGTCACACTTTGGTTATCACACAAATTTGGTTATTGCACAGCATCTTGTCATTGTCTAGA +s Anc0.Anc0refChr4 2590 26 - 45765 CA-------------------T----------------------------------ACAGCATCTTGTCATTGTCTAGA +s Anc1.Anc1refChr2 33293 26 + 144309 CA-------------------T----------------------------------ACAGCATCTTGTCATTGTCTAGA +s Anc2.Anc2refChr0 55619 26 + 56053 CA-------------------G----------------------------------ACAGCACCTTGTCATTGTCTAGA +s mr.mrrefChr0 52205 60 + 130230 TG-------------------TCACACTTTGGTTATCACACAAATTTGGTTATTGCACAGCATCTTGTCATTGTCTAGA +s simCow_chr6.simCow.chr6 59256 26 + 602619 CA-------------------C----------------------------------ATGGTACCTTGTCATTGTCGAGA +s simDog_chr6.simDog.chr6 53197 26 + 593897 CA-------------------G----------------------------------ACAGCACCTTGTCACTGTTTAGA +s simHuman_chr6.simHuman.chr6 53447 26 + 601863 CA-------------------T----------------------------------ACAGCATCTTGTCGTTGTCTAGA +s simMouse_chr6.simMouse.chr6 54571 5 + 636262 TG------------------------------------------------CAT-------------------------- +s simRat_chr6.simRat.chr6 47679 58 + 647215 ---------------------TCACACTTTGATTATCACATAAGTTTGATTATTGCACACCACCTTGTCATTGTTGAGA a s simMouse_chr6.simMouse.chr6 54847 5 + 636262 ATATG @@ -24063,25 +25122,88 @@ 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 +s simMouse_chr6.simMouse.chr6 64726 8 + 636262 ATTTGAGT +s Anc0.Anc0refChr4 10958 8 - 45765 GTTGGAGG +s Anc1.Anc1refChr2 41971 8 + 144309 GTTGGAGG +s Anc2.Anc2refChr4 8273 8 + 10050 GTTGGAGG +s mr.mrrefChr0 61478 8 + 130230 ATTTGAGT +s simCow_chr6.simCow.chr6 68944 8 + 602619 GTAGAAGG +s simDog_chr6.simDog.chr6 64842 8 + 593897 GATGGAGG +s simHuman_chr6.simHuman.chr6 62312 8 + 601863 GTTAGAGG +s simMouse_chr6.simMouse.chr6 64440 8 + 636262 ATTTGAGT +s simRat_chr6.simRat.chr6 57226 8 + 647215 ATTTGAGT + +a +s simMouse_chr6.simMouse.chr6 64734 14 + 636262 TTGGCTGATAGTAT +s Anc0.Anc0refChr4 10966 14 - 45765 TGAGTTAATAGCAT +s Anc1.Anc1refChr2 41979 14 + 144309 TGAGTTAATAGCAT +s Anc2.Anc2refChr4 8281 14 + 10050 TGAGTTAATTGCAT +s mr.mrrefChr0 61486 14 + 130230 TTGGCTGATAGTAT +s simCow_chr6.simCow.chr6 68952 14 + 602619 TGAGTTAATGGCAT +s simDog_chr6.simDog.chr6 64850 14 + 593897 TGAGTTAATTGCAC +s simHuman_chr6.simHuman.chr6 62320 14 + 601863 TGAGTTAATAACAT +s simMouse_chr6.simMouse.chr6 64452 14 + 636262 TTGGCTGATAGTAT +s simRat_chr6.simRat.chr6 57234 14 + 647215 TTGGCTGATAGCAT + +a +s simMouse_chr6.simMouse.chr6 64748 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 64466 1 + 636262 G +s simRat_chr6.simRat.chr6 57250 1 + 647215 G + +a +s simMouse_chr6.simMouse.chr6 64749 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 64467 1 + 636262 T +s simRat_chr6.simRat.chr6 57251 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 64750 101 + 636262 AAATCATAGGGAGGGACCTTGCAGACACAATGGTATGTTGAGGGTAGACAATAATTGTATATCTAAAATTTTAATCCAAGGTAGCAGGTTTTTGGGGGACA +s Anc0.Anc0refChr4 10984 96 - 45765 GTATCCAGTGGAGCG----TGCAGACACA-TTGTATGTAGAGGATACACAAAAATTATACAATTAAAACTTTAAGCCATGGTAGGAAGGTCTTGAGGGACA +s Anc1.Anc1refChr2 41997 96 + 144309 GTATCCAGTGGAGCG----TGCAGACACA-TTGTATGTAGAGGATACACAAAAATTATACAATTAAAACTTTAAGCCATGGTAGGAAGGTCTTGAGGGACA +s Anc2.Anc2refChr4 8299 96 + 10050 GTATTCTGTGGAGCA----TGTAGACACA-TTGTATGTAGAGGATACACAAAAATTATACAACTAAAACTTTAAGCCATGGTAGGAAGGTCTTAAGGGACA +s mr.mrrefChr0 61502 101 + 130230 AAATCAAAGGGAGGGACCTTGCAGACACAATGGTATGTTGAGGGTAGACAATAATTGTATATTTAACATTTTAATCCAAGGTAGCAGGTTTTTGGGGGACA +s simCow_chr6.simCow.chr6 68999 96 + 602619 GCATTCTGTGGAGCA----TGTAGACACA-TTGTATGTAGATGATACACAAGAATTATACAACTAAAACTTTAAGACATGGTAGGTACATCTTCAGGGACA +s simDog_chr6.simDog.chr6 64868 77 + 593897 TTA-----------------------ACA-TTGCAAGTACAGGAATAAAATAAGCTACACAACTAAAAGTTTAAGCCATGGTAGGAAGGTCTTAAGGGATG +s simHuman_chr6.simHuman.chr6 62338 96 + 601863 GTATCCAGAGGGCAG----TGCAGACACA-TTATATGCAGAGGATACGCAAAAATTATACAATGAAGACTTTAAGCTATGGTAGGAAGGACTTGAGAGACA +s simMouse_chr6.simMouse.chr6 64468 100 + 636262 AAATCAAA-GGAGGGACCTTGCAGATGCAATGGTATGTTGAGGGTAGACAATAATTGTATATTTAACATTTTAATCCAAGGTAGCGGGTTTTTGGGAGACA +s simRat_chr6.simRat.chr6 57252 101 + 647215 ATATCAAAGGGAGGGACCTTGCGGACACAATGGTATGCCGAGGGTAAACAATAACTATATATTAAACATTTTAATCCAAGGTAGCAGGTTTTTGGGGGACA + +a +s simMouse_chr6.simMouse.chr6 64851 61 + 636262 GGAGTGTGGCAATCGTAAAGAGGTTATTTGCGGAGACCTTCGTGTAACCAAAGGATGCACC +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 61 + 130230 GGAGTGTGGCAATCGTAAAGAGGTTATTTGCGGAGACCTTCGTGTAACCAAAGGATGCACC +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 64568 61 + 636262 GGAGTGTGGCAACCGTAAAGAGGTTATTTGCGGAGACATGCGTGTAAACAAAGGATGCACC +s simRat_chr6.simRat.chr6 57353 60 + 647215 -GAGTGTTACAATCATAAACAGGTTATTTGTGGAGACCTTTGTGTAACCAGAGGATGCACC + +a +s simMouse_chr6.simMouse.chr6 64912 66 + 636262 TTTGAAACTGGGTTGGGAGAGATTATGCCACTCAACTAGAAGGGCTACAAGGTATTACCGCCCAAT +s Anc0.Anc0refChr4 11094 4 - 45765 --------------------------------------------------------------ATAT +s Anc1.Anc1refChr2 42107 4 + 144309 --------------------------------------------------------------ATAT +s Anc2.Anc2refChr4 8410 4 + 10050 --------------------------------------------------------------ATAT +s mr.mrrefChr0 61664 66 + 130230 TTTGAAACTGAGTTGGGAGAGATTATGCTACTCAACTAGAAGGGCTACAAGGTATTACCGCCAAAT +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 simMouse_chr6.simMouse.chr6 64675 51 + 636262 TATGAAACTGAGTTGGGAGAGATTATGCTACTCAACTATACGTTGAATGAG--------------- +s simRat_chr6.simRat.chr6 57413 66 + 647215 TTTAAAACTGAGTTGGAAGAGTTTATGCTGCTCAACTAGATGGGCTACAAGTTATTGCCACTATAT a s simMouse_chr6.simMouse.chr6 64978 24 + 636262 AAAATGGGAAGGGGTAGTCAATTT @@ -30645,6 +31767,34 @@ s simRat_chr6.simRat.chr6 73122 4 + 647215 GGAA a +s simMouse_chr6.simMouse.chr6 80861 12 + 636262 ACTAGGCTCTGG +s Anc0.Anc0refChr4 24571 12 - 45765 ATTTGGCTCTGA +s Anc1.Anc1refChr2 55954 12 + 144309 ATTTGGCTCTGA +s Anc2.Anc2refChr7 24684 12 + 32194 ATTTGGCTCTGA +s mr.mrrefChr0 76535 12 + 130230 ACTAGGCTCTGG +s mr.mrrefChr0 76141 12 + 130230 AATAGGCTCTGG +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 80445 12 + 636262 AATAGGCTCTGG +s simRat_chr6.simRat.chr6 72730 12 + 647215 AATAGGCTCTGG +s simRat_chr6.simRat.chr6 73126 12 + 647215 ACAAGGCTCTGG + +a +s simMouse_chr6.simMouse.chr6 80873 19 + 636262 ATTCTCGGTTATACAATGA +s Anc0.Anc0refChr4 24583 19 - 45765 ATTTTTAATTGCACAACGA +s Anc1.Anc1refChr2 55966 19 + 144309 ATTTTTAATTGCACAACGA +s Anc2.Anc2refChr7 24696 19 + 32194 GTTTTTAATTGCACAACGC +s mr.mrrefChr0 76547 19 + 130230 ATTCTCGGTTATACAATGA +s mr.mrrefChr0 76153 19 + 130230 ATTCTCAGTTGCACAATGA +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 80457 19 + 636262 GTTCTCAGTTGCACAATGA +s simRat_chr6.simRat.chr6 72742 19 + 647215 ATTCTCAGTTGCACAATGA +s simRat_chr6.simRat.chr6 73138 19 + 647215 ATTCTCAGTTACACAATGA + +a s simMouse_chr6.simMouse.chr6 80892 4 + 636262 ATTA s Anc0.Anc0refChr4 24602 4 - 45765 ATTT s Anc1.Anc1refChr2 55985 4 + 144309 ATTT @@ -30656,6 +31806,34 @@ s simRat_chr6.simRat.chr6 73157 4 + 647215 ATTA a +s simMouse_chr6.simMouse.chr6 80896 14 + 636262 GATTTGGTACTCTT +s Anc0.Anc0refChr4 24606 14 - 45765 GGTTTGAGATTCAT +s Anc1.Anc1refChr2 55989 14 + 144309 GGTTTGAGATTCAT +s Anc2.Anc2refChr7 24719 14 + 32194 GGTTCCAGATTCAT +s mr.mrrefChr0 76570 14 + 130230 GATTTGGTACTCTT +s mr.mrrefChr0 76172 14 + 130230 TGATTGGTGTCCTT +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 80476 14 + 636262 CGATTGGTGTCCTT +s simRat_chr6.simRat.chr6 72761 14 + 647215 TGATTGGTGTTATT +s simRat_chr6.simRat.chr6 73161 14 + 647215 GATTTGGTATTCTT + +a +s simMouse_chr6.simMouse.chr6 80910 3 + 636262 AAC +s Anc0.Anc0refChr4 24620 3 - 45765 AAG +s Anc1.Anc1refChr2 56003 3 + 144309 AAG +s Anc2.Anc2refChr7 24733 3 + 32194 AAG +s mr.mrrefChr0 76584 3 + 130230 AAC +s mr.mrrefChr0 76186 3 + 130230 AAG +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 80490 3 + 636262 ACG +s simRat_chr6.simRat.chr6 72776 3 + 647215 AAG +s simRat_chr6.simRat.chr6 73175 3 + 647215 AAC + +a s simMouse_chr6.simMouse.chr6 80913 1 + 636262 A s Anc0.Anc0refChr4 24623 1 - 45765 A s Anc1.Anc1refChr2 56006 1 + 144309 A @@ -30667,12 +31845,176 @@ s simRat_chr6.simRat.chr6 73178 1 + 647215 A a +s simMouse_chr6.simMouse.chr6 80914 10 + 636262 GTCCAGTCAG +s Anc0.Anc0refChr4 24624 2 - 45765 TT-------- +s Anc1.Anc1refChr2 56007 10 + 144309 TTCCAATCAG +s Anc2.Anc2refChr7 24737 2 + 32194 TT-------- +s mr.mrrefChr0 76588 10 + 130230 GTCCAGTCAG +s mr.mrrefChr0 76189 10 + 130230 GTCCAATTAG +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 80493 10 + 636262 GTCCAATTAG +s simRat_chr6.simRat.chr6 72779 10 + 647215 GTCCAATTTG +s simRat_chr6.simRat.chr6 73179 10 + 647215 GTCCAATCAG + +a +s simMouse_chr6.simMouse.chr6 80924 14 + 636262 TGTGGCTATAAACT +s Anc0.Anc0refChr4 24626 14 - 45765 TGTGGTTACAAATG +s Anc1.Anc1refChr2 56017 14 + 144309 TGTGGTTACAAATG +s Anc2.Anc2refChr7 24739 14 + 32194 TATGGTTGAAAATG +s mr.mrrefChr0 76598 14 + 130230 TGTGGCTATAAACT +s mr.mrrefChr0 76199 14 + 130230 TGTGGCTACAAATT +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 80503 14 + 636262 TGTGGCTACAAATT +s simRat_chr6.simRat.chr6 72789 14 + 647215 TGTGGCTACAAATT +s simRat_chr6.simRat.chr6 73189 14 + 647215 TGTGGCTATAAACT + +a +s simMouse_chr6.simMouse.chr6 80938 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 76612 2 + 130230 GA +s mr.mrrefChr0 76213 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 80517 2 + 636262 GA +s simRat_chr6.simRat.chr6 72803 2 + 647215 GA +s simRat_chr6.simRat.chr6 73208 2 + 647215 GA + +a +s simMouse_chr6.simMouse.chr6 80940 7 + 636262 ATGAGCA +s Anc0.Anc0refChr4 24656 7 - 45765 ATAAGAA +s Anc1.Anc1refChr2 56047 7 + 144309 ATAAGAA +s Anc2.Anc2refChr7 24769 7 + 32194 CTAAGAA +s mr.mrrefChr0 76614 7 + 130230 ATGAGCA +s mr.mrrefChr0 76229 7 + 130230 ATGAAAA +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 80533 7 + 636262 ATGAAAA +s simRat_chr6.simRat.chr6 72819 7 + 647215 ATAATAA +s simRat_chr6.simRat.chr6 73210 7 + 647215 GTGATCA + +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 +s simMouse_chr6.simMouse.chr6 80948 28 + 636262 ATTCTCCTGTTTGTTTATCATCCATAAA +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 76622 28 + 130230 ATTCTCCTGTTTGTTTATCATCCATAAA +s mr.mrrefChr0 76236 28 + 130230 ATTATCTTGTTTGTTCACCATCCATAAC +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 80540 28 + 636262 ATTATCTTGTTTGTTCACCATCCATAAC +s simRat_chr6.simRat.chr6 72826 28 + 647215 ATTTTCTAGTTTGTTTATCATCCATAAA +s simRat_chr6.simRat.chr6 73218 28 + 647215 ATTATCCTGTTTGTTTGCCATCAATAAC + +a +s simMouse_chr6.simMouse.chr6 80976 16 + 636262 ATTGCGGGCAATTCTA +s Anc0.Anc0refChr4 24683 16 - 45765 ATTGCAGGCAATACTA +s Anc1.Anc1refChr2 56082 16 + 144309 ATTGCAGGCAATACTA +s Anc2.Anc2refChr7 24796 16 + 32194 ATTGCAGGTGAAACCA +s mr.mrrefChr0 76650 16 + 130230 ATTGCGGGCAATTCTA +s mr.mrrefChr0 76264 16 + 130230 ATTGCAGGCAATACTA +s simCow_chr6.simCow.chr6 83155 16 + 602619 ATTGTAGGTGTGACCA +s simDog_chr6.simDog.chr6 184276 16 + 593897 ATTGCAGGTGAAACCA +s simMouse_chr6.simMouse.chr6 80568 16 + 636262 ATTGCAGGCAATACTA +s simRat_chr6.simRat.chr6 72854 16 + 647215 ATTGCAAGCAATACCT +s simRat_chr6.simRat.chr6 73246 16 + 647215 ATTGCAGGCAATACCA + +a +s simMouse_chr6.simMouse.chr6 80992 21 + 636262 CAGATTTCAGTTTGACATATC +s Anc0.Anc0refChr4 24699 21 - 45765 CAAATTGTGGTTTGGCTTATC +s Anc1.Anc1refChr2 56098 21 + 144309 CAAATTGTGGTTTGGCTTATC +s Anc2.Anc2refChr7 24813 21 + 32194 CAAATTGTGGTTCGGCTTATA +s mr.mrrefChr0 76666 21 + 130230 CAGATTTCAGTTTGACATATC +s mr.mrrefChr0 76280 21 + 130230 CAAATTGTAGTTTTACCTACC +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 80584 21 + 636262 CAAATTGTAGTTTTACCTACC +s simRat_chr6.simRat.chr6 72870 21 + 647215 CAGATTTCAGTTTTATCTACC +s simRat_chr6.simRat.chr6 73262 21 + 647215 CAGATTTCAGTTTGACCTATC + +a +s simMouse_chr6.simMouse.chr6 81013 5 + 636262 TCCTT +s Anc0.Anc0refChr4 24722 5 - 45765 TCCTT +s Anc1.Anc1refChr2 56121 5 + 144309 TCCTT +s Anc2.Anc2refChr7 24836 5 + 32194 TCCTT +s mr.mrrefChr0 76687 5 + 130230 TCCTT +s mr.mrrefChr0 76301 5 + 130230 TTCTT +s simCow_chr6.simCow.chr6 83193 5 + 602619 CCCTT +s simDog_chr6.simDog.chr6 184313 5 + 593897 TCCTT +s simHuman_chr6.simHuman.chr6 76726 5 + 601863 TCCTT +s simMouse_chr6.simMouse.chr6 80605 5 + 636262 TTCTT +s simRat_chr6.simRat.chr6 72891 5 + 647215 TCCTT +s simRat_chr6.simRat.chr6 73283 5 + 647215 TCCTT + +a +s simMouse_chr6.simMouse.chr6 81018 2 + 636262 AT +s Anc0.Anc0refChr4 24727 2 - 45765 AC +s Anc1.Anc1refChr2 56126 2 + 144309 AC +s Anc2.Anc2refChr7 24841 2 + 32194 AC +s mr.mrrefChr0 76692 2 + 130230 AT +s mr.mrrefChr0 76306 2 + 130230 AT +s simCow_chr6.simCow.chr6 83198 2 + 602619 AC +s simDog_chr6.simDog.chr6 184318 2 + 593897 AC +s simHuman_chr6.simHuman.chr6 76731 2 + 601863 GC +s simMouse_chr6.simMouse.chr6 80611 2 + 636262 AT +s simRat_chr6.simRat.chr6 72896 2 + 647215 AT +s simRat_chr6.simRat.chr6 73288 2 + 647215 AT + +a +s simMouse_chr6.simMouse.chr6 81020 16 + 636262 CTGTAATTCAGTCAAG +s Anc0.Anc0refChr4 24729 16 - 45765 ATATAATTGGGCCAAG +s Anc1.Anc1refChr2 56128 16 + 144309 ATATAATTGGGCCAAG +s Anc2.Anc2refChr7 24843 16 + 32194 ATATAACTGGGCCAAG +s mr.mrrefChr0 76694 16 + 130230 CTGTAATTCAGTCAAG +s mr.mrrefChr0 76324 16 + 130230 ATGTAATGCAGCCAGG +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 80639 16 + 636262 ATGTAATGCAGCCAGG +s simRat_chr6.simRat.chr6 72914 16 + 647215 CTGTAATTAAACCAAG +s simRat_chr6.simRat.chr6 73290 16 + 647215 CTGTAATTCAGTCAAG + +a +s simMouse_chr6.simMouse.chr6 81036 16 + 636262 ATTCATCTGCATCTTG +s Anc0.Anc0refChr4 24748 14 - 45765 ATTCATCGGCAGC--G +s Anc1.Anc1refChr2 56147 14 + 144309 ATTCATCGGCAGC--G +s Anc2.Anc2refChr7 24862 14 + 32194 ATTCATGGCCGGC--A +s mr.mrrefChr0 76710 14 + 130230 ATTCATCTGCATC--G +s mr.mrrefChr0 76340 14 + 130230 ATTCATCTGCATC--T +s simCow_chr6.simCow.chr6 83219 14 + 602619 ATTTATGGCCGGC--A +s simDog_chr6.simDog.chr6 184339 14 + 593897 ATTCATGGCTGGC--A +s simHuman_chr6.simHuman.chr6 76752 14 + 601863 GTTCACAGGCAGC--G +s simMouse_chr6.simMouse.chr6 80655 14 + 636262 ATTCATCTGCATC--T +s simRat_chr6.simRat.chr6 72930 14 + 647215 ATTCATTTTCATC--T +s simRat_chr6.simRat.chr6 73306 14 + 647215 ACTTGTCTGCATC--A + +a +s simMouse_chr6.simMouse.chr6 81052 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 76724 3 + 130230 TAA +s mr.mrrefChr0 76356 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 80671 3 + 636262 TAA +s simRat_chr6.simRat.chr6 72946 3 + 647215 TAA +s simRat_chr6.simRat.chr6 73320 3 + 647215 TAA a s simMouse_chr6.simMouse.chr6 81055 5 + 636262 ATGCC @@ -30686,11 +32028,199 @@ s simRat_chr6.simRat.chr6 73323 5 + 647215 ATGCC a +s simMouse_chr6.simMouse.chr6 81060 1 + 636262 C +s Anc0.Anc0refChr4 24772 1 - 45765 T +s Anc1.Anc1refChr2 56171 1 + 144309 T +s Anc2.Anc2refChr7 24886 1 + 32194 T +s mr.mrrefChr0 76732 1 + 130230 C +s mr.mrrefChr0 76359 1 + 130230 T +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 80674 1 + 636262 T +s simRat_chr6.simRat.chr6 72949 1 + 647215 T +s simRat_chr6.simRat.chr6 73328 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 81061 8 + 636262 CATATGGC +s Anc0.Anc0refChr4 24773 8 - 45765 CATATGGC +s Anc1.Anc1refChr2 56172 8 + 144309 CATATGGC +s Anc2.Anc2refChr7 24887 8 + 32194 CATATGGC +s mr.mrrefChr0 76733 8 + 130230 CATATGGC +s mr.mrrefChr0 76360 8 + 130230 TACGTGGC +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 80675 8 + 636262 TACGTGGC +s simRat_chr6.simRat.chr6 72951 8 + 647215 CACATGGC +s simRat_chr6.simRat.chr6 73329 8 + 647215 CACATGGC + +a +s simMouse_chr6.simMouse.chr6 81069 22 + 636262 CCCACCTTATGTGCCCTCCCAA +s Anc0.Anc0refChr4 24781 22 - 45765 TCCACCTTATATGCCCTCTTAA +s Anc1.Anc1refChr2 56180 22 + 144309 TCCACCTTATATGCCCTCTTAA +s Anc2.Anc2refChr7 24895 22 + 32194 TCCACCTTGGTTGCCCTCTTAA +s mr.mrrefChr0 76741 22 + 130230 CCCACCTTATGTGCCCTCCCAA +s mr.mrrefChr0 76368 22 + 130230 CCCACTTGATATGCCCTCCTAA +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 80683 22 + 636262 CCCACTTGATATGCCCTCCTAA +s simRat_chr6.simRat.chr6 72959 22 + 647215 CCCACCTGATGCGCTCCCCCAA +s simRat_chr6.simRat.chr6 73337 22 + 647215 CCCACCTTATGTGCCTTCCCAA + +a +s simMouse_chr6.simMouse.chr6 81091 7 + 636262 TCTGCTC +s Anc0.Anc0refChr4 24803 4 - 45765 TCTG--- +s Anc1.Anc1refChr2 56202 7 + 144309 TCTGGTC +s Anc2.Anc2refChr7 24917 4 + 32194 TTTG--- +s mr.mrrefChr0 76763 7 + 130230 TCTGCTC +s mr.mrrefChr0 76390 7 + 130230 ACATGGC +s simCow_chr6.simCow.chr6 83278 4 + 602619 TTTG--- +s simDog_chr6.simDog.chr6 184398 4 + 593897 TTTG--- +s simMouse_chr6.simMouse.chr6 80705 7 + 636262 ACATGGC +s simRat_chr6.simRat.chr6 72981 7 + 647215 ACATGGC +s simRat_chr6.simRat.chr6 73360 7 + 647215 TCTGCCC + +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 81099 38 + 636262 CCCAATTTATTTGCCCTCCCAATTTATTTCGGACTCAG +s Anc0.Anc0refChr4 24807 12 - 45765 --------------------------TTTGGGACTCAG +s Anc1.Anc1refChr2 56209 38 + 144309 CCCACTTTAGTTCCCCTCCCAATTTTTTTGGGACTCAG +s Anc2.Anc2refChr7 24921 12 + 32194 --------------------------TTTGGGATTCAA +s mr.mrrefChr0 76771 38 + 130230 CCCAATTTATTTGCCCTCCCAATTTATTTCGGACTCAG +s mr.mrrefChr0 76397 38 + 130230 CCCACCTGAGGTCTCCTCCCAATTTTTTTGGGACTCAG +s simCow_chr6.simCow.chr6 83282 12 + 602619 --------------------------TTTGGGAGTCAA +s simDog_chr6.simDog.chr6 184402 12 + 593897 --------------------------TTTGGGATTCAA +s simMouse_chr6.simMouse.chr6 80712 38 + 636262 CCCACCTGAGGTCTCCTCCCAATTTTTTTGGGACTCAG +s simRat_chr6.simRat.chr6 72988 38 + 647215 CCGACCTGAGGTGCCCTCCCAATTTTTTTCAGACTCAG +s simRat_chr6.simRat.chr6 73368 38 + 647215 CCCAATTTATTTGACCTCACAATTTATTTGGGACTCAG + +a +s simMouse_chr6.simMouse.chr6 81137 1 + 636262 G +s Anc0.Anc0refChr4 24825 1 - 45765 A +s Anc1.Anc1refChr2 56253 1 + 144309 A +s Anc2.Anc2refChr7 24939 1 + 32194 A +s mr.mrrefChr0 76809 1 + 130230 G +s mr.mrrefChr0 76441 1 + 130230 A +s simDog_chr6.simDog.chr6 184420 1 + 593897 A +s simHuman_chr6.simHuman.chr6 76808 1 + 601863 A +s simMouse_chr6.simMouse.chr6 80756 1 + 636262 A +s simRat_chr6.simRat.chr6 73032 1 + 647215 A +s simRat_chr6.simRat.chr6 73406 1 + 647215 G + +a +s simMouse_chr6.simMouse.chr6 81138 3 + 636262 TAG +s Anc0.Anc0refChr4 24826 3 - 45765 TAT +s Anc1.Anc1refChr2 56254 3 + 144309 TAT +s Anc2.Anc2refChr7 24940 3 + 32194 TAT +s mr.mrrefChr0 76810 3 + 130230 TAG +s mr.mrrefChr0 76442 3 + 130230 TAG +s simDog_chr6.simDog.chr6 184421 3 + 593897 TAT +s simHuman_chr6.simHuman.chr6 76809 3 + 601863 TAT +s simMouse_chr6.simMouse.chr6 80757 3 + 636262 TAG +s simRat_chr6.simRat.chr6 73033 3 + 647215 TAA +s simRat_chr6.simRat.chr6 73413 3 + 647215 TAG + +a +s simMouse_chr6.simMouse.chr6 81141 9 + 636262 AGGACAACC +s Anc0.Anc0refChr4 24829 9 - 45765 AGAACAACC +s Anc1.Anc1refChr2 56257 9 + 144309 AGAACAACC +s Anc2.Anc2refChr7 24943 9 + 32194 AAAACAACC +s mr.mrrefChr0 76813 9 + 130230 AGGACAACC +s mr.mrrefChr0 76445 9 + 130230 AGAACAACC +s simDog_chr6.simDog.chr6 184424 9 + 593897 AAAACAACC +s simHuman_chr6.simHuman.chr6 76812 9 + 601863 AGGACAACC +s simMouse_chr6.simMouse.chr6 80763 9 + 636262 AGAACAACC +s simRat_chr6.simRat.chr6 73036 9 + 647215 GGAACAACC +s simRat_chr6.simRat.chr6 73416 9 + 647215 AGGACAACC + +a +s simMouse_chr6.simMouse.chr6 81150 13 + 636262 TTCTGTCTTCTGT +s Anc0.Anc0refChr4 24838 13 - 45765 TTGTGTCTCACAT +s Anc1.Anc1refChr2 56266 13 + 144309 TTGTGTCTCACAT +s Anc2.Anc2refChr7 24952 13 + 32194 TTGTGTCTCACAT +s mr.mrrefChr0 76822 13 + 130230 TTCTGTCTTCTGT +s mr.mrrefChr0 76454 13 + 130230 TTGTGTCTTCTGT +s simCow_chr6.simCow.chr6 83297 12 + 602619 -CGTGTCTCACAT +s simDog_chr6.simDog.chr6 184433 13 + 593897 TTGTGTCTCACAT +s simHuman_chr6.simHuman.chr6 76821 13 + 601863 TTGTGTCTCACAT +s simMouse_chr6.simMouse.chr6 80773 13 + 636262 TTGTGTCTTCTGT +s simRat_chr6.simRat.chr6 73045 13 + 647215 TTGTGTCTTTTGT +s simRat_chr6.simRat.chr6 73425 13 + 647215 TTCTGTCTTCTGT + +a +s simMouse_chr6.simMouse.chr6 81163 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 76835 5 + 130230 TCCAG +s mr.mrrefChr0 76467 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 80786 5 + 636262 TCCAG +s simRat_chr6.simRat.chr6 73058 5 + 647215 TCCAT +s simRat_chr6.simRat.chr6 73438 5 + 647215 TCCAG + +a +s simMouse_chr6.simMouse.chr6 81168 15 + 636262 AGGATTATTGGGGCT +s Anc0.Anc0refChr4 24857 15 - 45765 AGGTCTCCTGGCCCT +s Anc1.Anc1refChr2 56285 15 + 144309 AGGTCTCCTGGCCCT +s Anc2.Anc2refChr7 24971 15 + 32194 AGGTCTCCTGGCCCT +s mr.mrrefChr0 76840 15 + 130230 AGGATTATTGGGGCT +s mr.mrrefChr0 76472 15 + 130230 CGGATTAATGGGGTT +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 80791 15 + 636262 CGGATTAATGGGGTT +s simRat_chr6.simRat.chr6 73063 15 + 647215 TGGATTAATGGGGTT +s simRat_chr6.simRat.chr6 73443 15 + 647215 AGGATTATTGGAGCT + +a +s simMouse_chr6.simMouse.chr6 81183 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 76855 1 + 130230 G +s mr.mrrefChr0 76487 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 80806 1 + 636262 G +s simRat_chr6.simRat.chr6 73078 1 + 647215 G +s simRat_chr6.simRat.chr6 73458 1 + 647215 G + +a +s simMouse_chr6.simMouse.chr6 81184 23 + 636262 GACTCTATAGAACTCTGGATAAG +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 76856 23 + 130230 GACTCTATAGAACTCTGGATAAG +s mr.mrrefChr0 76490 23 + 130230 GAGTCTGCAGAACTCTGGATAAG +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 80809 23 + 636262 GAGTCTGCAGAACTCTGGATAAG +s simRat_chr6.simRat.chr6 73081 23 + 647215 GAATCTACAGAACTCTGCATAAA +s simRat_chr6.simRat.chr6 73459 23 + 647215 GACTCTTCAGAACTCTGTATAAG + +a +s simMouse_chr6.simMouse.chr6 81207 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 76879 2 + 130230 GC +s mr.mrrefChr0 76513 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 80832 2 + 636262 GC +s simRat_chr6.simRat.chr6 73104 2 + 647215 GC +s simRat_chr6.simRat.chr6 73482 2 + 647215 GC + +a s simMouse_chr6.simMouse.chr6 81209 15 + 636262 CACTCTGACAACTCA s Anc0.Anc0refChr4 24900 4 - 45765 ----CTAA------- s Anc1.Anc1refChr2 56330 4 + 144309 ----CTAA------- @@ -35665,21 +37195,16 @@ 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 +s simMouse_chr6.simMouse.chr6 94122 20 + 636262 ATTGTTATATTAACTGCCTG +s Anc0.Anc0refChr4 35645 2 - 45765 AT------------------ +s Anc1.Anc1refChr2 67459 2 + 144309 AT------------------ +s Anc1.Anc1refChr6 56112 18 - 197743 --TGTAATTTCAAAAAGTTG +s Anc2.Anc2refChr2 4569 2 + 27695 GT------------------ +s mr.mrrefChr0 89267 20 + 130230 ATTGTTATATTAACTGCCTG +s simCow_chr6.simCow.chr6 94876 2 + 602619 GT------------------ +s simDog_chr6.simDog.chr6 100281 2 + 593897 GT------------------ +s simHuman_chr6.simHuman.chr6 88716 18 + 601863 --TGTAATTTCAAAAAGTTG +s simRat_chr6.simRat.chr6 86251 20 + 647215 ATAGTAATATTAACTACCTG a s simMouse_chr6.simMouse.chr6 94142 15 + 636262 TGCCAAAGCATATTG @@ -38668,6 +40193,160 @@ s simRat_chr6.simRat.chr6 90589 29 + 647215 TTTAAA---TACATCCCACTGGCTTTGCAGAT a +s simMouse_chr6.simMouse.chr6 98471 4 + 636262 CATA +s Anc0.Anc0refChr4 39827 4 - 45765 AATG +s Anc1.Anc1refChr2 71801 4 + 144309 AATG +s Anc2.Anc2refChr2 9181 4 + 27695 AATG +s mr.mrrefChr0 93541 4 + 130230 CATA +s mr.mrrefChr0 93372 4 + 130230 AATG +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 98299 4 + 636262 AATG +s simRat_chr6.simRat.chr6 90440 4 + 647215 AATG +s simRat_chr6.simRat.chr6 90618 4 + 647215 CATA + +a +s simMouse_chr6.simMouse.chr6 98475 15 + 636262 TTGAATGACTATTAA +s Anc0.Anc0refChr4 39833 15 - 45765 TTGAAGGGCAATTAC +s Anc1.Anc1refChr2 71807 15 + 144309 TTGAAGGGCAATTAC +s Anc2.Anc2refChr2 9187 15 + 27695 CTGAAGGGCAATTAC +s mr.mrrefChr0 93545 15 + 130230 TTGAATGACTATTAA +s mr.mrrefChr0 93378 15 + 130230 TTTAGTGACAATTAA +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 98305 15 + 636262 TTTAGTGACAATTAA +s simRat_chr6.simRat.chr6 90446 15 + 647215 TTGAAGGACAATTAA +s simRat_chr6.simRat.chr6 90622 15 + 647215 TTGAAGGACCATTAA + +a +s simMouse_chr6.simMouse.chr6 98490 17 + 636262 TCGTTTTCTGAGTCCTG +s Anc0.Anc0refChr4 39848 17 - 45765 TCATTTTTTGTGGTCTA +s Anc1.Anc1refChr2 71822 17 + 144309 TCATTTTTTGTGGTCTA +s Anc2.Anc2refChr2 9202 17 + 27695 TCATTATGTGTGGTGTA +s mr.mrrefChr0 93560 17 + 130230 TCGTTTTCTGAGTCCTG +s mr.mrrefChr0 93393 17 + 130230 TCACTTTTTGAGGTCTG +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 98320 17 + 636262 TCACTTTTTGAGGTCTG +s simRat_chr6.simRat.chr6 90461 17 + 647215 TCATTTTTTAAAGTCTG +s simRat_chr6.simRat.chr6 90639 17 + 647215 TCATATTCTCAGGCCTG + +a +s simMouse_chr6.simMouse.chr6 98507 8 + 636262 CACGACCT +s Anc0.Anc0refChr4 39867 8 - 45765 CATGATCT +s Anc1.Anc1refChr2 71841 8 + 144309 CATGATCT +s Anc2.Anc2refChr2 9221 8 + 27695 CATGATCT +s mr.mrrefChr0 93577 8 + 130230 CACGACCT +s mr.mrrefChr0 93410 8 + 130230 CATGACCT +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 98337 8 + 636262 CATGACCT +s simRat_chr6.simRat.chr6 90478 8 + 647215 CATGACCC +s simRat_chr6.simRat.chr6 90656 8 + 647215 CCTGACCT + +a +s simMouse_chr6.simMouse.chr6 98515 4 + 636262 CTAT +s Anc0.Anc0refChr4 39876 4 - 45765 CTAG +s Anc1.Anc1refChr2 71850 4 + 144309 CTAG +s Anc2.Anc2refChr2 9230 4 + 27695 CTAG +s mr.mrrefChr0 93585 4 + 130230 CTAT +s mr.mrrefChr0 93418 4 + 130230 CTAA +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 98345 4 + 636262 CTAA +s simRat_chr6.simRat.chr6 90486 4 + 647215 CAAA +s simRat_chr6.simRat.chr6 90664 4 + 647215 CTAT + +a +s simMouse_chr6.simMouse.chr6 98519 8 + 636262 AATATCAA +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 93589 8 + 130230 AATATCAA +s mr.mrrefChr0 93422 8 + 130230 AATATCAG +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 98349 8 + 636262 AATATCAG +s simRat_chr6.simRat.chr6 90490 8 + 647215 AATATCAG +s simRat_chr6.simRat.chr6 90668 8 + 647215 AATATCAG + +a +s simMouse_chr6.simMouse.chr6 98527 1 + 636262 C +s Anc0.Anc0refChr4 39886 1 - 45765 G +s Anc1.Anc1refChr2 71862 1 + 144309 G +s Anc2.Anc2refChr2 9240 1 + 27695 G +s mr.mrrefChr0 93597 1 + 130230 C +s mr.mrrefChr0 93431 1 + 130230 T +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 98358 1 + 636262 T +s simRat_chr6.simRat.chr6 90499 1 + 647215 T +s simRat_chr6.simRat.chr6 90676 1 + 647215 C + +a +s simMouse_chr6.simMouse.chr6 98528 5 + 636262 TACCA +s Anc0.Anc0refChr4 39887 5 - 45765 CACCA +s Anc1.Anc1refChr2 71863 5 + 144309 CACCA +s Anc2.Anc2refChr2 9241 5 + 27695 CACTG +s mr.mrrefChr0 93598 5 + 130230 TACCA +s mr.mrrefChr0 93432 5 + 130230 TTCCA +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 98359 5 + 636262 TTCCA +s simRat_chr6.simRat.chr6 90500 5 + 647215 TACCA +s simRat_chr6.simRat.chr6 90678 5 + 647215 TAACG + +a +s simMouse_chr6.simMouse.chr6 98533 24 + 636262 ACTAACATTCAACCAGACAGTTCT +s Anc0.Anc0refChr4 39892 24 - 45765 ATTAGCATTTAACCATACAATTCG +s Anc1.Anc1refChr2 71868 24 + 144309 ATTAGCATTTAACCATACAATTCG +s Anc2.Anc2refChr2 9246 24 + 27695 ATTAGCATTTAACCATACAATGCG +s mr.mrrefChr0 93603 24 + 130230 ACTAGCATTCAACCATACAGTTCT +s mr.mrrefChr0 93437 24 + 130230 ACTAGCATTCAACCAGACAGTTTT +s simCow_chr6.simCow.chr6 99174 24 + 602619 ATTAGCGTTGCAACATACAATCCC +s simDog_chr6.simDog.chr6 495354 24 - 593897 ACTGGCATCTAACCATATAATGCG +s simHuman_chr6.simHuman.chr6 94624 24 + 601863 ATTAGCATTTAACCATACAATTCG +s simMouse_chr6.simMouse.chr6 98364 24 + 636262 ACTAGCATTCAACCAGACAGTTTT +s simRat_chr6.simRat.chr6 90513 24 + 647215 ACTAACATTCAACCAGACAGTTCT +s simRat_chr6.simRat.chr6 90683 23 + 647215 GCTAGCATT-ACTCCTTCAGTTGT + +a +s simMouse_chr6.simMouse.chr6 98557 1 + 636262 C +s Anc0.Anc0refChr4 39916 1 - 45765 C +s Anc1.Anc1refChr2 71892 1 + 144309 C +s Anc2.Anc2refChr2 9270 1 + 27695 C +s mr.mrrefChr0 93627 1 + 130230 C +s mr.mrrefChr0 93461 1 + 130230 T +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 98388 1 + 636262 T +s simRat_chr6.simRat.chr6 90537 1 + 647215 C +s simRat_chr6.simRat.chr6 90706 1 + 647215 C + +a +s simMouse_chr6.simMouse.chr6 98558 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 93628 6 + 130230 CTATCC +s mr.mrrefChr0 93474 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 98401 6 + 636262 CTATCC +s simRat_chr6.simRat.chr6 90550 6 + 647215 CTAGCC +s simRat_chr6.simRat.chr6 90707 6 + 647215 CTATCC + +a s simMouse_chr6.simMouse.chr6 98564 1 + 636262 G s Anc0.Anc0refChr4 39933 1 - 45765 T s Anc1.Anc1refChr2 71909 1 + 144309 T @@ -38679,6 +40358,48 @@ s simRat_chr6.simRat.chr6 90713 1 + 647215 T a +s simMouse_chr6.simMouse.chr6 98565 18 + 636262 ACTGTTTCCCATCAGATG +s Anc0.Anc0refChr4 39934 18 - 45765 ATTCCTTTTCATAAGATA +s Anc1.Anc1refChr2 71910 18 + 144309 ATTCCTTTTCATAAGATA +s Anc2.Anc2refChr2 9288 18 + 27695 ATTCCTGTTCATAAGATA +s mr.mrrefChr0 93635 18 + 130230 ATTGTTTCTCATAAGATG +s mr.mrrefChr0 93480 18 + 130230 ATCCTTTCCCACAAGATG +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 98407 18 + 636262 ATCCTTTCCCACAAGATG +s simRat_chr6.simRat.chr6 90557 18 + 647215 ATCCTGTCCCACAAGATG +s simRat_chr6.simRat.chr6 90714 18 + 647215 ATTGTTTCTCACAAGATG + +a +s simMouse_chr6.simMouse.chr6 98583 6 + 636262 GACCCC +s Anc0.Anc0refChr4 39952 6 - 45765 CATAGC +s Anc1.Anc1refChr2 71928 6 + 144309 CATAGC +s Anc2.Anc2refChr2 9306 6 + 27695 CATAGG +s mr.mrrefChr0 93653 6 + 130230 GACCCC +s mr.mrrefChr0 93498 6 + 130230 CCGACC +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 98425 6 + 636262 CCGACC +s simRat_chr6.simRat.chr6 90575 6 + 647215 CAGACC +s simRat_chr6.simRat.chr6 90734 6 + 647215 GACTAC + +a +s simMouse_chr6.simMouse.chr6 98589 8 + 636262 TTGCAAGG +s Anc0.Anc0refChr4 39958 8 - 45765 TTGCAAAA +s Anc1.Anc1refChr2 71934 8 + 144309 TTGCAAAA +s Anc2.Anc2refChr2 9312 8 + 27695 TTGCAAAA +s mr.mrrefChr0 93659 8 + 130230 TTGCAAGG +s mr.mrrefChr0 93504 8 + 130230 CTGTAAGA +s simCow_chr6.simCow.chr6 99240 8 + 602619 TTGCAGAA +s simDog_chr6.simDog.chr6 495503 8 - 593897 TTGCAAGA +s simHuman_chr6.simHuman.chr6 94690 8 + 601863 TTGTAAAA +s simMouse_chr6.simMouse.chr6 98431 8 + 636262 CTGTAAGA +s simRat_chr6.simRat.chr6 90581 8 + 647215 TTGTAAGG +s simRat_chr6.simRat.chr6 90743 6 + 647215 TTG--AGG + +a s simMouse_chr6.simMouse.chr6 98597 5 + 636262 TTTAA s Anc0.Anc0refChr4 39966 5 - 45765 TTTAA s Anc1.Anc1refChr2 71942 5 + 144309 TTTAA @@ -44894,59 +46615,129 @@ 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 +s simMouse_chr6.simMouse.chr6 114184 12 + 636262 TATTCCCAAACA +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 108883 12 + 130230 TATTCCCAAACA +s mr.mrrefChr0 108712 12 + 130230 TATTCCTAAAAA +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 114030 12 + 636262 TATTCCTAAAAA +s simRat_chr6.simRat.chr6 106355 12 + 647215 TCTTCCTAGAAG +s simRat_chr6.simRat.chr6 106541 12 + 647215 TATTCCCAAGGA + +a +s simMouse_chr6.simMouse.chr6 114196 29 + 636262 AGAAGTCCTCTCTATTTTGATCTTGGCTG +s Anc0.Anc0refChr1 7572 29 - 62388 AAAATCATTCTTCATTCTGATCTTGGCTG +s Anc1.Anc1refChr2 85753 29 + 144309 AAAATCATTCTTCATTCTGATCTTGGCTG +s Anc2.Anc2refChr2 23288 29 + 27695 AAAATCATACTTAATTCTGATCTTGGCTG +s mr.mrrefChr0 108895 29 + 130230 AGAAGTCCTCTCTATTTTGATCTTGGCTG +s mr.mrrefChr0 108726 29 + 130230 ATAAGCACTCTTCTGTCTGAGCTTGGCTG +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 114044 29 + 636262 ATAAGCACTCTTCTGTCTAAGCTTGGCTG +s simRat_chr6.simRat.chr6 106369 29 + 647215 ACAAGCACTCTTTAGTCTGAGCTTGGCTG +s simRat_chr6.simRat.chr6 106553 29 + 647215 AAAAGTACTCTCTATTTTGATCTTGGCTG + +a +s simMouse_chr6.simMouse.chr6 114225 24 + 636262 CTAAGGCTTTGATAGACACTGCAT +s Anc0.Anc0refChr1 7602 24 - 62388 CTAAGGCTTTGAGAGGCTCAGGAA +s Anc1.Anc1refChr2 85783 24 + 144309 CTAAGGCTTTGAGAGGCTCAGGAA +s Anc2.Anc2refChr2 23318 24 + 27695 CTAAGGCTTTGAGAGGCTCAGGAA +s mr.mrrefChr0 108924 24 + 130230 CTAAGGCTTTGATAGACACTGCAT +s mr.mrrefChr0 108756 24 + 130230 CCAAGGCTTTGATAGGCAAAAGGA +s simCow_chr6.simCow.chr6 117468 24 + 602619 CTAGGTCTTTGAGAGGCTCATGAT +s simDog_chr6.simDog.chr6 510182 24 - 593897 CTAAGGCTTTGAGAGGCTTAGGGA +s simHuman_chr6.simHuman.chr6 109742 24 + 601863 ATAAGGCTTTGAGGGGCTCACGAA +s simMouse_chr6.simMouse.chr6 114074 23 + 636262 CCAAGGCTTTGATAGGC-AAAGGA +s simRat_chr6.simRat.chr6 106399 24 + 647215 CCAAGGCTTTGATAGGCAAAAGGA +s simRat_chr6.simRat.chr6 106607 24 + 647215 CTAAGACTTTGATAAGCACTGCAT + +a +s simMouse_chr6.simMouse.chr6 114249 8 + 636262 CACAGGTT +s Anc0.Anc0refChr1 7626 8 - 62388 CAGAGGTC +s Anc1.Anc1refChr2 85807 8 + 144309 CAGAGGTC +s Anc2.Anc2refChr2 23342 8 + 27695 CAGAGGTC +s mr.mrrefChr0 108948 8 + 130230 CACAGGTT +s mr.mrrefChr0 108780 8 + 130230 CACAGGTT +s simCow_chr6.simCow.chr6 117492 8 + 602619 CAGAAACT +s simDog_chr6.simDog.chr6 510207 8 - 593897 CAGAGGTC +s simHuman_chr6.simHuman.chr6 109766 8 + 601863 CAGAGGTC +s simMouse_chr6.simMouse.chr6 114097 8 + 636262 CACAGGTT +s simRat_chr6.simRat.chr6 106423 8 + 647215 TACAGGAT +s simRat_chr6.simRat.chr6 106631 8 + 647215 CACAGGTT + +a +s simMouse_chr6.simMouse.chr6 114257 2 + 636262 GA +s Anc0.Anc0refChr1 7634 2 - 62388 GA +s Anc1.Anc1refChr2 85815 2 + 144309 GA +s Anc2.Anc2refChr2 23350 2 + 27695 GA +s mr.mrrefChr0 108956 2 + 130230 GA +s mr.mrrefChr0 108788 2 + 130230 GA +s simCow_chr6.simCow.chr6 117500 2 + 602619 GA +s simDog_chr6.simDog.chr6 510215 2 - 593897 GG +s simHuman_chr6.simHuman.chr6 109774 2 + 601863 AA +s simMouse_chr6.simMouse.chr6 114105 2 + 636262 GA +s simRat_chr6.simRat.chr6 106639 2 + 647215 GG + +a +s simMouse_chr6.simMouse.chr6 114259 4 + 636262 CATC +s Anc0.Anc0refChr1 7636 4 - 62388 GGGC +s Anc1.Anc1refChr2 85817 4 + 144309 GGGC +s Anc2.Anc2refChr2 23352 4 + 27695 GGGC +s mr.mrrefChr0 108958 4 + 130230 CATC +s mr.mrrefChr0 108790 4 + 130230 GGGC +s simCow_chr6.simCow.chr6 117502 4 + 602619 GGGC +s simDog_chr6.simDog.chr6 510217 4 - 593897 GGGC +s simHuman_chr6.simHuman.chr6 109776 4 + 601863 GGGC +s simMouse_chr6.simMouse.chr6 114107 4 + 636262 GGGC +s simRat_chr6.simRat.chr6 106431 4 + 647215 AGGC +s simRat_chr6.simRat.chr6 106641 4 + 647215 CAGC + +a +s simMouse_chr6.simMouse.chr6 114263 25 + 636262 CAGAGCCAAGTGGGAATGTCAATGG +s Anc0.Anc0refChr1 7660 16 - 62388 C---------CAGGAGTGTTGATGG +s Anc1.Anc1refChr2 85841 16 + 144309 C---------CAGGAGTGTTGATGG +s Anc2.Anc2refChr2 23376 16 + 27695 T---------CAGGAGTGTTGATGG +s mr.mrrefChr0 108962 16 + 130230 C---------TGGGAATGTCAATGG +s mr.mrrefChr0 108818 16 + 130230 A---------TGGGGATGTTGATCG +s simCow_chr6.simCow.chr6 117526 16 + 602619 T---------TAGGATTGTCAATGG +s simDog_chr6.simDog.chr6 510245 16 - 593897 T---------CATGAGTGTTGATGG +s simHuman_chr6.simHuman.chr6 109800 16 + 601863 C---------CAGGAGTGTTGGTGG +s simMouse_chr6.simMouse.chr6 114135 13 + 636262 A---------TGGGGATGTTGA--- +s simRat_chr6.simRat.chr6 106467 16 + 647215 A---------TGGAGATGTCAATCG +s simRat_chr6.simRat.chr6 106645 16 + 647215 T---------TGGCACCTTTATTGG + +a +s simMouse_chr6.simMouse.chr6 114288 30 + 636262 GGAAGGTATTATTGGACCATACTTTTTTCA +s Anc0.Anc0refChr1 7676 30 - 62388 GGGAGGTCTTATTGAACCTTGCTTTTGTCC +s Anc1.Anc1refChr2 85857 30 + 144309 GGGAGGTCTTATTGAACCTTGCTTTTGTCC +s Anc2.Anc2refChr2 23392 30 + 27695 GGGAGGTCGTATTGAACCTTGCTTTTGTCC +s mr.mrrefChr0 108978 30 + 130230 GGAAGGTATTATTGGACCATACTTTTTTCA +s mr.mrrefChr0 108834 30 + 130230 GGGAAGTCTTCTTGAACCTGGCTTTTGACC +s simCow_chr6.simCow.chr6 117542 30 + 602619 GGGGGTTCCTATTGAACCTTGCCTTTGTTC +s simDog_chr6.simDog.chr6 510261 30 - 593897 GGGAGGTTGTATTAGACCTTGCTTTTGGCC +s simHuman_chr6.simHuman.chr6 109816 30 + 601863 GGGAGGTCTTATTGAACTTCGCTCTTGTCT +s simMouse_chr6.simMouse.chr6 114148 24 + 636262 ------TCTTCTGAAACCTGGCTTTTGACC +s simRat_chr6.simRat.chr6 106483 30 + 647215 GGGAAGTCTTCTTGGACCTGGCTTTTGACC +s simRat_chr6.simRat.chr6 106664 30 + 647215 GGAAGGTATTATTGAGCCGTACTGTTGTCA + +a +s simMouse_chr6.simMouse.chr6 114318 6 + 636262 TCTATG +s Anc0.Anc0refChr1 7708 6 - 62388 AAGATG +s Anc1.Anc1refChr2 85889 6 + 144309 AAGATG +s Anc2.Anc2refChr2 23424 6 + 27695 AAGATG +s mr.mrrefChr0 109008 6 + 130230 TCTATG +s mr.mrrefChr0 108864 6 + 130230 AAGATG +s simCow_chr6.simCow.chr6 117573 6 + 602619 AAGCTG +s simDog_chr6.simDog.chr6 510293 6 - 593897 AAGATA +s simHuman_chr6.simHuman.chr6 109848 6 + 601863 AAGATG +s simMouse_chr6.simMouse.chr6 114172 1 + 636262 A----- +s simRat_chr6.simRat.chr6 106513 6 + 647215 AAGATG +s simRat_chr6.simRat.chr6 106694 6 + 647215 TCTAGG a s simMouse_chr6.simMouse.chr6 114324 15 + 636262 ATTATCTCAAGCCAT @@ -44973,6 +46764,20 @@ s simRat_chr6.simRat.chr6 106715 2 + 647215 AT a +s simMouse_chr6.simMouse.chr6 114341 11 + 636262 TGCTGCTTGAT +s Anc0.Anc0refChr1 7728 11 - 62388 TGCTATTGGAC +s Anc1.Anc1refChr2 85909 11 + 144309 TGCTATTGGAC +s Anc2.Anc2refChr2 23444 11 + 27695 TGCTATTGGAC +s mr.mrrefChr0 109031 11 + 130230 TGCTACTTGAT +s mr.mrrefChr0 108872 11 + 130230 TGCTATTGGAT +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 114173 11 + 636262 TGCTATTGGAT +s simRat_chr6.simRat.chr6 106530 11 + 647215 TGCTATTGACT +s simRat_chr6.simRat.chr6 106717 11 + 647215 TGTTACTTGAT + +a s simMouse_chr6.simMouse.chr6 114352 7 + 636262 TAGAGTA s Anc0.Anc0refChr1 7739 7 - 62388 TCTAGTA s Anc1.Anc1refChr2 85920 7 + 144309 TCTAGTA @@ -45261,6 +47066,76 @@ s simRat_chr6.simRat.chr6 107152 9 + 647215 TGCCT---TTCA a +s simMouse_chr6.simMouse.chr6 114790 23 + 636262 GGCTTACAACCCATATTCCCTTA +s Anc0.Anc0refChr1 54231 23 + 62388 GGCTTCCAACCCATAACCCCTAA +s Anc1.Anc1refChr2 57965 23 - 144309 GGCTTCCAACCCATAACCCCTAA +s Anc2.Anc2refChr2 3773 23 - 27695 GGCTTCCAACCCCTAACCCCCAA +s mr.mrrefChr0 109480 23 + 130230 GGCTTACAACCCATATTCCCTTA +s mr.mrrefChr0 20762 23 - 130230 GGTTCCTATCCCATAACACCTAG +s simCow_chr6.simCow.chr6 484552 23 - 602619 GGCTTCCAACCCCTACCCCGCCA +s simDog_chr6.simDog.chr6 83061 23 + 593897 GGCTTCCAACCCCTAACCCCCAA +s simHuman_chr6.simHuman.chr6 491574 23 - 601863 GGCTTCTGACCCATAACCCCTAA +s simMouse_chr6.simMouse.chr6 521484 23 - 636262 GGTTCCCATCCCATAACACCTAG +s simRat_chr6.simRat.chr6 540063 23 - 647215 GGTTCCTATCCCATAACACCTAG +s simRat_chr6.simRat.chr6 107161 23 + 647215 GGCTTGCAACTCACATTCCCCTA + +a +s simMouse_chr6.simMouse.chr6 114813 4 + 636262 TCAA +s Anc0.Anc0refChr1 54254 4 + 62388 TCAA +s Anc1.Anc1refChr2 57988 4 - 144309 TCAA +s Anc2.Anc2refChr2 3796 4 - 27695 GCAA +s mr.mrrefChr0 109503 4 + 130230 TCAA +s mr.mrrefChr0 20785 4 - 130230 TCGA +s simCow_chr6.simCow.chr6 484575 4 - 602619 CCAA +s simDog_chr6.simDog.chr6 83085 4 + 593897 GCAA +s simHuman_chr6.simHuman.chr6 491597 4 - 601863 TCAA +s simMouse_chr6.simMouse.chr6 521507 4 - 636262 TCGA +s simRat_chr6.simRat.chr6 540086 4 - 647215 TTGA +s simRat_chr6.simRat.chr6 107184 4 + 647215 TCAA + +a +s simMouse_chr6.simMouse.chr6 114817 14 + 636262 ATATCTAAGTGTGC +s Anc0.Anc0refChr1 54258 14 + 62388 ATATCTAAGTATGT +s Anc1.Anc1refChr2 57992 14 - 144309 ATATCTAAGTATGT +s Anc2.Anc2refChr2 3821 14 - 27695 ATATCCAAGTATGT +s mr.mrrefChr0 109507 14 + 130230 ATATCTAAGTGTGC +s mr.mrrefChr0 20789 14 - 130230 ATATCTAACTGTGA +s simCow_chr6.simCow.chr6 484605 14 - 602619 ATATCTAGGGATGT +s simDog_chr6.simDog.chr6 83110 14 + 593897 ATATCCAAGTATGT +s simHuman_chr6.simHuman.chr6 491601 14 - 601863 ATATCTAAGTATGT +s simMouse_chr6.simMouse.chr6 521511 14 - 636262 ATATCTAACTGTGA +s simRat_chr6.simRat.chr6 540090 14 - 647215 ATATCTAACTGTGC +s simRat_chr6.simRat.chr6 107188 14 + 647215 ATATCTAAGTGTGC + +a +s simMouse_chr6.simMouse.chr6 114831 8 + 636262 CTGTTAAC +s Anc0.Anc0refChr1 54272 8 + 62388 CTGTAACA +s Anc1.Anc1refChr2 58006 8 - 144309 CTGTAACA +s Anc2.Anc2refChr2 3835 8 - 27695 TTGTAACA +s mr.mrrefChr0 109521 8 + 130230 CTGTTAAC +s mr.mrrefChr0 20803 8 - 130230 ATGTGAAA +s simCow_chr6.simCow.chr6 484619 8 - 602619 TTATGATA +s simDog_chr6.simDog.chr6 83145 8 + 593897 TTGTAACA +s simHuman_chr6.simHuman.chr6 491615 8 - 601863 CTGTAACA +s simMouse_chr6.simMouse.chr6 521525 8 - 636262 ATGTGAAA +s simRat_chr6.simRat.chr6 540104 8 - 647215 ATATGGAA +s simRat_chr6.simRat.chr6 107202 8 + 647215 CTGTCAAC + +a +s simMouse_chr6.simMouse.chr6 114839 36 + 636262 TGGCTAGCATGTCCAATTGAATATCTTACTAACTGC +s Anc0.Anc0refChr1 54281 36 + 62388 TGATTAGTATGGTAATTTGAATATCACATTAATTGC +s Anc1.Anc1refChr2 58015 36 - 144309 TGATTAGTATGGTAATTTGAATATCACATTAATTGC +s Anc2.Anc2refChr2 3844 36 - 27695 TGATTAGGATGGTAATTTGGATATCACATTAATTGC +s mr.mrrefChr0 109529 36 + 130230 TGGCTAGCATGTCCAATTGAATATCTTACTAACTGC +s mr.mrrefChr0 20812 36 - 130230 TGGCTAGTATTGTCATTCAAATATCATGCTAATAGC +s simCow_chr6.simCow.chr6 484628 36 - 602619 TGATTAGGATGGTATTCTGGATATCGTATTATTTGC +s simDog_chr6.simDog.chr6 83154 36 + 593897 TGATTGGGATGGTAACTTGGATATTACACTAATTGC +s simHuman_chr6.simHuman.chr6 491624 36 - 601863 TGATTAATATGGTAATTCAAATATCACATTACTTGC +s simMouse_chr6.simMouse.chr6 521534 36 - 636262 TGGCTAGTATTGTCATTCAAGTATCATGCTAATAGC +s simRat_chr6.simRat.chr6 540113 36 - 647215 TGGCTAGAATTGCCATCCAGATATCATGCTAGCAGT +s simRat_chr6.simRat.chr6 107210 36 + 647215 TGGCTAGCCTGTTCAATCGAATATCCTACTAACTGC + +a s simMouse_chr6.simMouse.chr6 114875 74 + 636262 AGCTGCAGGAAAACACTTCTATTTCTGTGATAGGTCCATGTCAGGAACAGTGCTGGCAAAACTAGTAATTGCCG s Anc0.Anc0refChr1 8169 42 - 62388 --------------------------------GGTCCCTCTAGGAGACAATGCTGGCAAAGCTAGTAATTGCTG s Anc1.Anc1refChr2 86356 42 + 144309 --------------------------------GGTCCCTCTAGGAGACAATGCTGGCAAAGCTAGTAATTGCTG @@ -51477,9 +53352,82 @@ 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 +s simMouse_chr6.simMouse.chr6 130311 63 + 636262 AATGCTTACGGAGCGGTCCCCAGTAATTACTAGTTTATGTACACACTAATTGTTTAAAAATGG +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 129990 63 + 636262 AATGCTTACGGAGCGGTCCCCAGTAACTACTAGTTTATGTACACACTAATTGTTTAAAAATGG +s simRat_chr6.simRat.chr6 128177 43 + 647215 --------------------CAGTAATTACTAGTTTATGTACACACTAATTGTTTAAAAATGG + +a +s simMouse_chr6.simMouse.chr6 130374 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 130053 32 + 636262 CTTATTAAAAATCTAAGCTTGGGCTAACCCCT +s simRat_chr6.simRat.chr6 128221 32 + 647215 CTTATTAAAAATCTAAGCTTGGGCTGACCCCT + +a +s simMouse_chr6.simMouse.chr6 130406 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 130085 40 + 636262 CCTTAGTTGGAATTGAAATCGAACAATATTATCTTAAGGA +s simRat_chr6.simRat.chr6 128253 36 + 647215 CCTTCGTTGG----AACATCCAACAATATTATCTTAACAA + +a +s simMouse_chr6.simMouse.chr6 130446 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 130125 19 + 636262 ACAATGTGGCAATCAGTAG +s simRat_chr6.simRat.chr6 128303 19 + 647215 ACAATCAGCCAATCAGCAG + +a +s simMouse_chr6.simMouse.chr6 130465 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 130144 11 + 636262 CGGTTGCTTTG +s simRat_chr6.simRat.chr6 128322 11 + 647215 GGGTTTCTTTG + +a +s simMouse_chr6.simMouse.chr6 130476 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 130155 94 + 636262 TTATTCTTTTGGTAATCTACAAGAATGTGTGCCGTTAACAGGCTGGAACGGGGACTCATGTAATACAGCTCCTTGTTTGGTGGATTACAGCTTA +s simRat_chr6.simRat.chr6 128333 91 + 647215 CTATTCTTTTGATTATC---AAGAATGTGTGCTGTTAACAGGTTGGAAGGGAGACTTATGTAATGCAGCTCCTTGGTCGGTGGATTACAGCTTA + +a +s simMouse_chr6.simMouse.chr6 130570 114 + 636262 CCCTCTTGTTTAATTAGTGAGGGGGCTTGAACCTCTTGCAGCTCCTTGTTTAGTGGTTCTTACCCTTTCAGTCCGATTGATGAGGGTGTGACCCTAATGTCTCTCAGACCGATA +s mr.mrrefChr0 125030 114 + 130230 CCCTCTTGTTTAATTAATGAGGGGGCTTGAACCTCTTGCAGCTCCTTGTTTAGTGGTTCTTACCCCTTCAGTCCGATTGATGAGGGTGTGACCCTAATGTCTCTCAGACCGATA +s simMouse_chr6.simMouse.chr6 130249 62 + 636262 CCCTCTTGTTTAATTAATGAGGGGGCTTGAACCTCTTGCAGCTCCTTGTTTAGTGGTTCTTA---------------------------------------------------- +s simRat_chr6.simRat.chr6 128441 113 + 647215 CCCTCTTGTATAATTAATGAAAGGCCAAGGGTCCCATGCAGCTCCTTGTGTGGTGATTC-TACCCCTTCCATCCGGTTGATGAGGGTGTGACCCTAAAGTCCCTCAGTCTGATA a s simMouse_chr6.simMouse.chr6 130684 71 + 636262 CCACCCAAAACACATTACAAAATAGAGTTGAGTGCTACAGTATCAAGATTTTATGTAGACTTGAATATGTG @@ -54444,48 +56392,136 @@ 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 +s simMouse_chr6.simMouse.chr6 137198 11 + 636262 GTTGCAGTTTT +s Anc0.Anc0refChr1 28337 11 - 62388 GTTGAGGTATT +s Anc1.Anc1refChr2 107233 11 + 144309 GTTGAGGTATT +s Anc2.Anc2refChr3 17199 11 + 53186 GTTGAGGTATT +s mr.mrrefChr5 910 11 + 294540 GTTGCAGTATT +s simCow_chr6.simCow.chr6 144580 11 + 602619 GTTGAGGCATT +s simDog_chr6.simDog.chr6 429557 11 - 593897 TCCAAGGTATT +s simHuman_chr6.simHuman.chr6 131385 11 + 601863 GTTGAGGTATT +s simMouse_chr6.simMouse.chr6 136958 1 + 636262 ------G---- +s simRat_chr6.simRat.chr6 135071 11 + 647215 GTTGCAGTATT + +a +s simMouse_chr6.simMouse.chr6 137209 12 + 636262 ACTGAATGATAC +s Anc0.Anc0refChr1 28378 12 - 62388 ATTCAGTCAGAC +s Anc1.Anc1refChr2 107274 12 + 144309 ATTCAGTCAGAC +s Anc2.Anc2refChr3 17240 12 + 53186 ATCCAGCCAGAC +s mr.mrrefChr5 921 12 + 294540 ACTGAGTGATAC +s simCow_chr6.simCow.chr6 144621 12 + 602619 ATCCAGCCTGAC +s simDog_chr6.simDog.chr6 429599 9 - 593897 AT---GCCAAAC +s simHuman_chr6.simHuman.chr6 131426 12 + 601863 ATTAAGTCAGAC +s simMouse_chr6.simMouse.chr6 136959 4 + 636262 --------ATAC +s simRat_chr6.simRat.chr6 135082 12 + 647215 ATTGAGTGATAC + +a +s simMouse_chr6.simMouse.chr6 137221 8 + 636262 TTCTCGAA +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 136963 8 + 636262 ATCTAGAG +s simRat_chr6.simRat.chr6 135094 8 + 647215 AACTAGAG + +a +s simMouse_chr6.simMouse.chr6 137229 17 + 636262 CATGCTCTGTGTACTCC +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 136971 17 + 636262 CATGCTCTGTGTGCTCC +s simRat_chr6.simRat.chr6 135102 17 + 647215 TGTGCTCTGTATGCTCC + +a +s simMouse_chr6.simMouse.chr6 137246 17 + 636262 TCTTCTAATGGAGTGCA +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 136988 17 + 636262 TCTTCTAATGGGGTGCA +s simRat_chr6.simRat.chr6 135119 17 + 647215 TGTTCTAATGGAGTGCA + +a +s simMouse_chr6.simMouse.chr6 137263 8 + 636262 CTGCTCCT +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 137005 8 + 636262 GTGCTCCT +s simRat_chr6.simRat.chr6 135149 8 + 647215 ATGCTCCT + +a +s simMouse_chr6.simMouse.chr6 137271 48 + 636262 CTTAGTTGATGCAGCACATTTCTTGTGGATATGCGGCGACTTTCTAGT +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 137013 48 + 636262 CTAAGTTGATGCAGCACATTCCTTGTAGATAAGAGGCGACTTTCTAGC +s simRat_chr6.simRat.chr6 135179 46 + 647215 CCAAGTTGAAGCAGCACATTTCTTGTAGATAAGAGGCAACTTTC--GG + +a +s simMouse_chr6.simMouse.chr6 137319 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 137061 4 + 636262 AAGT +s simRat_chr6.simRat.chr6 135225 4 + 647215 ATGT + +a +s simMouse_chr6.simMouse.chr6 137323 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 137065 8 + 636262 ATCAAATG +s simRat_chr6.simRat.chr6 135230 8 + 647215 ATCAAAGG + +a +s simMouse_chr6.simMouse.chr6 137331 19 + 636262 AGAACTAATGAACTCAATG +s Anc0.Anc0refChr1 28477 19 - 62388 CATGCCAATGAACTCCCTG +s Anc1.Anc1refChr2 107373 19 + 144309 CATGCCAATGAACTCCCTG +s Anc2.Anc2refChr3 17350 19 + 53186 GATGCCAATGAACTCCCTG +s mr.mrrefChr5 1076 19 + 294540 CAAACTAATGAACTCAATG +s simCow_chr6.simCow.chr6 144742 18 + 602619 AATGCCAATGAAATCCCT- +s simDog_chr6.simDog.chr6 429720 17 - 593897 GAT--TGAGGAACTCCCTG +s simHuman_chr6.simHuman.chr6 131525 19 + 601863 CACGCCAATTAACCCCCTG +s simMouse_chr6.simMouse.chr6 137073 19 + 636262 CAAACCAATGAACTCAGTG +s simRat_chr6.simRat.chr6 135238 19 + 647215 CAAGTTGATGAACTCAATG + +a +s simMouse_chr6.simMouse.chr6 137350 28 + 636262 TTAAATTGTCTGTGCCTCGTGTATATAA +s Anc0.Anc0refChr1 28496 25 - 62388 TAAGATTGTCTATGCCCCATATAT---G +s Anc1.Anc1refChr2 107392 28 + 144309 TAAGATTGTCTATGCCCCATATATATCG +s Anc2.Anc2refChr3 17369 25 + 53186 TAAGATTGTCTATGCCCCATATAT---G +s mr.mrrefChr5 1095 28 + 294540 TTAGATTGTCTGTGCCCCATGTATATAA +s simCow_chr6.simCow.chr6 144760 24 + 602619 -AATACTGTCTATCCCTCATATAT---A +s simDog_chr6.simDog.chr6 429737 25 - 593897 TTAGATCATCTACGCCCCATATAT---G +s simHuman_chr6.simHuman.chr6 131544 21 + 601863 TAAGATTGTCTATGCC-------TATCG +s simMouse_chr6.simMouse.chr6 137093 9 + 636262 TTAGATTGC------------------- +s simRat_chr6.simRat.chr6 135257 28 + 647215 TTAGATTGTCTGTGCCCTATGTATATAT a s simMouse_chr6.simMouse.chr6 137378 14 + 636262 AGTAGTGCCATGTG @@ -55495,25 +57531,15 @@ 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 +s simMouse_chr6.simMouse.chr6 139680 41 + 636262 TCCAAAGTAGTTTCCTGAGACTCTATAATTAGGAAATAGAG +s Anc0.Anc0refChr1 30720 41 - 62388 TGCAGAAGAAATTCTTTACATTCTATAGTTAGGCAATAGAG +s Anc1.Anc1refChr2 109696 41 + 144309 TGCAGAAGAAATTCTTTACATTCTATAGTTAGGCAATAGAG +s Anc2.Anc2refChr3 19769 41 + 53186 TGCAGTAGAAATTCTTTACATTTTATAGTTTAGCAATAGAG +s mr.mrrefChr5 3311 41 + 294540 TCCAAAGTAGATTCCTGAGACTCTATAATTAGGAAATAGAG +s simCow_chr6.simCow.chr6 147333 41 + 602619 TGCAGTAGAAATTCTTTACATTTGGTAATTTAGTAATAGAG +s simDog_chr6.simDog.chr6 431518 23 - 593897 --------------TTTACATTTTATAG----GCGATAGAG +s simHuman_chr6.simHuman.chr6 133887 41 + 601863 TGCACATGAAATCCTTCACATTCTATAGTTAGGGAATAGAG +s simRat_chr6.simRat.chr6 137488 41 + 647215 TCCAAAGTAGATGCCTGAGACTCTTTAATTAGGAAAGAGAG a s simMouse_chr6.simMouse.chr6 139721 6 + 636262 TCACAG @@ -62023,16 +64049,82 @@ 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 +s simMouse_chr6.simMouse.chr6 157460 45 + 636262 CAGATAAAGTGCAAACCATACCTGCGTCAAAACAAATAAGGTGGG +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 157305 45 + 636262 CAGATAAAGTGCAAACTATACCTGCGTCAAAACAAATAATGTGGG +s simRat_chr6.simRat.chr6 154908 45 + 647215 CAGATAAAGTGCAGACCATACCTGCTTCAGGACTAACAAGGGGGG + +a +s simMouse_chr6.simMouse.chr6 157505 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 157350 52 + 636262 CTAACTCTGGAATAGATATCTCACTAACCCTTATTATAAGAGGATGTAGTGT +s simRat_chr6.simRat.chr6 154953 52 + 647215 CTAACTTTGGAATAGATATTTCACTAACCCTTATTATATGAAGGTGTAGTGT + +a +s simMouse_chr6.simMouse.chr6 157557 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 157402 37 + 636262 TTTCTTTTAATACCAGATGAGTTCTGTATCTGCCTAG +s simRat_chr6.simRat.chr6 155005 37 + 647215 TTTCTTTCAAAACCAGATGAGTTCTGTGTCTGCCTAC + +a +s simMouse_chr6.simMouse.chr6 157594 6 + 636262 TCCCTT +s Anc0.Anc0refChr5 78947 6 - 87904 TTTTTT +s Anc1.Anc1refChr8 35548 6 - 57822 TTTTTT +s Anc2.Anc2refChr15 84571 6 - 86568 TTTTTT +s mr.mrrefChr5 20437 6 + 294540 TCCCTT +s simCow_chr6.simCow.chr6 418656 6 - 602619 TTTTTT +s simCow_chr6.simCow.chr6 417426 6 - 602619 TTTTTT +s simDog_chr6.simDog.chr6 127192 6 + 593897 TTCTTT +s simHuman_chr6.simHuman.chr6 413667 6 - 601863 TTTATT +s simMouse_chr6.simMouse.chr6 157439 6 + 636262 TCCCTT +s simRat_chr6.simRat.chr6 155042 5 + 647215 -CCTTT + +a +s simMouse_chr6.simMouse.chr6 157600 5 + 636262 TTTCT +s Anc0.Anc0refChr5 78956 5 - 87904 TTTCT +s Anc1.Anc1refChr8 35557 5 - 57822 TTTCT +s Anc2.Anc2refChr15 84580 5 - 86568 TTTCT +s mr.mrrefChr5 20446 5 + 294540 TTTCT +s simCow_chr6.simCow.chr6 418665 5 - 602619 TTTGT +s simCow_chr6.simCow.chr6 417435 5 - 602619 TTTGT +s simDog_chr6.simDog.chr6 127201 5 + 593897 TTTCT +s simHuman_chr6.simHuman.chr6 413676 5 - 601863 TACCT +s simMouse_chr6.simMouse.chr6 157448 5 + 636262 TTTCT +s simRat_chr6.simRat.chr6 155047 5 + 647215 TTTCT + +a +s simMouse_chr6.simMouse.chr6 157605 22 + 636262 GCCCTCAGGGCCCTCACCCATT +s Anc0.Anc0refChr5 78961 22 - 87904 GCCCCCATGGCCCCCAGCTATT +s Anc1.Anc1refChr8 35562 22 - 57822 GCCCCCATGGCCCCCAGCTATT +s Anc2.Anc2refChr15 84585 22 - 86568 AGACCCATGGCTCCCAGCTGTT +s mr.mrrefChr5 20451 22 + 294540 GCCCACAGGGCCCCCAGCTATT +s simCow_chr6.simCow.chr6 418670 20 - 602619 C--CACATGGCTCCCAGTTGAT +s simCow_chr6.simCow.chr6 417440 20 - 602619 A--CACATCACTCCCAGTTGAT +s simDog_chr6.simDog.chr6 127206 22 + 593897 AGACCCATTGCTCCTAGCTGTT +s simHuman_chr6.simHuman.chr6 413681 22 - 601863 GCCCCCATGGTCTCCAGCTATT +s simMouse_chr6.simMouse.chr6 157453 7 + 636262 GCCCAAA--------------- +s simRat_chr6.simRat.chr6 155056 22 + 647215 ACCCATGGGGCCACCTGCTGTT a s simMouse_chr6.simMouse.chr6 157627 14 + 636262 AGACACCCAACACC @@ -63288,6 +65380,156 @@ s simRat_chr6.simRat.chr6 157368 17 + 647215 ATGGTTTCCAGAGATCC a +s simMouse_chr6.simMouse.chr6 159666 3 + 636262 GCA +s Anc0.Anc0refChr1 58907 3 - 62388 ACT +s Anc1.Anc1refChr2 140636 3 + 144309 ACT +s Anc1.Anc1refChr2 140470 3 + 144309 ACT +s Anc2.Anc2refChr3 49250 3 + 53186 ACT +s Anc2.Anc2refChr3 49419 3 + 53186 ACT +s mr.mrrefChr5 22582 3 + 294540 ACA +s mr.mrrefChr5 22413 3 + 294540 ACT +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 175729 3 + 601863 ACT +s simHuman_chr6.simHuman.chr6 175895 3 + 601863 ACT +s simMouse_chr6.simMouse.chr6 159497 3 + 636262 ACT +s simRat_chr6.simRat.chr6 157216 3 + 647215 ATC +s simRat_chr6.simRat.chr6 157385 3 + 647215 ACA + +a +s simMouse_chr6.simMouse.chr6 159669 1 + 636262 T +s Anc0.Anc0refChr1 58910 1 - 62388 T +s Anc1.Anc1refChr2 140639 1 + 144309 T +s Anc1.Anc1refChr2 140473 1 + 144309 T +s Anc2.Anc2refChr3 49253 1 + 53186 T +s Anc2.Anc2refChr3 49422 1 + 53186 T +s mr.mrrefChr5 22585 1 + 294540 T +s mr.mrrefChr5 22416 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 175732 1 + 601863 T +s simHuman_chr6.simHuman.chr6 175898 1 + 601863 T +s simMouse_chr6.simMouse.chr6 159500 1 + 636262 T +s simRat_chr6.simRat.chr6 157219 1 + 647215 T +s simRat_chr6.simRat.chr6 157388 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 159670 6 + 636262 ATAGCT +s Anc0.Anc0refChr1 58968 6 - 62388 ATAACC +s Anc1.Anc1refChr2 140640 6 + 144309 CTAGCC +s Anc1.Anc1refChr2 140529 6 + 144309 ATAACC +s Anc2.Anc2refChr3 49311 6 + 53186 ATAACC +s Anc2.Anc2refChr3 49485 6 + 53186 TTAGCC +s mr.mrrefChr5 22586 6 + 294540 ATAGCT +s mr.mrrefChr5 22478 6 + 294540 CTGAGC +s simCow_chr6.simCow.chr6 178449 6 + 602619 CTAGGC +s simCow_chr6.simCow.chr6 178302 6 + 602619 ATAGCC +s simDog_chr6.simDog.chr6 461775 6 - 593897 TTAGCC +s simDog_chr6.simDog.chr6 461584 6 - 593897 ATAACC +s simHuman_chr6.simHuman.chr6 175788 6 + 601863 TTAACC +s simHuman_chr6.simHuman.chr6 175899 2 + 601863 G----A +s simMouse_chr6.simMouse.chr6 159556 6 + 636262 CTGAGC +s simRat_chr6.simRat.chr6 157281 6 + 647215 CTCAGC +s simRat_chr6.simRat.chr6 157389 6 + 647215 ATAGCT + +a +s simMouse_chr6.simMouse.chr6 159676 5 + 636262 TGGCT +s Anc0.Anc0refChr1 58974 5 - 62388 TGGCT +s Anc1.Anc1refChr2 140646 5 + 144309 TGGCT +s Anc1.Anc1refChr2 140535 5 + 144309 TGGCT +s Anc2.Anc2refChr3 49317 5 + 53186 TGGCT +s Anc2.Anc2refChr3 49491 5 + 53186 TGGCT +s mr.mrrefChr5 22592 5 + 294540 TGGCT +s mr.mrrefChr5 22484 5 + 294540 TTGCA +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 175794 5 + 601863 TGGCT +s simHuman_chr6.simHuman.chr6 175901 5 + 601863 TAGAT +s simMouse_chr6.simMouse.chr6 159562 5 + 636262 TTACA +s simRat_chr6.simRat.chr6 157287 5 + 647215 TTGCA +s simRat_chr6.simRat.chr6 157395 5 + 647215 TGGCT + +a +s simMouse_chr6.simMouse.chr6 159681 2 + 636262 AA +s Anc0.Anc0refChr1 58979 2 - 62388 AA +s Anc1.Anc1refChr2 140651 2 + 144309 AA +s Anc1.Anc1refChr2 140540 2 + 144309 AA +s Anc2.Anc2refChr3 49322 2 + 53186 AA +s Anc2.Anc2refChr3 49496 2 + 53186 AA +s mr.mrrefChr5 22597 2 + 294540 AA +s mr.mrrefChr5 22489 2 + 294540 TG +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 175799 2 + 601863 AA +s simHuman_chr6.simHuman.chr6 175906 2 + 601863 AA +s simMouse_chr6.simMouse.chr6 159567 2 + 636262 TG +s simRat_chr6.simRat.chr6 157292 2 + 647215 CT +s simRat_chr6.simRat.chr6 157400 2 + 647215 GA + +a +s simMouse_chr6.simMouse.chr6 159683 5 + 636262 TCACT +s Anc0.Anc0refChr1 58981 5 - 62388 ACTCT +s Anc1.Anc1refChr2 140653 5 + 144309 ACACT +s Anc1.Anc1refChr2 140542 5 + 144309 ATTCT +s Anc2.Anc2refChr3 49324 5 + 53186 ATTCT +s Anc2.Anc2refChr3 49498 5 + 53186 ACACT +s mr.mrrefChr5 22599 5 + 294540 ACACT +s mr.mrrefChr5 22491 5 + 294540 CTCCT +s simCow_chr6.simCow.chr6 178470 5 + 602619 ACACT +s simCow_chr6.simCow.chr6 178315 5 + 602619 AAGCT +s simDog_chr6.simDog.chr6 461788 5 - 593897 ACACT +s simDog_chr6.simDog.chr6 461597 5 - 593897 ATTTT +s simHuman_chr6.simHuman.chr6 175801 5 + 601863 ATACT +s simHuman_chr6.simHuman.chr6 175908 5 + 601863 ACACT +s simMouse_chr6.simMouse.chr6 159569 5 + 636262 CTCCT +s simRat_chr6.simRat.chr6 157294 5 + 647215 CTTCT +s simRat_chr6.simRat.chr6 157402 5 + 647215 ACACG + +a +s simMouse_chr6.simMouse.chr6 159688 3 + 636262 AAT +s Anc0.Anc0refChr1 58986 3 - 62388 AAG +s Anc1.Anc1refChr2 140658 3 + 144309 CAG +s Anc1.Anc1refChr2 140547 3 + 144309 ACA +s Anc2.Anc2refChr3 49329 3 + 53186 AAA +s Anc2.Anc2refChr3 49503 3 + 53186 CAG +s mr.mrrefChr5 22604 3 + 294540 AAT +s mr.mrrefChr5 22496 3 + 294540 ACA +s simCow_chr6.simCow.chr6 178475 3 + 602619 TAG +s simCow_chr6.simCow.chr6 178320 3 + 602619 AAA +s simDog_chr6.simDog.chr6 461793 3 - 593897 CAG +s simDog_chr6.simDog.chr6 461602 3 - 593897 AAA +s simHuman_chr6.simHuman.chr6 175806 3 + 601863 ACA +s simHuman_chr6.simHuman.chr6 175913 3 + 601863 CAG +s simMouse_chr6.simMouse.chr6 159580 3 + 636262 ACA +s simRat_chr6.simRat.chr6 157299 3 + 647215 ACA +s simRat_chr6.simRat.chr6 157407 3 + 647215 AAT + +a +s simMouse_chr6.simMouse.chr6 159691 3 + 636262 CGT +s Anc0.Anc0refChr1 58989 3 - 62388 CAT +s Anc1.Anc1refChr2 140661 3 + 144309 CAT +s Anc1.Anc1refChr2 140550 3 + 144309 CAT +s Anc2.Anc2refChr3 49332 3 + 53186 CAT +s Anc2.Anc2refChr3 49506 3 + 53186 CAT +s mr.mrrefChr5 22607 3 + 294540 CAT +s mr.mrrefChr5 22508 3 + 294540 CAG +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 175809 3 + 601863 CAT +s simHuman_chr6.simHuman.chr6 175916 3 + 601863 CAT +s simMouse_chr6.simMouse.chr6 159592 3 + 636262 CGG +s simRat_chr6.simRat.chr6 157311 3 + 647215 CAG +s simRat_chr6.simRat.chr6 157410 3 + 647215 CAT + +a s simMouse_chr6.simMouse.chr6 159694 1 + 636262 C s Anc0.Anc0refChr1 58992 1 - 62388 C s Anc1.Anc1refChr2 140664 1 + 144309 C @@ -63302,6 +65544,25 @@ s simRat_chr6.simRat.chr6 157413 1 + 647215 C a +s simMouse_chr6.simMouse.chr6 159695 7 + 636262 CCTTAAT +s Anc0.Anc0refChr1 58993 7 - 62388 CCTTAAT +s Anc1.Anc1refChr2 140665 7 + 144309 CCTTAAT +s Anc1.Anc1refChr2 140553 7 + 144309 CCTTAAT +s Anc2.Anc2refChr3 49336 7 + 53186 CCTTAAT +s Anc2.Anc2refChr3 49510 7 + 53186 CCTTAAT +s mr.mrrefChr5 22611 7 + 294540 CCTTAAT +s mr.mrrefChr5 22511 7 + 294540 CTATTAA +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 175812 7 + 601863 CCTTAAT +s simHuman_chr6.simHuman.chr6 175920 7 + 601863 CATTAAT +s simMouse_chr6.simMouse.chr6 159595 7 + 636262 CTATTAA +s simRat_chr6.simRat.chr6 157314 7 + 647215 CAATTAA +s simRat_chr6.simRat.chr6 157414 7 + 647215 CCTTAAT + +a s simMouse_chr6.simMouse.chr6 159702 5 + 636262 AGATG s Anc0.Anc0refChr1 59000 5 - 62388 AGATG s Anc1.Anc1refChr2 140672 5 + 144309 AGATG @@ -64004,20 +66265,146 @@ 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 +s simMouse_chr6.simMouse.chr6 161225 7 + 636262 CATCACA +s Anc0.Anc0refChr1 60448 7 - 62388 TCCCGCA +s Anc1.Anc1refChr2 142263 7 + 144309 TCTTACA +s Anc1.Anc1refChr2 142144 7 + 144309 TCCCCCT +s Anc2.Anc2refChr3 50978 7 + 53186 TCCCGCT +s Anc2.Anc2refChr3 51093 7 + 53186 TCTTGCA +s mr.mrrefChr5 269600 7 - 294540 CATCACA +s mr.mrrefChr5 269543 7 - 294540 TCCCCCT +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 177357 7 + 601863 TCCCCCT +s simHuman_chr6.simHuman.chr6 177476 7 + 601863 ACTGACT +s simMouse_chr6.simMouse.chr6 161168 7 + 636262 TCCCCCT +s simRat_chr6.simRat.chr6 487492 7 - 647215 CATCACA + +a +s simMouse_chr6.simMouse.chr6 161232 11 + 636262 ATAAAAATGCT +s Anc0.Anc0refChr1 60455 11 - 62388 GTCACAATTTC +s Anc1.Anc1refChr2 142270 11 + 144309 GTCACAATTTC +s Anc1.Anc1refChr2 142151 11 + 144309 AGCACAGTGTC +s Anc2.Anc2refChr3 50985 11 + 53186 GGCACAATGTC +s Anc2.Anc2refChr3 51100 11 + 53186 GTCACAATTTC +s mr.mrrefChr5 269607 11 - 294540 ATAAAAATTTC +s mr.mrrefChr5 269550 11 - 294540 AGCACAGTGTT +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 177364 11 + 601863 AGCACAGTGTC +s simHuman_chr6.simHuman.chr6 177483 11 + 601863 GTCCCAATGTA +s simMouse_chr6.simMouse.chr6 161175 11 + 636262 AGCACAGTGTT +s simRat_chr6.simRat.chr6 487429 11 - 647215 AGTACAGTTTT +s simRat_chr6.simRat.chr6 487499 11 - 647215 ATATAAATTTC + +a +s simMouse_chr6.simMouse.chr6 161243 1 + 636262 C +s Anc0.Anc0refChr1 60466 1 - 62388 C +s Anc1.Anc1refChr2 142281 1 + 144309 C +s Anc1.Anc1refChr2 142162 1 + 144309 C +s Anc2.Anc2refChr3 50996 1 + 53186 C +s Anc2.Anc2refChr3 51111 1 + 53186 C +s mr.mrrefChr5 269618 1 - 294540 C +s mr.mrrefChr5 269561 1 - 294540 C +s simCow_chr6.simCow.chr6 180043 1 + 602619 C +s simCow_chr6.simCow.chr6 179957 1 + 602619 C +s simDog_chr6.simDog.chr6 463420 1 - 593897 C +s simDog_chr6.simDog.chr6 463305 1 - 593897 C +s simHuman_chr6.simHuman.chr6 177375 1 + 601863 A +s simHuman_chr6.simHuman.chr6 177494 1 + 601863 C +s simMouse_chr6.simMouse.chr6 161186 1 + 636262 C +s simRat_chr6.simRat.chr6 487440 1 - 647215 C +s simRat_chr6.simRat.chr6 487510 1 - 647215 C + +a +s simMouse_chr6.simMouse.chr6 161244 8 + 636262 TTAGACAG +s Anc0.Anc0refChr1 60467 8 - 62388 TATGCCAA +s Anc1.Anc1refChr2 142282 8 + 144309 TTTGACAA +s Anc1.Anc1refChr2 142163 8 + 144309 TATGCCTA +s Anc2.Anc2refChr3 50997 8 + 53186 CATGCCTA +s Anc2.Anc2refChr3 51112 8 + 53186 TTTGACAA +s mr.mrrefChr5 269619 8 - 294540 TTAGACAA +s mr.mrrefChr5 269562 7 - 294540 TCTG-TTA +s simCow_chr6.simCow.chr6 180044 8 + 602619 TTCACTGA +s simCow_chr6.simCow.chr6 179958 6 + 602619 CCTGCC-- +s simDog_chr6.simDog.chr6 463421 8 - 593897 TTTGACAA +s simDog_chr6.simDog.chr6 463306 8 - 593897 CATGCCTA +s simHuman_chr6.simHuman.chr6 177376 8 + 601863 TAAGACTA +s simHuman_chr6.simHuman.chr6 177495 8 + 601863 TCGGAGAG +s simMouse_chr6.simMouse.chr6 161187 7 + 636262 TCTG-TTA +s simRat_chr6.simRat.chr6 487511 8 - 647215 TTGGGCAA + +a +s simMouse_chr6.simMouse.chr6 161252 2 + 636262 TT +s Anc0.Anc0refChr1 60475 2 - 62388 TC +s Anc1.Anc1refChr2 142290 2 + 144309 TC +s Anc1.Anc1refChr2 142171 2 + 144309 TT +s Anc2.Anc2refChr3 51005 2 + 53186 TT +s Anc2.Anc2refChr3 51120 2 + 53186 TC +s mr.mrrefChr5 269627 2 - 294540 TT +s mr.mrrefChr5 269569 2 - 294540 TT +s simCow_chr6.simCow.chr6 180052 2 + 602619 TT +s simCow_chr6.simCow.chr6 179964 2 + 602619 TT +s simDog_chr6.simDog.chr6 463429 2 - 593897 TC +s simDog_chr6.simDog.chr6 463314 2 - 593897 TT +s simHuman_chr6.simHuman.chr6 177384 2 + 601863 TT +s simHuman_chr6.simHuman.chr6 177503 2 + 601863 TC +s simMouse_chr6.simMouse.chr6 161194 2 + 636262 TT +s simRat_chr6.simRat.chr6 487441 2 - 647215 TG +s simRat_chr6.simRat.chr6 487519 2 - 647215 TT + +a +s simMouse_chr6.simMouse.chr6 161254 4 + 636262 AATT +s Anc0.Anc0refChr1 60478 4 - 62388 AACT +s Anc1.Anc1refChr2 142293 4 + 144309 AACT +s Anc1.Anc1refChr2 142173 4 + 144309 AACT +s Anc2.Anc2refChr3 51007 4 + 53186 AACT +s Anc2.Anc2refChr3 51123 4 + 53186 AACT +s mr.mrrefChr5 269629 4 - 294540 AATT +s mr.mrrefChr5 269571 4 - 294540 CACT +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 177386 4 + 601863 AACT +s simHuman_chr6.simHuman.chr6 177506 4 + 601863 AACT +s simMouse_chr6.simMouse.chr6 161196 4 + 636262 CACT +s simRat_chr6.simRat.chr6 487443 4 - 647215 CACC +s simRat_chr6.simRat.chr6 487521 4 - 647215 AATT + +a +s simMouse_chr6.simMouse.chr6 161258 1 + 636262 T +s Anc0.Anc0refChr1 60482 1 - 62388 T +s Anc1.Anc1refChr2 142297 1 + 144309 T +s Anc1.Anc1refChr2 142177 1 + 144309 T +s Anc2.Anc2refChr3 51127 1 + 53186 T +s mr.mrrefChr5 269633 1 - 294540 T +s mr.mrrefChr5 269575 1 - 294540 A +s simCow_chr6.simCow.chr6 180058 1 + 602619 T +s simDog_chr6.simDog.chr6 463442 1 - 593897 T +s simHuman_chr6.simHuman.chr6 177390 1 + 601863 T +s simHuman_chr6.simHuman.chr6 177510 1 + 601863 T +s simMouse_chr6.simMouse.chr6 161200 1 + 636262 A +s simRat_chr6.simRat.chr6 487447 1 - 647215 G +s simRat_chr6.simRat.chr6 487525 1 - 647215 T + +a +s simMouse_chr6.simMouse.chr6 161259 3 + 636262 TAC +s Anc0.Anc0refChr1 60483 3 - 62388 TAC +s Anc1.Anc1refChr2 142298 3 + 144309 TAC +s Anc1.Anc1refChr2 142178 3 + 144309 TAA +s Anc2.Anc2refChr3 51128 3 + 53186 TTC +s mr.mrrefChr5 269634 3 - 294540 TAC +s mr.mrrefChr5 269576 3 - 294540 TAA +s simCow_chr6.simCow.chr6 180059 3 + 602619 TGC +s simDog_chr6.simDog.chr6 463451 3 - 593897 CTC +s simHuman_chr6.simHuman.chr6 177391 3 + 601863 TAA +s simHuman_chr6.simHuman.chr6 177511 3 + 601863 TAC +s simMouse_chr6.simMouse.chr6 161201 3 + 636262 TAA +s simRat_chr6.simRat.chr6 487448 3 - 647215 TAA +s simRat_chr6.simRat.chr6 487526 3 - 647215 TAC a s simMouse_chr6.simMouse.chr6 161262 5 + 636262 AAAAT @@ -70678,18 +73065,76 @@ 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 +s simMouse_chr6.simMouse.chr6 178753 24 + 636262 AACCTTGCCCTAGCTAGGTTAACA +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 178580 24 + 636262 CACCTTGCCCTGGCTAGGTTCATG +s simRat_chr6.simRat.chr6 373379 20 + 647215 CACCCTGCCCTGGCTATTTT---- + +a +s simMouse_chr6.simMouse.chr6 178777 31 + 636262 TGGTCTTTTCCCTTCGAGGAAAACTAATAAT +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 178604 31 + 636262 TGGTCTCGTCCCTTCGAGGGAGACTAATAAT +s simRat_chr6.simRat.chr6 373399 31 + 647215 CCATCTTGTCCCAGCTAGGGAAACTAATAAT + +a +s simMouse_chr6.simMouse.chr6 178808 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 178635 1 + 636262 T +s simRat_chr6.simRat.chr6 373430 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 178809 45 + 636262 CTGGTGACTTACTGTGTGGTAGGTCTAGGTCCTGGGTAGTTACAT +s Anc0.Anc0refChr3 7936 43 + 222631 CTGGTAATTTGCTGTT--GTGGGCCTGGTCCCTGGGTGGCTACCG +s Anc1.Anc1refChr6 40728 43 + 197743 CTGGTAATTTGCTGTT--GTGGGCCTGGTCCCTGGGTGGCTACCG +s Anc2.Anc2refChr13 10480 43 + 96486 CTGGTAATTTGCTGTT--GTGGGCCTGGTCTCTCGGTGGCTACCG +s mr.mrrefChr5 227814 43 + 294540 CTGGTGACTTACTGTG--GTAGGTCTAGGTCCTGGGTAGATACAT +s simCow_chr6.simCow.chr6 365987 40 + 602619 CTGGGAA--TGTTGTT--GTGCACCTGGTCTCTAGGTAGCT-CTG +s simDog_chr6.simDog.chr6 356849 43 + 593897 CTGGTAATTTGCCATT--ATGGGCTTGGTCTTGCAGTGGCTACCT +s simHuman_chr6.simHuman.chr6 364554 43 + 601863 CTGATAATCCGCTGTT--GTGAGCCCGGTCCCTGGGTGTCTACCG +s simMouse_chr6.simMouse.chr6 178636 43 + 636262 CTGGTGACTTACTGTG--GTAGGTCTAGGTCCTGGGTAGATACAT +s simRat_chr6.simRat.chr6 373441 43 + 647215 CTGGTGACTTGCTGCG--GTAGGCCTGGGTTTTGGGTAGATACAT + +a +s simMouse_chr6.simMouse.chr6 178854 26 + 636262 AATTTAGTTCCATACATTAATGTGAG +s Anc0.Anc0refChr3 7979 26 + 222631 AATTTAGTTCCATACATTAGTATGGG +s Anc1.Anc1refChr6 40771 26 + 197743 AATTTAGTTCCATACATTAGTATGGG +s Anc2.Anc2refChr13 10523 26 + 96486 AATTAAGTTCCATACATTAGTATGGG +s mr.mrrefChr5 227857 26 + 294540 AATTTAGTTCCATACATTAATGTGAG +s simCow_chr6.simCow.chr6 366030 26 + 602619 AACTAAGATCCATACATTAGCATGGA +s simDog_chr6.simDog.chr6 356892 26 + 593897 GATCAAGTTCCATCCATTAGTATGGG +s simHuman_chr6.simHuman.chr6 364597 26 + 601863 AATTTAGTTTCATACATTTGTATGGG +s simMouse_chr6.simMouse.chr6 178679 26 + 636262 GATTTAATTCCATACATTAATGTGAG +s simRat_chr6.simRat.chr6 373484 26 + 647215 AATTTAGTTCCATACATTCGTGTGAG + +a +s simMouse_chr6.simMouse.chr6 178880 137 + 636262 AAAGGTGTGTCCACACCTCTAAGGCTAGCCTGGCGAGACAGCAATCAATTGGGCCTGCTGCCATCATGTTCTTCTGATCCGGCTACTCTTCATTTCGGGTTGGTTAAAAAGGATATAACATGGACCGCCAGGCTCTG +s Anc0.Anc0refChr3 8011 19 + 222631 AAAAGT----------------------------------------------------------------------------------------------------------------------CCGCTAAGTTCTG +s Anc1.Anc1refChr6 40803 19 + 197743 AAAAGT----------------------------------------------------------------------------------------------------------------------CCGCTAAGTTCTG +s Anc2.Anc2refChr13 10555 19 + 96486 AACAGT----------------------------------------------------------------------------------------------------------------------TTGCTAAGTTCTG +s mr.mrrefChr5 227889 55 + 294540 AAAGGTGTGGCCACACCTCTAAGGCTAGCCTGGCGAGACAGC----------------------------------------------------------------------------------CCGCCAGGCTCTG +s simCow_chr6.simCow.chr6 366057 17 + 602619 --CAGG----------------------------------------------------------------------------------------------------------------------ATGCTAAGTTCTG +s simDog_chr6.simDog.chr6 356924 19 + 593897 AACAGT----------------------------------------------------------------------------------------------------------------------TTGCTATGTTCTG +s simHuman_chr6.simHuman.chr6 364629 19 + 601863 AAAAAT----------------------------------------------------------------------------------------------------------------------CCACTAAGTCCAG +s simMouse_chr6.simMouse.chr6 178711 42 + 636262 AAAGGTGTGGCCACACCTCTAAGTCTAGCCTGGCTAGACAGC----------------------------------------------------------------------------------------------- +s simRat_chr6.simRat.chr6 373516 19 + 647215 AAAGGT----------------------------------------------------------------------------------------------------------------------CTGCCAGGCTCTG a s simMouse_chr6.simMouse.chr6 179017 9 + 636262 AGTAGAATA @@ -97612,6 +100057,75 @@ s simRat_chr6.simRat.chr6 240280 4 + 647215 GGAG a +s simMouse_chr6.simMouse.chr6 250251 20 + 636262 TGGGGGCCCACTGTTATAAC +s Anc0.Anc0refChr5 67371 20 + 87904 TGGTGGCCCTTTGTGATACC +s Anc1.Anc1refChr7 26097 20 - 47259 TGGTGGCCCTTTGTGATACC +s Anc2.Anc2refChr15 64245 20 + 86568 TGGTGGCCCTTTGTGATACC +s mr.mrrefChr5 102945 20 + 294540 TGGGGGCCCACTGTGATAAC +s mr.mrrefChr5 194189 20 - 294540 TGGGGGCTCATCTTTTCTGC +s simCow_chr6.simCow.chr6 245807 20 + 602619 ACATGGCCCCTTGTGGTACC +s simDog_chr6.simDog.chr6 236631 19 + 593897 TGGTGGCTCTT-GTGATACA +s simHuman_chr6.simHuman.chr6 328423 20 - 601863 TGGTGGCCCTTAGTGATACC +s simMouse_chr6.simMouse.chr6 388684 20 - 636262 TGGGGGCTCATCTTTTCTGC +s simRat_chr6.simRat.chr6 409548 20 - 647215 GGGGGGCTCATCTTTTCTGG +s simRat_chr6.simRat.chr6 240284 20 + 647215 TGGGGGCCCCCTGTGACAAC + +a +s simMouse_chr6.simMouse.chr6 250271 21 + 636262 AAGGAGTCGGTCGTGGAGACA +s Anc0.Anc0refChr5 67391 21 + 87904 AAGCAATGGGTCTTGGAGTCA +s Anc1.Anc1refChr7 26117 21 - 47259 AAGCAATGGGTCTTGGAGTCA +s Anc2.Anc2refChr15 64265 21 + 86568 AAGCAATGGGACTTGGAGTCA +s mr.mrrefChr5 102965 21 + 294540 AAGCAGTGGGTCGTGGAGACA +s mr.mrrefChr5 194209 21 - 294540 GAGCAGTGGGTCTCAAAGGCA +s simCow_chr6.simCow.chr6 245827 19 + 602619 TAGCAATGGGACTTT--GTCA +s simDog_chr6.simDog.chr6 236650 21 + 593897 AAGCAATAGGACTTGGAGTCA +s simHuman_chr6.simHuman.chr6 328452 21 - 601863 ATGCAATGGGTTTTGGAGTTG +s simMouse_chr6.simMouse.chr6 388704 21 - 636262 GAGCAGTGGGTCTCAAAGGCA +s simRat_chr6.simRat.chr6 409568 21 - 647215 CAGCGGTGGGTCTTGAAGGCA +s simRat_chr6.simRat.chr6 240304 21 + 647215 AAGCCCTGGGTCACGGAGGCA + +a +s simMouse_chr6.simMouse.chr6 250292 23 + 636262 CTTAGATAGTTAAGAGTGGGTTT +s Anc0.Anc0refChr5 67412 23 + 87904 TCTAGATAATCAGGAGTAGGTTC +s Anc1.Anc1refChr7 26138 23 - 47259 TCTAGATAATCAGGAGTAGGTTC +s Anc2.Anc2refChr15 64286 23 + 86568 TCTTGATAATCAGGGGTAGGGTC +s mr.mrrefChr5 102986 23 + 294540 CTTAGATAGTTAAGAGTGGGTTT +s mr.mrrefChr5 194230 23 - 294540 CCTAGATAGTCGGGAGTGAGTTT +s simCow_chr6.simCow.chr6 245846 23 + 602619 TCTTGATAAATAGGGATACGGCT +s simDog_chr6.simDog.chr6 236671 23 + 593897 TCTTGATCATCAAGGGTAGGGTC +s simHuman_chr6.simHuman.chr6 328473 23 - 601863 TCTGGATAATAAGGAGTAAGTTC +s simMouse_chr6.simMouse.chr6 388725 23 - 636262 CCTAGATAGTCGGGAGTGAGTTT +s simRat_chr6.simRat.chr6 409589 23 - 647215 CCTAGATAGTCAAGAGTGGGATT +s simRat_chr6.simRat.chr6 240330 23 + 647215 CTTAGATAGTTAAGAGTGGGTTT + +a +s simMouse_chr6.simMouse.chr6 250315 6 + 636262 CTTAAT +s Anc0.Anc0refChr5 67435 6 + 87904 TTAACT +s Anc1.Anc1refChr7 26161 6 - 47259 TTAACT +s Anc2.Anc2refChr15 64311 6 + 86568 TTAACT +s mr.mrrefChr5 103009 6 + 294540 TTTAAT +s mr.mrrefChr5 194253 6 - 294540 CTTAAT +s simCow_chr6.simCow.chr6 245871 6 + 602619 TTATCT +s simDog_chr6.simDog.chr6 236696 5 + 593897 TTAAC- +s simHuman_chr6.simHuman.chr6 328496 6 - 601863 TTAACC +s simMouse_chr6.simMouse.chr6 388748 6 - 636262 CTTAAT +s simRat_chr6.simRat.chr6 409612 6 - 647215 CTTAAT +s simRat_chr6.simRat.chr6 240353 6 + 647215 TTTAAT + +a +s simMouse_chr6.simMouse.chr6 250321 1 + 636262 G +s Anc0.Anc0refChr5 67441 1 + 87904 A +s Anc1.Anc1refChr7 26167 1 - 47259 A +s Anc2.Anc2refChr15 64317 1 + 86568 A +s mr.mrrefChr5 103015 1 + 294540 G +s mr.mrrefChr5 194259 1 - 294540 A +s simCow_chr6.simCow.chr6 245877 1 + 602619 A +s simHuman_chr6.simHuman.chr6 328502 1 - 601863 A +s simMouse_chr6.simMouse.chr6 388754 1 - 636262 A +s simRat_chr6.simRat.chr6 409618 1 - 647215 G +s simRat_chr6.simRat.chr6 240360 1 + 647215 G + +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 @@ -97623,6 +100137,48 @@ s simRat_chr6.simRat.chr6 240361 1 + 647215 A---------- a +s simMouse_chr6.simMouse.chr6 250333 16 + 636262 GAATTCAACAAATATG +s Anc0.Anc0refChr5 67451 16 + 87904 AATATAATGAAATAAC +s Anc1.Anc1refChr7 26177 16 - 47259 AATATAATGAAATAAC +s Anc2.Anc2refChr15 64327 16 + 86568 AATATAATGAAATAAC +s mr.mrrefChr5 103025 16 + 294540 GAATTCAACAAATATG +s mr.mrrefChr5 194260 16 - 294540 GAATTAAGCAAATATG +s simCow_chr6.simCow.chr6 245887 16 + 602619 AGCACAATGAGACAAC +s simDog_chr6.simDog.chr6 236703 16 + 593897 AATATAATTAAATAAA +s simHuman_chr6.simHuman.chr6 328512 16 - 601863 AATATCATGAAATAAC +s simMouse_chr6.simMouse.chr6 388755 16 - 636262 GAATTAAGCAAATATG +s simRat_chr6.simRat.chr6 409619 16 - 647215 GAATTAAACAAATAGA +s simRat_chr6.simRat.chr6 240362 14 + 647215 --ATTCAACTAATATG + +a +s simMouse_chr6.simMouse.chr6 250349 16 + 636262 TACAGGTGTCTGAACG +s Anc0.Anc0refChr5 67481 16 + 87904 TACCGGTGTCAAGAGG +s Anc1.Anc1refChr7 26207 16 - 47259 TACCGGTGTCAAGAGG +s Anc2.Anc2refChr15 64357 16 + 86568 TACCAGTGTTAAGAGG +s mr.mrrefChr5 103050 16 + 294540 TACAGGTGTCTGAACG +s mr.mrrefChr5 194283 16 - 294540 TAGGGGTGTCTGAAAG +s simCow_chr6.simCow.chr6 245917 16 + 602619 TACCAGTGTTAAGAGG +s simDog_chr6.simDog.chr6 236734 16 + 593897 TACCAGTGTTTAGAGG +s simHuman_chr6.simHuman.chr6 328542 16 - 601863 TACCGGTCTGAAGAGG +s simMouse_chr6.simMouse.chr6 388780 16 - 636262 TAGGGGTGTCTGAAAG +s simRat_chr6.simRat.chr6 409642 16 - 647215 TACCAGTGTCCAGAGG +s simRat_chr6.simRat.chr6 240385 16 + 647215 TATGGGTGTCTGAATA + +a +s simMouse_chr6.simMouse.chr6 250365 5 + 636262 AGTTG +s Anc0.Anc0refChr5 67497 5 + 87904 AGTAG +s Anc1.Anc1refChr7 26223 5 - 47259 AGTAG +s Anc2.Anc2refChr15 64378 5 + 86568 AGGAT +s mr.mrrefChr5 103066 5 + 294540 AGTTG +s mr.mrrefChr5 194299 5 - 294540 AGTTG +s simCow_chr6.simCow.chr6 245938 5 + 602619 GGGAT +s simDog_chr6.simDog.chr6 236755 5 + 593897 AGGAT +s simHuman_chr6.simHuman.chr6 328558 5 - 601863 AGTAG +s simMouse_chr6.simMouse.chr6 388796 5 - 636262 AGTTG +s simRat_chr6.simRat.chr6 409658 5 - 647215 AGTTG +s simRat_chr6.simRat.chr6 240401 5 + 647215 AGCTG + +a s simMouse_chr6.simMouse.chr6 250370 1 + 636262 T s Anc0.Anc0refChr5 67502 1 + 87904 T s Anc1.Anc1refChr7 26228 1 - 47259 T @@ -97634,6 +100190,90 @@ s simRat_chr6.simRat.chr6 240406 1 + 647215 T a +s simMouse_chr6.simMouse.chr6 250371 3 + 636262 TCC +s Anc0.Anc0refChr5 67503 3 + 87904 TTA +s Anc1.Anc1refChr7 26229 3 - 47259 TTA +s Anc2.Anc2refChr15 64384 3 + 86568 TGA +s mr.mrrefChr5 103072 3 + 294540 TTC +s mr.mrrefChr5 194304 3 - 294540 TTC +s simCow_chr6.simCow.chr6 245944 3 + 602619 TGA +s simDog_chr6.simDog.chr6 236761 3 + 593897 TGA +s simHuman_chr6.simHuman.chr6 328564 3 - 601863 TTA +s simMouse_chr6.simMouse.chr6 388801 3 - 636262 TTC +s simRat_chr6.simRat.chr6 409663 3 - 647215 TTC +s simRat_chr6.simRat.chr6 240407 3 + 647215 TTC + +a +s simMouse_chr6.simMouse.chr6 250374 39 + 636262 TAGCTAAAATGATACAAATATAAGGCTACCCAACTGACC +s Anc0.Anc0refChr5 67514 39 + 87904 TAACTAATATGATGCAACTTTAGGGCTACCCAACCGACC +s Anc1.Anc1refChr7 26240 39 - 47259 TAACTAATATGATGCAACTTTAGGGCTACCCAACCGACC +s Anc2.Anc2refChr15 64395 39 + 86568 CAACTAATATGAAGAAACTTCAGGGCTACCCAACCTACC +s mr.mrrefChr5 103083 39 + 294540 TAGCTAAAATGATACAAATATAAGGCTACCCAACTGACC +s mr.mrrefChr5 194315 39 - 294540 GAGCAAAAATGATATAAGTTGAATGCTACCCAGCTGACA +s simCow_chr6.simCow.chr6 245955 39 + 602619 CAACTAACATTAGGAAACTTCAGGGCTACCCAACCGACC +s simDog_chr6.simDog.chr6 236772 39 + 593897 CGACCAATATGAACAAACTTCAAGGCTACTCAACCTAAC +s simHuman_chr6.simHuman.chr6 328575 39 - 601863 TAACTAATATAATGCCACTTTAGGGCTACCCAACCAACT +s simMouse_chr6.simMouse.chr6 388812 39 - 636262 GAGCAAAAATGATATAAGTTGAATGCTACCCAGCTGACA +s simRat_chr6.simRat.chr6 409674 39 - 647215 TAGCTAAGACGTCATGAGTTCAGGGCTATGTGGCTGACT +s simRat_chr6.simRat.chr6 240418 38 + 647215 TAGCTAAAATGATACAAGT-CAAGGCTACCCAGCAGACC + +a +s simMouse_chr6.simMouse.chr6 250413 17 + 636262 TATCAAACAACGAAGTC +s Anc0.Anc0refChr5 67572 17 + 87904 TGTTAAGAAACACAATT +s Anc1.Anc1refChr7 26298 17 - 47259 TGTTAAGAAACACAATT +s Anc2.Anc2refChr15 64453 17 + 86568 TGTTAAGACACACAATT +s mr.mrrefChr5 103122 17 + 294540 TGTCAAACAACAAAGTC +s mr.mrrefChr5 194354 17 - 294540 TGTCAAAGAATGAAGTC +s simCow_chr6.simCow.chr6 246013 17 + 602619 TGTTAACACACACAATC +s simDog_chr6.simDog.chr6 236831 17 + 593897 TGTTAAGACACACAATT +s simHuman_chr6.simHuman.chr6 328633 17 - 601863 TGTTAGGAAGCACAATT +s simMouse_chr6.simMouse.chr6 388851 17 - 636262 TGTCAAAGAATGAAGTC +s simRat_chr6.simRat.chr6 409713 17 - 647215 TGTCAAAGAACAAAGTC +s simRat_chr6.simRat.chr6 240456 17 + 647215 TGCCAAAGAACAGGGTC + +a +s simMouse_chr6.simMouse.chr6 250430 10 + 636262 TATATCAGGT +s Anc0.Anc0refChr5 67589 8 + 87904 --TACCAGGT +s Anc1.Anc1refChr7 26315 10 - 47259 TATACCAGGT +s Anc2.Anc2refChr15 64470 8 + 86568 --TTCCAGGT +s mr.mrrefChr5 103139 10 + 294540 TATACCAGGT +s mr.mrrefChr5 194372 10 - 294540 TATATCAGGT +s simCow_chr6.simCow.chr6 246030 8 + 602619 --TTCCAACC +s simDog_chr6.simDog.chr6 236848 8 + 593897 --TTCCAGGT +s simHuman_chr6.simHuman.chr6 328650 8 - 601863 --TACCAGGT +s simMouse_chr6.simMouse.chr6 388879 10 - 636262 TATATCAGGT +s simRat_chr6.simRat.chr6 409731 10 - 647215 TATATCAGGT +s simRat_chr6.simRat.chr6 240473 10 + 647215 TATACCAGGT + +a +s simMouse_chr6.simMouse.chr6 250440 5 + 636262 TGCAG +s Anc0.Anc0refChr5 67597 5 + 87904 AGCAG +s Anc1.Anc1refChr7 26325 5 - 47259 AGCAG +s Anc2.Anc2refChr15 64478 5 + 86568 ACCAG +s mr.mrrefChr5 103149 5 + 294540 TGCAG +s mr.mrrefChr5 194382 5 - 294540 CACCC +s simCow_chr6.simCow.chr6 246043 5 + 602619 ACCAG +s simDog_chr6.simDog.chr6 236856 5 + 593897 ACCAT +s simHuman_chr6.simHuman.chr6 328658 4 - 601863 AG-AG +s simMouse_chr6.simMouse.chr6 388889 5 - 636262 CACCC +s simRat_chr6.simRat.chr6 409741 5 - 647215 CACCC +s simRat_chr6.simRat.chr6 240483 5 + 647215 CGCAG + +a +s simMouse_chr6.simMouse.chr6 250445 3 + 636262 GCC +s Anc0.Anc0refChr5 67602 3 + 87904 GCC +s Anc1.Anc1refChr7 26330 3 - 47259 GCC +s Anc2.Anc2refChr15 64483 3 + 86568 GCC +s mr.mrrefChr5 103154 3 + 294540 GCC +s mr.mrrefChr5 194387 3 - 294540 CAA +s simCow_chr6.simCow.chr6 246048 3 + 602619 ACC +s simDog_chr6.simDog.chr6 236861 3 + 593897 GCA +s simHuman_chr6.simHuman.chr6 328662 3 - 601863 GCC +s simMouse_chr6.simMouse.chr6 388896 3 - 636262 CAA +s simRat_chr6.simRat.chr6 409746 3 - 647215 CAG +s simRat_chr6.simRat.chr6 240488 3 + 647215 GCC + +a s simMouse_chr6.simMouse.chr6 250448 11 + 636262 TATGACATATC s Anc0.Anc0refChr5 67605 11 + 87904 TGTGACACATA s Anc1.Anc1refChr7 26333 11 - 47259 TGTGACACATA @@ -98479,57 +101119,246 @@ 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 +s simMouse_chr6.simMouse.chr6 251622 2 + 636262 AC +s Anc0.Anc0refChr5 19201 2 - 87904 GC +s Anc1.Anc1refChr7 19788 2 + 47259 GC +s Anc2.Anc2refChr15 20962 2 - 86568 GT +s mr.mrrefChr5 104283 2 + 294540 AC +s mr.mrrefChr5 190282 2 - 294540 AC +s simCow_chr6.simCow.chr6 355422 2 - 602619 GG +s simDog_chr6.simDog.chr6 356040 2 - 593897 AT +s simHuman_chr6.simHuman.chr6 272027 2 + 601863 GA +s simMouse_chr6.simMouse.chr6 384668 2 - 636262 AC + +a +s simMouse_chr6.simMouse.chr6 251624 13 + 636262 TGTGTACCCTCTC +s Anc0.Anc0refChr5 19203 13 - 87904 TGTGTACTCTATC +s Anc1.Anc1refChr7 19790 13 + 47259 TGTGTACTCTATC +s Anc2.Anc2refChr15 20964 13 - 86568 TGTGTACTCTACC +s mr.mrrefChr5 104285 13 + 294540 TGTGTACCCTCTC +s mr.mrrefChr5 190284 13 - 294540 TGTATACCCTCGC +s simCow_chr6.simCow.chr6 355424 13 - 602619 CATGTACCCTAAC +s simDog_chr6.simDog.chr6 356042 13 - 593897 TGTGTACTCTACC +s simHuman_chr6.simHuman.chr6 272029 13 + 601863 TGTATACTCTATC +s simMouse_chr6.simMouse.chr6 384671 13 - 636262 TGTATACCCTCGC +s simRat_chr6.simRat.chr6 241465 6 + 647215 -------TCTATC + +a +s simMouse_chr6.simMouse.chr6 251637 3 + 636262 ACA +s Anc0.Anc0refChr5 19279 3 - 87904 ACG +s Anc1.Anc1refChr7 19866 3 + 47259 ACG +s Anc2.Anc2refChr15 21043 3 - 86568 ATG +s mr.mrrefChr5 104298 3 + 294540 ACA +s mr.mrrefChr5 190344 3 - 294540 ACA +s simCow_chr6.simCow.chr6 355504 3 - 602619 ATA +s simDog_chr6.simDog.chr6 356121 3 - 593897 TTG +s simHuman_chr6.simHuman.chr6 272105 3 + 601863 AAG +s simMouse_chr6.simMouse.chr6 384731 3 - 636262 ACA +s simRat_chr6.simRat.chr6 241471 3 + 647215 ACA + +a +s simMouse_chr6.simMouse.chr6 251640 56 + 636262 TCTTTCTATTACTCATCCCTGAGAACACTCGGGTCATCTAACCCAGAAACTGGATA +s Anc0.Anc0refChr5 19282 52 - 87904 GCATTTT-TTAGTCATCCTTCATAACACTGAGGTCATCTAAACTAGAAATC---TA +s Anc1.Anc1refChr7 19869 52 + 47259 GCATTTT-TTAGTCATCCTTCATAACACTGAGGTCATCTAAACTAGAAATC---TA +s Anc2.Anc2refChr15 21046 52 - 86568 GCATTTT-TTAGTCATCCTTCATAACACAGATGTCATCTAAACTAGAAATC---TA +s mr.mrrefChr5 104301 56 + 294540 TCTTTCTATTACTCATCCCTGAGAACACTCGGGTCATCTAACCCAGAAACTGGATA +s mr.mrrefChr5 190347 51 - 294540 GCATTTT-TCATTTATCCTTGA-AACACTAGGGTCATCTAAACTAGAAATC---TG +s simCow_chr6.simCow.chr6 355507 52 - 602619 GCATTTT-TTCGTTATTCTTCATAATACTAATGTCATCCCAATTAGAAGTC---TA +s simDog_chr6.simDog.chr6 356124 48 - 593897 GCATTTG-CTAGTCATCCTTCACGACACAGATG----CTAAACAAGAAATC---TA +s simHuman_chr6.simHuman.chr6 272108 52 + 601863 GCATTTT-TTAGTCATCCTTCATAACATGTAGGTCATCTAAACTTGAAATC---TA +s simMouse_chr6.simMouse.chr6 384734 51 - 636262 GCATTTT-TCATTTATCCTTGA-AACACTAGGGTCATCTAAACTAGAAATC---TG +s simRat_chr6.simRat.chr6 241475 56 + 647215 TGCATCTTTTACTCATCCTTGAGAACAGTTGGGTCATCTGAACTAGAAACTGGACA + +a +s simMouse_chr6.simMouse.chr6 251696 5 + 636262 GCAAA +s Anc0.Anc0refChr5 19334 5 - 87904 GGAGA +s Anc1.Anc1refChr7 19921 5 + 47259 GGAGA +s Anc2.Anc2refChr15 21098 5 - 86568 GGTGA +s mr.mrrefChr5 104357 5 + 294540 GCAAA +s mr.mrrefChr5 190398 5 - 294540 TGAAA +s simCow_chr6.simCow.chr6 355559 5 - 602619 GGTGA +s simDog_chr6.simDog.chr6 356172 5 - 593897 GGTGA +s simHuman_chr6.simHuman.chr6 272160 5 + 601863 GGAGT +s simMouse_chr6.simMouse.chr6 384849 5 - 636262 TGAAA +s simRat_chr6.simRat.chr6 241531 5 + 647215 ATAAT + +a +s simMouse_chr6.simMouse.chr6 251701 16 + 636262 GCAGAGAGAGCAAAAT +s Anc0.Anc0refChr5 19339 14 - 87904 ACAGAAAG--CATAAT +s Anc1.Anc1refChr7 19926 14 + 47259 ACAGAAAG--CATAAT +s Anc2.Anc2refChr15 21106 14 - 86568 ACAGAAAG--GATAAT +s mr.mrrefChr5 104362 16 + 294540 GCAGAGAGAGCAAAAT +s mr.mrrefChr5 190403 14 - 294540 ACAGAGAG--CAAGAT +s simCow_chr6.simCow.chr6 355567 14 - 602619 AAAGAAAG--GATAAT +s simDog_chr6.simDog.chr6 356181 14 - 593897 ACAGAAAG--GACAAT +s simHuman_chr6.simHuman.chr6 272165 14 + 601863 TCAAAAGG--CATAAT +s simMouse_chr6.simMouse.chr6 384854 14 - 636262 ACAGAGAG--CAAGAT +s simRat_chr6.simRat.chr6 241536 16 + 647215 GCAGAGAGAGCAAGAT + +a +s simMouse_chr6.simMouse.chr6 251717 4 + 636262 TGAT +s Anc0.Anc0refChr5 19354 4 - 87904 TGAC +s Anc1.Anc1refChr7 19941 4 + 47259 TGAC +s Anc2.Anc2refChr15 21121 4 - 86568 TGAC +s mr.mrrefChr5 104378 4 + 294540 TGAT +s mr.mrrefChr5 190418 4 - 294540 TGAT +s simCow_chr6.simCow.chr6 355582 4 - 602619 TAAC +s simDog_chr6.simDog.chr6 356196 4 - 593897 TGAC +s simHuman_chr6.simHuman.chr6 272180 4 + 601863 TGAC +s simMouse_chr6.simMouse.chr6 384869 4 - 636262 TGAT +s simRat_chr6.simRat.chr6 241553 4 + 647215 TGAT + +a +s simMouse_chr6.simMouse.chr6 251721 2 + 636262 GT +s Anc0.Anc0refChr5 19359 2 - 87904 GT +s Anc1.Anc1refChr7 19946 2 + 47259 GT +s Anc2.Anc2refChr15 21126 2 - 86568 AT +s mr.mrrefChr5 104382 2 + 294540 GT +s mr.mrrefChr5 190422 2 - 294540 TT +s simCow_chr6.simCow.chr6 355587 2 - 602619 AT +s simDog_chr6.simDog.chr6 356201 2 - 593897 AT +s simHuman_chr6.simHuman.chr6 272185 2 + 601863 GT +s simMouse_chr6.simMouse.chr6 384873 2 - 636262 TT +s simRat_chr6.simRat.chr6 241557 2 + 647215 GT + +a +s simMouse_chr6.simMouse.chr6 251723 6 + 636262 ATAGAC +s Anc0.Anc0refChr5 19361 6 - 87904 CAAGAC +s Anc1.Anc1refChr7 19948 6 + 47259 CAAGAC +s Anc2.Anc2refChr15 21128 6 - 86568 CAAGAC +s mr.mrrefChr5 104384 6 + 294540 ATAGAC +s mr.mrrefChr5 190424 5 - 294540 G-AGAC +s simCow_chr6.simCow.chr6 355589 6 - 602619 TAAGCC +s simDog_chr6.simDog.chr6 356203 5 - 593897 CAAGA- +s simHuman_chr6.simHuman.chr6 272187 6 + 601863 CAAGAC +s simMouse_chr6.simMouse.chr6 384875 5 - 636262 G-AGAC +s simRat_chr6.simRat.chr6 241560 6 + 647215 CTAGAT + +a +s simMouse_chr6.simMouse.chr6 251729 8 + 636262 TGCTGGAA +s Anc0.Anc0refChr5 19367 8 - 87904 TTCTAGAA +s Anc1.Anc1refChr7 19954 8 + 47259 TTCTAGAA +s Anc2.Anc2refChr15 21134 8 - 86568 ATCAAGAC +s mr.mrrefChr5 104390 8 + 294540 TGCTGGAA +s mr.mrrefChr5 190429 8 - 294540 TGCTAGAA +s simCow_chr6.simCow.chr6 355595 8 - 602619 ATTAAGAC +s simDog_chr6.simDog.chr6 356208 7 - 593897 -TCAAGAC +s simHuman_chr6.simHuman.chr6 272193 8 + 601863 TTCTGGAA +s simMouse_chr6.simMouse.chr6 384880 8 - 636262 TGCTAGAG +s simRat_chr6.simRat.chr6 405750 8 - 647215 TGCTTGAA +s simRat_chr6.simRat.chr6 241566 8 + 647215 TGCTGGAA + +a +s simMouse_chr6.simMouse.chr6 251737 3 + 636262 AAC +s Anc0.Anc0refChr5 19378 3 - 87904 AAG +s Anc1.Anc1refChr7 19965 3 + 47259 AAG +s Anc2.Anc2refChr15 21145 3 - 86568 TAG +s mr.mrrefChr5 104398 3 + 294540 AAC +s mr.mrrefChr5 190440 3 - 294540 AAG +s simCow_chr6.simCow.chr6 355606 3 - 602619 TTG +s simDog_chr6.simDog.chr6 356218 3 - 593897 TAG +s simHuman_chr6.simHuman.chr6 272204 3 + 601863 GAG +s simMouse_chr6.simMouse.chr6 384891 3 - 636262 AAG +s simRat_chr6.simRat.chr6 405761 3 - 647215 AAG +s simRat_chr6.simRat.chr6 241574 3 + 647215 CAC + +a +s simMouse_chr6.simMouse.chr6 251740 2 + 636262 TT +s Anc0.Anc0refChr5 19387 2 - 87904 TT +s Anc1.Anc1refChr7 19974 2 + 47259 TT +s Anc2.Anc2refChr15 21154 2 - 86568 TT +s mr.mrrefChr5 104401 2 + 294540 TT +s mr.mrrefChr5 190443 2 - 294540 TT +s simCow_chr6.simCow.chr6 355620 2 - 602619 TT +s simDog_chr6.simDog.chr6 356221 1 - 593897 -T +s simHuman_chr6.simHuman.chr6 272215 2 + 601863 CT +s simMouse_chr6.simMouse.chr6 384894 2 - 636262 TT +s simRat_chr6.simRat.chr6 405764 2 - 647215 TT +s simRat_chr6.simRat.chr6 241577 2 + 647215 TG + +a +s simMouse_chr6.simMouse.chr6 251742 5 + 636262 TCGAC +s Anc0.Anc0refChr5 19389 4 - 87904 -AGAT +s Anc1.Anc1refChr7 19976 5 + 47259 TAGAT +s Anc2.Anc2refChr15 21156 4 - 86568 -AGAT +s mr.mrrefChr5 104403 5 + 294540 TCGAC +s mr.mrrefChr5 190445 5 - 294540 TAAAT +s simCow_chr6.simCow.chr6 355622 4 - 602619 -ATAT +s simDog_chr6.simDog.chr6 356222 4 - 593897 -AGAT +s simHuman_chr6.simHuman.chr6 272217 5 + 601863 TAGAT +s simMouse_chr6.simMouse.chr6 384896 5 - 636262 TGAAT +s simRat_chr6.simRat.chr6 405771 5 - 647215 TAAGT +s simRat_chr6.simRat.chr6 241579 5 + 647215 TGAAC + +a +s simMouse_chr6.simMouse.chr6 251747 1 + 636262 G +s Anc0.Anc0refChr5 19393 1 - 87904 A +s Anc1.Anc1refChr7 19981 1 + 47259 A +s Anc2.Anc2refChr15 21160 1 - 86568 A +s mr.mrrefChr5 104408 1 + 294540 G +s mr.mrrefChr5 190450 1 - 294540 A +s simCow_chr6.simCow.chr6 355626 1 - 602619 G +s simDog_chr6.simDog.chr6 356226 1 - 593897 A +s simHuman_chr6.simHuman.chr6 272222 1 + 601863 A +s simMouse_chr6.simMouse.chr6 384901 1 - 636262 A +s simRat_chr6.simRat.chr6 405792 1 - 647215 A +s simRat_chr6.simRat.chr6 241584 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 251748 17 + 636262 AGACTTCTGAAAAAATT +s Anc0.Anc0refChr5 19394 17 - 87904 CACCATGTGAAAAAATC +s Anc1.Anc1refChr7 19982 17 + 47259 CACCATGTGAAAAAATC +s Anc2.Anc2refChr15 21161 17 - 86568 CACCATGTTATAAATTC +s mr.mrrefChr5 104409 17 + 294540 AGACTTCTGAAAAAATT +s mr.mrrefChr5 190451 17 - 294540 ATACTTGTGAAAAAATT +s simCow_chr6.simCow.chr6 355628 17 - 602619 CACAGTGTGAAAAATTA +s simDog_chr6.simDog.chr6 356227 15 - 593897 CACCA--TTATAAATTC +s simHuman_chr6.simHuman.chr6 272223 15 + 601863 CACCATGTCA--AAACC +s simMouse_chr6.simMouse.chr6 384902 12 - 636262 ATACTTGTGA-----TT +s simRat_chr6.simRat.chr6 405793 17 - 647215 ATACTTGTGAAAAAATT +s simRat_chr6.simRat.chr6 241585 17 + 647215 AAACTTCTGGACAAATG + +a +s simMouse_chr6.simMouse.chr6 251765 4 + 636262 AAGT +s Anc0.Anc0refChr5 19411 4 - 87904 AAGT +s Anc1.Anc1refChr7 19999 4 + 47259 AAGT +s Anc2.Anc2refChr15 21178 4 - 86568 AAGT +s mr.mrrefChr5 104426 4 + 294540 AAGT +s mr.mrrefChr5 190468 4 - 294540 AAGT +s simCow_chr6.simCow.chr6 355657 4 - 602619 ATGT +s simDog_chr6.simDog.chr6 356242 4 - 593897 AAGT +s simHuman_chr6.simHuman.chr6 272238 4 + 601863 AAGT +s simMouse_chr6.simMouse.chr6 384914 4 - 636262 AAGT +s simRat_chr6.simRat.chr6 405810 4 - 647215 AAAT +s simRat_chr6.simRat.chr6 241602 4 + 647215 AAAT + +a +s simMouse_chr6.simMouse.chr6 251769 16 + 636262 GGACCAGGCACAGGAG +s Anc0.Anc0refChr5 19415 15 - 87904 TAGCCAGGTATAGG-A +s Anc1.Anc1refChr7 20003 15 + 47259 TAGCCAGGTATAGG-A +s Anc2.Anc2refChr15 21182 15 - 86568 TAGCCAGGTATAGG-A +s mr.mrrefChr5 104430 15 + 294540 GGACCAGGCACAGG-G +s mr.mrrefChr5 190472 15 - 294540 TGCCCATGTACAGG-A +s simCow_chr6.simCow.chr6 355661 15 - 602619 TAGACAGGTATGGG-A +s simDog_chr6.simDog.chr6 356246 14 - 593897 T-GCCAGGTACAGG-A +s simHuman_chr6.simHuman.chr6 272242 15 + 601863 TAGCCAGGTATAGA-A +s simMouse_chr6.simMouse.chr6 384918 15 - 636262 TGCCCCTGTACAGG-A +s simRat_chr6.simRat.chr6 405814 15 - 647215 TGCCCATGTACAGG-A +s simRat_chr6.simRat.chr6 241709 15 + 647215 GGAGCAGGCACAGG-G + +a +s simMouse_chr6.simMouse.chr6 251785 12 + 636262 CACTGGAAACCC +s Anc0.Anc0refChr5 19431 12 - 87904 GATTGGAAACTC +s Anc1.Anc1refChr7 20019 12 + 47259 GATTGGAAACTC +s Anc2.Anc2refChr15 21198 12 - 86568 GATTCAAAACAC +s mr.mrrefChr5 104445 12 + 294540 CACTGGAAACCC +s mr.mrrefChr5 190488 12 - 294540 CATTGGAAACTC +s simCow_chr6.simCow.chr6 355677 12 - 602619 GATACAAACCAC +s simDog_chr6.simDog.chr6 356261 12 - 593897 GATTCAAAAACC +s simHuman_chr6.simHuman.chr6 272258 10 + 601863 GATTGGAAAC-- +s simMouse_chr6.simMouse.chr6 384934 12 - 636262 CATTGGAATCTC +s simRat_chr6.simRat.chr6 405830 12 - 647215 CATTGGAAACTC +s simRat_chr6.simRat.chr6 241724 12 + 647215 CATTGGCAACTC a s simMouse_chr6.simMouse.chr6 251797 2 + 636262 AT @@ -98537,20 +101366,58 @@ 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 +s simMouse_chr6.simMouse.chr6 251799 1 + 636262 T +s Anc0.Anc0refChr5 19443 1 - 87904 T +s Anc1.Anc1refChr7 20031 1 + 47259 T +s Anc2.Anc2refChr15 21210 1 - 86568 C +s mr.mrrefChr5 104459 1 + 294540 T +s mr.mrrefChr5 190500 1 - 294540 C +s simCow_chr6.simCow.chr6 355689 1 - 602619 C +s simDog_chr6.simDog.chr6 356273 1 - 593897 C +s simMouse_chr6.simMouse.chr6 384946 1 - 636262 C +s simRat_chr6.simRat.chr6 405842 1 - 647215 T +s simRat_chr6.simRat.chr6 241738 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 251800 84 + 636262 TGTCCACCTGTGTTGGACGTTATGCTGCAAAATTAGTGAATCTCTTCCTACTAGATAGCATGTGGAATCAGTAATTCAAACCCT +s Anc0.Anc0refChr5 19444 73 - 87904 TGT---------TGGGGCGTTCTACTGACAAATTAGTACACTT--TCCTACTAAGTAACATGTGGAATAAGTATTCCAAACTCT +s Anc1.Anc1refChr7 20032 82 + 47259 TGTCCACCTGTGTGGGGCGTTCTACTGACAAATTAGTACACTT--TCCTACTAAGTAACATGTGGAATAAGTATTCCAAACTCT +s Anc2.Anc2refChr15 21211 73 - 86568 TAT---------TGGGGCGTTCTACTCACAAATTAGTACACTT--TCCTACTAAGTAACATATGGAATAAGTATTCCAAACTCT +s mr.mrrefChr5 104460 82 + 294540 TGTCCACCTGTGTTGGACGTTATGCTGCAAAATTAGTGAATCT--TCCTACTAGATAGCATGTGGAATCAGTAATTCAAACCCT +s mr.mrrefChr5 190501 82 - 294540 TGTGCACTTGTGTGGGGTGTTATACTGCAAAATTAGTGCATTT--TCCAACTAAGTAACATGTAGCATATGTAGTTCAAACTTT +s simCow_chr6.simCow.chr6 355690 68 - 602619 TTG---------TGGGGAGTTCGACCAACAAATTAGTACACTT--TCCTACAAAGGAAGATATGGAATAAGCAGCCAAG----- +s simDog_chr6.simDog.chr6 356274 73 - 593897 TAT---------TGGGGCATTCTACTCACATATCAGTACACTT--TCCTCCTAGGTATCATATGAAATAAGTATTTCAAACTCT +s simHuman_chr6.simHuman.chr6 272268 77 + 601863 -----ACCTGTGTGGGGCGTTCAGCTGACAAGTTAGTACACTT--TCCTACTAAGCAACATGTGGCATAAGTATTCTAAATTCT +s simMouse_chr6.simMouse.chr6 384949 77 - 636262 TGTGCACTTGTGTGGGGTGTTAT-----AAAATTAGTGCATTT--TCCAACTAAGTAACATGTAGCATATGTAGTTCAAACTTT +s simRat_chr6.simRat.chr6 405843 82 - 647215 TGTGCACTTGTGTGGGGTGTTATACTGCAAAATTAGTGCAGTT--TTTGACGAAATAACATGTAGAATATGTCGTTCAAACTTT +s simRat_chr6.simRat.chr6 241739 82 + 647215 TGTGCACCTGTGTTGGATGTTATACCGCAAAATTAGTTAATCT--TCCGACTACGTAACATGGGAAATAAGTAATTCAAACCCT + +a +s simMouse_chr6.simMouse.chr6 251884 2 + 636262 TC +s Anc0.Anc0refChr5 19520 2 - 87904 TT +s Anc1.Anc1refChr7 20117 2 + 47259 TT +s Anc2.Anc2refChr15 21287 2 - 86568 TT +s mr.mrrefChr5 104542 2 + 294540 TC +s mr.mrrefChr5 190586 2 - 294540 TC +s simDog_chr6.simDog.chr6 356350 2 - 593897 TT +s simHuman_chr6.simHuman.chr6 272348 2 + 601863 TT +s simMouse_chr6.simMouse.chr6 385029 2 - 636262 TC +s simRat_chr6.simRat.chr6 405928 2 - 647215 TC +s simRat_chr6.simRat.chr6 241821 2 + 647215 TC + +a +s simMouse_chr6.simMouse.chr6 251886 13 + 636262 AAAAGTAGCTACG +s Anc0.Anc0refChr5 19530 13 - 87904 GCAAGTAGCTAAG +s Anc1.Anc1refChr7 20127 13 + 47259 GCAAGTAGCTAAG +s Anc2.Anc2refChr15 21297 13 - 86568 GCAAGTAGCTAAG +s mr.mrrefChr5 104544 13 + 294540 AAAAGTAGCTACG +s mr.mrrefChr5 190588 13 - 294540 ACAAGAAGCATTG +s simCow_chr6.simCow.chr6 355766 13 - 602619 GCATGTAGCTAAG +s simDog_chr6.simDog.chr6 356360 13 - 593897 GCAAGTAGCTAAG +s simHuman_chr6.simHuman.chr6 272358 13 + 601863 GCACGTAGCTGAG +s simMouse_chr6.simMouse.chr6 385031 13 - 636262 ACAAGAAGCATTG +s simRat_chr6.simRat.chr6 405930 13 - 647215 ACAAGAAGCATTG +s simRat_chr6.simRat.chr6 241823 13 + 647215 AGAAATAGCTTAG a s simMouse_chr6.simMouse.chr6 251899 2 + 636262 AG @@ -98564,6 +101431,62 @@ s simRat_chr6.simRat.chr6 241836 2 + 647215 AG a +s simMouse_chr6.simMouse.chr6 251901 9 + 636262 CATCCAGTA +s Anc0.Anc0refChr5 19545 9 - 87904 CGTCCAGTA +s Anc1.Anc1refChr7 20142 9 + 47259 CGTCCAGTA +s Anc2.Anc2refChr15 21312 9 - 86568 CGCCCAGTG +s mr.mrrefChr5 104559 9 + 294540 CATCCAGTA +s mr.mrrefChr5 190601 9 - 294540 CATCCAGGA +s simCow_chr6.simCow.chr6 355781 9 - 602619 CGCCCAGTG +s simDog_chr6.simDog.chr6 356375 7 - 593897 CGCCTAG-- +s simHuman_chr6.simHuman.chr6 272373 9 + 601863 TGTCCAGCA +s simMouse_chr6.simMouse.chr6 385044 9 - 636262 CACCCAGGA +s simRat_chr6.simRat.chr6 405943 9 - 647215 CATCCAGTA +s simRat_chr6.simRat.chr6 241838 9 + 647215 TATCCAGTA + +a +s simMouse_chr6.simMouse.chr6 251910 10 + 636262 GGGAGTGGTA +s Anc0.Anc0refChr5 19555 10 - 87904 AGGAGTGGTA +s Anc1.Anc1refChr7 20152 10 + 47259 AGGAGTGGTA +s Anc2.Anc2refChr15 21322 10 - 86568 ATGAGTGGTA +s mr.mrrefChr5 104568 10 + 294540 GGGAGTGGTA +s mr.mrrefChr5 190611 10 - 294540 AGAAGTGGTA +s simCow_chr6.simCow.chr6 355791 10 - 602619 ATGAGTGGTA +s simDog_chr6.simDog.chr6 356382 6 - 593897 ----ATGATA +s simHuman_chr6.simHuman.chr6 272383 10 + 601863 AGGGGTGGGG +s simMouse_chr6.simMouse.chr6 385054 10 - 636262 AGAAGTGGTA +s simRat_chr6.simRat.chr6 405953 10 - 647215 AGAAGTGGTA +s simRat_chr6.simRat.chr6 241848 10 + 647215 AGGAGTGGTA + +a +s simMouse_chr6.simMouse.chr6 251920 14 + 636262 CTGGACATCTTAGT +s Anc0.Anc0refChr5 19565 5 - 87904 TAAG---------C +s Anc1.Anc1refChr7 20162 14 + 47259 TAAGACATCTTAGC +s Anc2.Anc2refChr15 21332 5 - 86568 TAAG---------C +s mr.mrrefChr5 104578 14 + 294540 CTGGACATCTTAGT +s mr.mrrefChr5 190621 14 - 294540 TAAGATGTCTTAGC +s simCow_chr6.simCow.chr6 355808 5 - 602619 TGAG---------C +s simDog_chr6.simDog.chr6 356388 5 - 593897 TACC---------C +s simHuman_chr6.simHuman.chr6 272393 5 + 601863 TA---------AGC +s simMouse_chr6.simMouse.chr6 385064 14 - 636262 TAAGATGTCTTAGC +s simRat_chr6.simRat.chr6 405963 14 - 647215 TAGGATGTCTAAAC +s simRat_chr6.simRat.chr6 241858 14 + 647215 CTGGACATCTTAGT + +a +s simMouse_chr6.simMouse.chr6 251934 7 + 636262 GACAGAT +s Anc0.Anc0refChr5 19570 7 - 87904 AACAGAT +s Anc1.Anc1refChr7 20176 7 + 47259 AACAGAT +s Anc2.Anc2refChr15 21337 7 - 86568 AACACAT +s mr.mrrefChr5 104592 7 + 294540 GACAGAT +s mr.mrrefChr5 190635 7 - 294540 AGCAGAT +s simCow_chr6.simCow.chr6 355813 7 - 602619 AGCGGAT +s simDog_chr6.simDog.chr6 356395 7 - 593897 AACACAT +s simHuman_chr6.simHuman.chr6 272398 7 + 601863 AACAAAT +s simMouse_chr6.simMouse.chr6 385078 7 - 636262 AGCAGAT +s simRat_chr6.simRat.chr6 405977 7 - 647215 AGCAGAT +s simRat_chr6.simRat.chr6 241872 7 + 647215 GACAGAT + +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 @@ -103651,6 +106574,49 @@ s simRat_chr6.simRat.chr6 253830 4 + 647215 cgtg a +s simMouse_chr6.simMouse.chr6 264056 3 + 636262 tat +s Anc0.Anc0refChr3 196027 3 - 222631 TAT +s Anc1.Anc1refChr6 141548 3 - 197743 TAT +s Anc2.Anc2refChr13 66400 3 - 96486 CAT +s mr.mrrefChr5 116616 3 + 294540 tat +s mr.mrrefChr5 46492 3 - 294540 TGT +s simCow_chr6.simCow.chr6 216407 3 - 602619 CAT +s simHuman_chr6.simHuman.chr6 221271 3 - 601863 TAT +s simHuman_chr6.simHuman.chr6 156409 3 - 601863 TAT +s simMouse_chr6.simMouse.chr6 552370 3 - 636262 TGT +s simRat_chr6.simRat.chr6 252712 3 - 647215 TAT +s simRat_chr6.simRat.chr6 253834 3 + 647215 tgt + +a +s simMouse_chr6.simMouse.chr6 264059 7 + 636262 ttatggc +s Anc0.Anc0refChr3 196030 7 - 222631 CTAGAAC +s Anc1.Anc1refChr6 141551 7 - 197743 CTAGAAC +s Anc2.Anc2refChr13 66403 7 - 96486 CTAGAAC +s mr.mrrefChr5 116619 7 + 294540 ttatggc +s mr.mrrefChr5 46495 7 - 294540 TTACAAC +s simCow_chr6.simCow.chr6 216410 7 - 602619 CTAGAGC +s simDog_chr6.simDog.chr6 217218 2 - 593897 -----AC +s simHuman_chr6.simHuman.chr6 156412 7 - 601863 CTAGAAC +s simMouse_chr6.simMouse.chr6 552373 7 - 636262 TTACAAC +s simRat_chr6.simRat.chr6 252715 7 - 647215 TCACAAC +s simRat_chr6.simRat.chr6 253837 7 + 647215 tttcagc + +a +s simMouse_chr6.simMouse.chr6 264066 4 + 636262 aagt +s Anc0.Anc0refChr3 196038 4 - 222631 AAGT +s Anc1.Anc1refChr6 141559 4 - 197743 AAGT +s Anc2.Anc2refChr13 66411 4 - 96486 AAGT +s mr.mrrefChr5 116626 4 + 294540 aagt +s mr.mrrefChr5 46502 4 - 294540 AAGT +s simCow_chr6.simCow.chr6 216418 4 - 602619 AAGT +s simDog_chr6.simDog.chr6 217221 4 - 593897 AAGA +s simHuman_chr6.simHuman.chr6 221274 4 - 601863 TTGT +s simHuman_chr6.simHuman.chr6 156420 4 - 601863 TTGT +s simMouse_chr6.simMouse.chr6 552380 4 - 636262 AAGT +s simRat_chr6.simRat.chr6 252722 4 - 647215 AAAT +s simRat_chr6.simRat.chr6 253844 4 + 647215 aagt + +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 @@ -103671,6 +106637,20 @@ s simRat_chr6.simRat.chr6 254455 17 + 647215 ATGCATATATCCCCACA--------------------------------------------- a +s simMouse_chr6.simMouse.chr6 264924 1 + 636262 G +s Anc0.Anc0refChr3 196042 1 - 222631 A +s Anc1.Anc1refChr6 141563 1 - 197743 A +s Anc2.Anc2refChr13 66415 1 - 96486 A +s mr.mrrefChr5 117276 1 + 294540 G +s mr.mrrefChr5 46506 1 - 294540 A +s simCow_chr6.simCow.chr6 216422 1 - 602619 A +s simDog_chr6.simDog.chr6 217225 1 - 593897 A +s simHuman_chr6.simHuman.chr6 221278 1 - 601863 A +s simHuman_chr6.simHuman.chr6 156424 1 - 601863 A +s simMouse_chr6.simMouse.chr6 552384 1 - 636262 A +s simRat_chr6.simRat.chr6 252726 1 - 647215 A + +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 @@ -106207,6 +109187,47 @@ s simRat_chr6.simRat.chr6 258626 7 + 647215 CCTAATA a +s simMouse_chr6.simMouse.chr6 269671 19 + 636262 TTGAAAATTTGTTGTATAC +s Anc0.Anc0refChr3 2036 19 + 222631 TTGGGGATCAATTGTGTAC +s Anc1.Anc1refChr5 4363 19 + 6477 TTGGGGATCAATTGTGTAC +s Anc2.Anc2refChr13 4198 19 + 96486 TTGGGGATCAATGTTGTAT +s mr.mrrefChr5 121169 19 + 294540 TTGGAAATTTGTTGTATAC +s mr.mrrefChr5 121004 19 + 294540 TTAGGAATTTACTGTGTAC +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 269486 19 + 636262 TTAGGAATTTACTGTGTAC +s simRat_chr6.simRat.chr6 258469 19 + 647215 TTAGAAGTTTGTTGTGTAC +s simRat_chr6.simRat.chr6 258633 19 + 647215 TTGGAAATTTGTTGTGTAC + +a +s simMouse_chr6.simMouse.chr6 269690 16 + 636262 GTTGCAACAGAGAGGC +s Anc0.Anc0refChr3 2055 16 + 222631 GTTGCAACACAAGATG +s Anc1.Anc1refChr5 4382 16 + 6477 GTTGCAACACAAGATG +s Anc2.Anc2refChr13 4217 16 + 96486 TTTGCAACACAAGATA +s mr.mrrefChr5 121188 16 + 294540 GTTGCAACAGAAAGGC +s mr.mrrefChr5 121038 16 + 294540 GTAGCAACACAAGAAG +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 269520 16 + 636262 GTAGCAACACAAGAAG +s simRat_chr6.simRat.chr6 258503 16 + 647215 GTAGCAACACAAGAAG +s simRat_chr6.simRat.chr6 258652 16 + 647215 ATTGCAGCAGAAAGGC + +a +s simMouse_chr6.simMouse.chr6 269706 29 + 636262 TGTTTAACTCTCTGTCATAGTACTATGAA +s Anc0.Anc0refChr3 2071 29 + 222631 TATTTAATTCTCCCTCTTAGTACTATGTA +s Anc1.Anc1refChr5 4398 29 + 6477 TATTTAATTCTCCCTCTTAGTACTATGTA +s Anc2.Anc2refChr13 4233 29 + 96486 TATGTAATCCGCCCTCTCAGTACTATGTA +s mr.mrrefChr5 121204 29 + 294540 TGTTTAACTCTCTGTCATAGTACTATGAA +s mr.mrrefChr5 121054 29 + 294540 TATTTAATTGTCTGTCTTGGTACTATGTA +s simDog_chr6.simDog.chr6 350306 29 + 593897 TATGTAATCCGCCCTCTCAGTACTATGTA +s simHuman_chr6.simHuman.chr6 248421 29 + 601863 TGTATAATTCTCCCTATGAGTACTATGCA +s simMouse_chr6.simMouse.chr6 269536 29 + 636262 TATTTAATTGTCTGTCTTGGTACTATGTA +s simRat_chr6.simRat.chr6 258519 29 + 647215 TATATACTTGTCTGTCTTGGTACTATGTA +s simRat_chr6.simRat.chr6 258668 29 + 647215 TGTTTAACTCTCTGTCATAGTACTATGAA + +a s simMouse_chr6.simMouse.chr6 269735 2 + 636262 GC s Anc0.Anc0refChr3 2100 2 + 222631 GC s Anc1.Anc1refChr5 4427 2 + 6477 GC @@ -106217,15 +109238,31 @@ 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 +s simMouse_chr6.simMouse.chr6 269737 9 + 636262 AACTTAGTA +s Anc0.Anc0refChr3 2102 9 + 222631 AACTTGGCA +s Anc1.Anc1refChr5 4429 9 + 6477 AACTTGGCA +s Anc2.Anc2refChr13 4264 9 + 96486 AACTTGGCA +s mr.mrrefChr5 121235 9 + 294540 AACTTAGTA +s mr.mrrefChr5 121083 1 + 294540 --------A +s simCow_chr6.simCow.chr6 359704 3 + 602619 ------GCA +s simDog_chr6.simDog.chr6 350347 9 + 593897 AACTTGGCA +s simHuman_chr6.simHuman.chr6 248452 9 + 601863 AACTTGGCA +s simMouse_chr6.simMouse.chr6 269565 1 + 636262 --------A +s simRat_chr6.simRat.chr6 258699 9 + 647215 AACTTAGTA + +a +s simMouse_chr6.simMouse.chr6 269746 6 + 636262 TTCTAC +s Anc0.Anc0refChr3 2111 6 + 222631 TCCTAT +s Anc1.Anc1refChr5 4438 6 + 6477 TCCTAT +s Anc2.Anc2refChr13 4273 6 + 96486 TCCCAA +s mr.mrrefChr5 121244 6 + 294540 TTCTAC +s mr.mrrefChr5 121084 6 + 294540 TCCTAT +s simCow_chr6.simCow.chr6 359707 2 + 602619 TA---- +s simDog_chr6.simDog.chr6 350356 6 + 593897 TCCCAA +s simHuman_chr6.simHuman.chr6 248461 6 + 601863 TCCTAT +s simMouse_chr6.simMouse.chr6 269581 6 + 636262 TCCTAT +s simRat_chr6.simRat.chr6 258548 6 + 647215 TCCTAT +s simRat_chr6.simRat.chr6 258708 6 + 647215 TTCTAC a s simMouse_chr6.simMouse.chr6 269752 5 + 636262 ATCAA @@ -106238,6 +109275,90 @@ s simRat_chr6.simRat.chr6 258714 5 + 647215 ATTAA a +s simMouse_chr6.simMouse.chr6 269757 16 + 636262 CTTTTTTAAAGTTGGG +s Anc0.Anc0refChr3 2122 16 + 222631 ATTATTGAAAATCAGG +s Anc1.Anc1refChr5 4449 16 + 6477 ATTATTGAAAATCAGG +s Anc2.Anc2refChr13 4284 16 + 96486 ATTCTTGAAAATCAGG +s mr.mrrefChr5 121255 16 + 294540 CTTTTTGAAAATTGGG +s mr.mrrefChr5 121090 16 + 294540 CTCATTTAATATCAAG +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 269587 16 + 636262 CTCATTTAATATCAAG +s simRat_chr6.simRat.chr6 258554 16 + 647215 CTCATTTAAAATCAAG +s simRat_chr6.simRat.chr6 258719 16 + 647215 CTTTTTGAAAATTGGG + +a +s simMouse_chr6.simMouse.chr6 269773 2 + 636262 AG +s Anc0.Anc0refChr3 2139 2 + 222631 AG +s Anc1.Anc1refChr5 4466 2 + 6477 AG +s Anc2.Anc2refChr13 4301 2 + 96486 AG +s mr.mrrefChr5 121271 2 + 294540 AG +s mr.mrrefChr5 121107 2 + 294540 AG +s simCow_chr6.simCow.chr6 359723 2 + 602619 AG +s simDog_chr6.simDog.chr6 350384 2 + 593897 TG +s simHuman_chr6.simHuman.chr6 248489 2 + 601863 AG +s simMouse_chr6.simMouse.chr6 269604 2 + 636262 AG +s simRat_chr6.simRat.chr6 258571 2 + 647215 AG +s simRat_chr6.simRat.chr6 258735 2 + 647215 AG + +a +s simMouse_chr6.simMouse.chr6 269775 5 + 636262 TACTT +s Anc0.Anc0refChr3 2145 5 + 222631 TATCA +s Anc1.Anc1refChr5 4472 5 + 6477 TATCA +s Anc2.Anc2refChr13 4307 5 + 96486 TATCA +s mr.mrrefChr5 121277 5 + 294540 TACTT +s mr.mrrefChr5 121113 5 + 294540 TATTG +s simCow_chr6.simCow.chr6 359729 5 + 602619 TATCA +s simDog_chr6.simDog.chr6 350390 5 + 593897 TATCA +s simHuman_chr6.simHuman.chr6 248495 5 + 601863 TATCA +s simMouse_chr6.simMouse.chr6 269610 5 + 636262 TATTG +s simRat_chr6.simRat.chr6 258577 5 + 647215 TATTG +s simRat_chr6.simRat.chr6 258741 5 + 647215 TACTT + +a +s simMouse_chr6.simMouse.chr6 269780 4 + 636262 TCTA +s Anc0.Anc0refChr3 2150 4 + 222631 TCAA +s Anc1.Anc1refChr5 4477 4 + 6477 TCAA +s Anc2.Anc2refChr13 4312 4 + 96486 TCAA +s mr.mrrefChr5 121282 4 + 294540 TCAA +s mr.mrrefChr5 121118 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 269615 4 + 636262 TCAA +s simRat_chr6.simRat.chr6 258582 4 + 647215 TCAA +s simRat_chr6.simRat.chr6 258747 4 + 647215 TCAA + +a +s simMouse_chr6.simMouse.chr6 269784 7 + 636262 AGACACT +s Anc0.Anc0refChr3 2154 7 + 222631 ACACATT +s Anc1.Anc1refChr5 4481 7 + 6477 ACACATT +s Anc2.Anc2refChr13 4316 7 + 96486 ACACATT +s mr.mrrefChr5 121286 7 + 294540 AGACATT +s mr.mrrefChr5 121122 7 + 294540 AGACATC +s simCow_chr6.simCow.chr6 359738 7 + 602619 ACACATT +s simDog_chr6.simDog.chr6 350399 7 + 593897 GCATATT +s simHuman_chr6.simHuman.chr6 248506 7 + 601863 ACACATT +s simMouse_chr6.simMouse.chr6 269619 7 + 636262 AGACATC +s simRat_chr6.simRat.chr6 258586 7 + 647215 AGACATC +s simRat_chr6.simRat.chr6 258751 7 + 647215 AGACATT + +a +s simMouse_chr6.simMouse.chr6 269791 26 + 636262 CAGACAGAAACAAACTCCTCAACCAA +s Anc0.Anc0refChr3 2161 26 + 222631 AAGACATAGACAAACTCTTCAACTAA +s Anc1.Anc1refChr5 4488 26 + 6477 AAGACATAGACAAACTCTTCAACTAA +s Anc2.Anc2refChr13 4323 26 + 96486 AAAACATAGACAAACTCTTCAACTAA +s mr.mrrefChr5 121293 26 + 294540 AAGACAGAAACAAACTCCTCAACCAA +s mr.mrrefChr5 121129 26 + 294540 AAGGCAGAAACACACTCTTTAACTAG +s simCow_chr6.simCow.chr6 359745 26 + 602619 AGAACATAGACAAAATCTTTAACTAA +s simDog_chr6.simDog.chr6 350406 23 + 593897 AA---CTAGACAAACTTTTCAACTAG +s simHuman_chr6.simHuman.chr6 248513 26 + 601863 AAGACATAGACAAACTCTTCAACCAA +s simMouse_chr6.simMouse.chr6 269631 26 + 636262 AAGGCAGAAACACACTCTTTAACTAG +s simRat_chr6.simRat.chr6 258593 26 + 647215 AAGGTAGAAATAAACTCTTTAACTGG +s simRat_chr6.simRat.chr6 258758 26 + 647215 AAGACAGAAACAAACTCCTCAAGTAG + +a s simMouse_chr6.simMouse.chr6 269817 4 + 636262 TTCC s Anc0.Anc0refChr3 2187 1 + 222631 T--- s Anc1.Anc1refChr5 4514 1 + 6477 T--- @@ -106249,6 +109370,20 @@ s simRat_chr6.simRat.chr6 258784 4 + 647215 TTCC a +s simMouse_chr6.simMouse.chr6 269821 14 + 636262 TGAACTAATTCAAG +s Anc0.Anc0refChr3 2188 9 + 222631 AGAA-----ACAAA +s Anc1.Anc1refChr5 4515 14 + 6477 AGAACTGATACAAA +s Anc2.Anc2refChr13 4350 9 + 96486 TGAA-----AGAAA +s mr.mrrefChr5 121323 14 + 294540 TGAACTAATTCAAG +s mr.mrrefChr5 121155 14 + 294540 AGATGTACTTAAAG +s simCow_chr6.simCow.chr6 359772 9 + 602619 TGAA-----AGAAG +s simDog_chr6.simDog.chr6 350430 9 + 593897 TGAA-----AGAAA +s simHuman_chr6.simHuman.chr6 248540 9 + 601863 -----TGATACAAA +s simMouse_chr6.simMouse.chr6 269657 14 + 636262 AGATGTACTTAAAG +s simRat_chr6.simRat.chr6 258619 14 + 647215 AGATGTACCTAATA +s simRat_chr6.simRat.chr6 258788 13 + 647215 TCAACT-ATTCAAG + +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 @@ -107395,33 +110530,74 @@ 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 +s simMouse_chr6.simMouse.chr6 272147 5 + 636262 CTGTT +s Anc0.Anc0refChr5 279 5 - 87904 ATTTT +s Anc1.Anc1refChr7 287 5 + 47259 ATTTT +s Anc2.Anc2refChr15 1511 5 - 86568 ATTTT +s mr.mrrefChr5 123702 5 + 294540 CTGTT +s mr.mrrefChr5 123539 5 + 294540 ATCTT +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 271988 5 + 636262 ATCTA +s simRat_chr6.simRat.chr6 261021 5 + 647215 ATCTT +s simRat_chr6.simRat.chr6 261188 5 + 647215 CTGTT + +a +s simMouse_chr6.simMouse.chr6 272152 22 + 636262 AGATTACACAGAATTTTATGTA +s Anc0.Anc0refChr5 284 9 - 87904 -TATTACCCA------------ +s Anc1.Anc1refChr7 292 13 + 47259 ATATTACCCAGA---------T +s Anc2.Anc2refChr15 1516 9 - 86568 -TATTATCCA------------ +s mr.mrrefChr5 123707 13 + 294540 AGATTACACAGA---------A +s mr.mrrefChr5 123547 13 + 294540 ATGTTTCCTATA---------T +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 271996 13 + 636262 ATGTTTCTTATA---------T +s simRat_chr6.simRat.chr6 261029 13 + 647215 ATGTTTCCCACT---------T +s simRat_chr6.simRat.chr6 261193 13 + 647215 AGCTTACACAGA---------A + +a +s simMouse_chr6.simMouse.chr6 272174 34 + 636262 TTTTAGTGTGGACCAGCAACTCTCACCAAATCAG +s Anc0.Anc0refChr5 293 34 - 87904 TTTTAGTGCTAACCATCAACTCTAGCTAACTCAA +s Anc1.Anc1refChr7 305 34 + 47259 TTTTAGTGCTAACCATCAACTCTAGCTAACTCAA +s Anc2.Anc2refChr15 1525 34 - 86568 TTTTAGTGCTAACCATAAACTCTAGCTAACTCAA +s mr.mrrefChr5 123720 34 + 294540 TTTTAGTGTGGACCAGCAACTCTCACCAAATCAG +s mr.mrrefChr5 123563 34 + 294540 TTTTAGTGCTAACATTCAACTAGGGCCAACTCAG +s simCow_chr6.simCow.chr6 335144 34 - 602619 TTTAAGTGCTAACCATCAACTCTAGCTAACCCAA +s simDog_chr6.simDog.chr6 335778 34 - 593897 TTTTAGTGCTAACCGTAAACTTTAGCTAAATCAA +s simHuman_chr6.simHuman.chr6 250796 34 + 601863 TTTTAGTGGTAACTATTAACTCAAGATAGCTCAA +s simMouse_chr6.simMouse.chr6 272012 28 + 636262 TTCTAGTGCTAACATTC-AG-----CCTATTCAG +s simRat_chr6.simRat.chr6 261045 34 + 647215 TTTTAGTGCCAAGCTTCAACTAGGGCCAACTCAG +s simRat_chr6.simRat.chr6 261206 34 + 647215 TTCTAGTGTGGACCAACAACTTTGACCAAATCAG + +a +s simMouse_chr6.simMouse.chr6 272208 14 + 636262 CAAATCAATGTCAA +s Anc0.Anc0refChr5 327 14 - 87904 CAAAGCAAAGCCAA +s Anc1.Anc1refChr7 339 14 + 47259 CAAAGCAAAGCCAA +s Anc2.Anc2refChr15 1559 14 - 86568 CAAGGCAAAGCAAG +s mr.mrrefChr5 123754 14 + 294540 CAAATCAATGTCAA +s mr.mrrefChr5 123597 14 + 294540 CACAGCAAAGCCAA +s simCow_chr6.simCow.chr6 335178 14 - 602619 TAAGGCAAAGCAAC +s simDog_chr6.simDog.chr6 335812 14 - 593897 CAAGGCAAAGCAAG +s simHuman_chr6.simHuman.chr6 250830 14 + 601863 CAAAGCGAAGCCAA +s simMouse_chr6.simMouse.chr6 272042 14 + 636262 CACAGCAAAGCCGA +s simRat_chr6.simRat.chr6 261079 14 + 647215 CACAGCAAAGCCAA +s simRat_chr6.simRat.chr6 261240 14 + 647215 CAAATCAATGTCAA + +a +s simMouse_chr6.simMouse.chr6 272222 37 + 636262 GAGTCCCGTCCCTTAGATATTGGTAGCAAATGTTACT +s Anc0.Anc0refChr5 361 37 - 87904 AAGTCCCATCCCTTAAACATTGGTAGCAAATGCTACT +s Anc1.Anc1refChr7 373 37 + 47259 AAGTCCCATCCCTTAAACATTGGTAGCAAATGCTACT +s Anc2.Anc2refChr15 1593 37 - 86568 AAGTCCCATCCCTTAAACATTGGTAGGAAATGTTACT +s mr.mrrefChr5 123768 37 + 294540 GAGTCCCGTCCCTTAGATATTGGTAGCAAATGCTACT +s mr.mrrefChr5 123631 37 + 294540 ACTTCCCATCCCTGCAACATTAGTAGCAAATGCTTCT +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 272076 37 + 636262 ACTTCTGATCCCTGCAACATTAGTAGCAAATGCTTCT +s simRat_chr6.simRat.chr6 261113 37 + 647215 ACTTCCCATCCCTGTAACATTGCAAGCAGATGCTACT +s simRat_chr6.simRat.chr6 261274 37 + 647215 AAGTCCCATTACTTAGATATAGGTAGCAAAGGCTACT a s simMouse_chr6.simMouse.chr6 272259 4 + 636262 CCCA @@ -107435,6 +110611,48 @@ s simRat_chr6.simRat.chr6 261311 4 + 647215 CCCA a +s simMouse_chr6.simMouse.chr6 272263 3 + 636262 CAA +s Anc0.Anc0refChr5 402 3 - 87904 CAA +s Anc1.Anc1refChr7 414 3 + 47259 CAA +s Anc2.Anc2refChr15 1634 3 - 86568 CAA +s mr.mrrefChr5 123809 3 + 294540 CAA +s mr.mrrefChr5 123668 3 + 294540 TGA +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 272113 3 + 636262 TGA +s simRat_chr6.simRat.chr6 261150 3 + 647215 TGA +s simRat_chr6.simRat.chr6 261315 3 + 647215 CAA + +a +s simMouse_chr6.simMouse.chr6 272266 1 + 636262 C +s Anc0.Anc0refChr5 405 1 - 87904 T +s Anc1.Anc1refChr7 417 1 + 47259 T +s Anc2.Anc2refChr15 1637 1 - 86568 T +s mr.mrrefChr5 123812 1 + 294540 C +s mr.mrrefChr5 123671 1 + 294540 G +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 272116 1 + 636262 G +s simRat_chr6.simRat.chr6 261153 1 + 647215 A +s simRat_chr6.simRat.chr6 261318 1 + 647215 C + +a +s simMouse_chr6.simMouse.chr6 272267 30 + 636262 CTAATCTCATTTCAAAAAACCATTACATCT +s Anc0.Anc0refChr5 406 30 - 87904 TTAATCTCCTTTTAGAAAACCACTACATCT +s Anc1.Anc1refChr7 418 30 + 47259 TTAATCTCCTTTTAGAAAACCACTACATCT +s Anc2.Anc2refChr15 1638 30 - 86568 TTAATCTCCTTTTAGAAAACCACTACATCT +s mr.mrrefChr5 123813 30 + 294540 CTAATCTCATTTCAAAAAACCATTACATCT +s mr.mrrefChr5 123672 30 + 294540 CTAGTCTAATCTTAGGAAACTACTGTACCT +s simCow_chr6.simCow.chr6 335257 30 - 602619 TTAATCTCCTTTTAGAAAACCACTACATCG +s simDog_chr6.simDog.chr6 335890 30 - 593897 TTGATCTCCTTCTAGAAAACCACACCATCT +s simHuman_chr6.simHuman.chr6 250909 30 + 601863 TTAATCTCCCTTTAGAAAACCACTACATCT +s simMouse_chr6.simMouse.chr6 272117 30 + 636262 CTAGTCTAATCTTAGGAAACTACTGTACCT +s simRat_chr6.simRat.chr6 261158 30 + 647215 CTAGTCTAATTTTAGAAAACTACTGTATCT +s simRat_chr6.simRat.chr6 261319 22 + 647215 CTAATCCCAT--------AACATGACATCT + +a s simMouse_chr6.simMouse.chr6 272297 53 + 636262 AGAGTGTAGTCGATATGAATCTGATGTCTACCAACCAATTTCTATTGAGATGT s Anc0.Anc0refChr5 436 53 - 87904 CCATTGTAGACAATGTGAATTAGATCTCTACCAACCTATGTCTATTAAGATGA s Anc1.Anc1refChr7 448 53 + 47259 CCATTGTAGACAATGTGAATTAGATCTCTACCAACCTATGTCTATTAAGATGA @@ -110665,17 +113883,98 @@ 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 +s simMouse_chr6.simMouse.chr6 278578 13 + 636262 CGTCGGCGTTAAG +s Anc0.Anc0refChr3 221456 10 - 222631 CTTTATCTT---G +s Anc1.Anc1refChr5 2979 10 - 6477 CTTTATCTT---G +s Anc2.Anc2refChr13 93178 10 - 96486 CTTTATCTT---G +s mr.mrrefChr5 130035 10 + 294540 CGTCGGCGT---G +s mr.mrrefChr5 129812 10 + 294540 CTGTATTTT---G +s simCow_chr6.simCow.chr6 243819 10 - 602619 TTTTATCTT---G +s simDog_chr6.simDog.chr6 244504 10 - 593897 CTTTATCTT---G +s simHuman_chr6.simHuman.chr6 354293 10 - 601863 CCTTATCTT---G +s simMouse_chr6.simMouse.chr6 278355 10 + 636262 CTGTATTTT---G +s simRat_chr6.simRat.chr6 267588 10 + 647215 TGTGATTTT---A + +a +s simMouse_chr6.simMouse.chr6 278591 51 + 636262 CTGCAAGTTCTCTTTGCATCCTTCTTGCCTTTGAATGAACTATACCATACT +s Anc0.Anc0refChr3 221469 49 - 222631 CATCTAGTCCTCTCTGCCCACTTATTGTCTTTG--TGAACTCTACAAAATT +s Anc1.Anc1refChr5 2992 51 - 6477 CATCTAGTCCTCTCTGCCCACTTATTGTCTTTGAATGAACTCTACAAAATT +s Anc2.Anc2refChr13 93202 49 - 96486 CATCTAGTCCTCTCTGCCCACTTATTGTTTTTG--TGAACTCTTGAAAATT +s mr.mrrefChr5 130045 51 + 294540 CTGCAAGTTCTCTTTGCATCCTTCTTGCCTTTGAATGAACTATACCATACT +s mr.mrrefChr5 129824 38 + 294540 CTTCTAGTTCTCTCTGC-------------CCGAATGAACTATACAATACT +s simCow_chr6.simCow.chr6 243843 49 - 602619 CATCTGGTCCTCTCTGTCCATTCCTTGTTTTCG--TGAACTCTGGAAAAGT +s simDog_chr6.simDog.chr6 244529 49 - 593897 CATCTAGACCTCTCTGCCGACTTATTGCTTTTG--TTCACTCTTGAAAATT +s simHuman_chr6.simHuman.chr6 354306 51 - 601863 CATTTAGTCCTCTCTGCCCTCTTTTCATCTTTGAATGAACTCTCAATAATT +s simMouse_chr6.simMouse.chr6 278367 38 + 636262 CTTCTAGTTCTCTCTGC-------------CCGAATGAACTATACAATACT +s simRat_chr6.simRat.chr6 267600 38 + 647215 CTTCTAGTTCTCTCTGT-------------CGGAATGAACTATACAATACT + +a +s simMouse_chr6.simMouse.chr6 278642 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 130096 4 + 294540 GCAG +s mr.mrrefChr5 129862 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 278405 4 + 636262 GCAG +s simRat_chr6.simRat.chr6 267638 4 + 647215 GCAG + +a +s simMouse_chr6.simMouse.chr6 278646 19 + 636262 GGAAGCTTTGAATACTACT +s Anc0.Anc0refChr3 221522 19 - 222631 AGGGGTTTTGAATGTCATT +s Anc1.Anc1refChr5 3047 19 - 6477 AGGGGTTTTGAATGTCATT +s Anc2.Anc2refChr13 93255 19 - 96486 AGGGGTTTTGCATGTCATT +s mr.mrrefChr5 130100 19 + 294540 GGAAGCTTTGAATACTACT +s mr.mrrefChr5 129866 19 + 294540 GGGCATTTTGAATATCACT +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 278409 19 + 636262 GGGCATTTTGAATATCACT +s simRat_chr6.simRat.chr6 267642 19 + 647215 GGGTGATTTGAATATCATT + +a +s simMouse_chr6.simMouse.chr6 278665 21 + 636262 AGACCCAGGCTTTTGGTTGTC +s Anc0.Anc0refChr3 221541 21 - 222631 TGACCAGGGCTTCTGGCTATT +s Anc1.Anc1refChr5 3066 21 - 6477 TGACCAGGGCTTCTGGCTATT +s Anc2.Anc2refChr13 93274 21 - 96486 TGACCAGGGCTTCTGGCTATT +s mr.mrrefChr5 130119 21 + 294540 AGACCCGGGCTTTTGGTTGTC +s mr.mrrefChr5 129885 21 + 294540 TGACCTGGACATCTGGCTATT +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 278428 21 + 636262 TGACCTGGACATCTGGCTATT +s simRat_chr6.simRat.chr6 267661 21 + 647215 TGACCCGGGCTTCTAGCTCTC +s simRat_chr6.simRat.chr6 267790 21 + 647215 AGACCCGGGCTTTTGGCTCTC + +a +s simMouse_chr6.simMouse.chr6 278686 8 + 636262 ACCCTAAC +s Anc0.Anc0refChr3 221562 8 - 222631 GCCCTAAG +s Anc1.Anc1refChr5 3087 8 - 6477 GCCCTAAG +s Anc2.Anc2refChr13 93295 8 - 96486 GTACTAAG +s mr.mrrefChr5 130140 8 + 294540 ACCCTAAC +s mr.mrrefChr5 129906 8 + 294540 GCCATAAG +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 278449 8 + 636262 GCCATAAG +s simRat_chr6.simRat.chr6 267682 8 + 647215 ACTATAAG +s simRat_chr6.simRat.chr6 267811 8 + 647215 ACCCTAAG + +a +s simMouse_chr6.simMouse.chr6 278694 5 + 636262 ACTGG +s Anc0.Anc0refChr3 221570 5 - 222631 AATGG +s Anc1.Anc1refChr5 3095 5 - 6477 AATGG +s Anc2.Anc2refChr13 93304 5 - 96486 AATGG +s mr.mrrefChr5 130148 5 + 294540 ACTGG +s mr.mrrefChr5 129914 5 + 294540 AATGG +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 278457 5 + 636262 AATGG +s simRat_chr6.simRat.chr6 267690 5 + 647215 AATGG +s simRat_chr6.simRat.chr6 267819 5 + 647215 AATGG a s simMouse_chr6.simMouse.chr6 278699 17 + 636262 TCTGTGAGAGGAACTCT @@ -110683,11 +113982,111 @@ 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 +s simMouse_chr6.simMouse.chr6 278716 30 + 636262 AGTGTGAGAGGAAGTCTGGCACACTGTAAG +s Anc0.Anc0refChr3 221575 30 - 222631 ACCATGAAGGGAACACTAGAATACTGCAAT +s Anc1.Anc1refChr5 3100 30 - 6477 ACCATGAAGGGAACACTAGAATACTGCAAT +s Anc2.Anc2refChr13 93309 30 - 96486 ACCATGAAGGGAACACTAGAATACTGCACT +s mr.mrrefChr5 130170 30 + 294540 ACCATGAGAGGAAGTCTAGAACACTGTAAG +s mr.mrrefChr5 129919 30 + 294540 ACTAGCAGAGGAGGTCTATATTACTGTAAG +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 278462 30 + 636262 ACTAGCAGAGGAGGTCTATATTACTGTAAG +s simRat_chr6.simRat.chr6 267695 30 + 647215 ACTAGGAGAGGATGTCTAGAATACTGTAGG +s simRat_chr6.simRat.chr6 267841 30 + 647215 ACCATGAGAGGAAGTCTAGAACCCTGTAGG + +a +s simMouse_chr6.simMouse.chr6 278746 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 130200 5 + 294540 TGCTG +s mr.mrrefChr5 129950 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 278493 5 + 636262 TGCTG +s simRat_chr6.simRat.chr6 267726 5 + 647215 TGTTA +s simRat_chr6.simRat.chr6 267871 5 + 647215 TGCTA + +a +s simMouse_chr6.simMouse.chr6 278751 7 + 636262 AACACAT +s Anc0.Anc0refChr3 221610 7 - 222631 GCCACGT +s Anc1.Anc1refChr5 3135 7 - 6477 GCCACGT +s Anc2.Anc2refChr13 93344 7 - 96486 GCCACGT +s mr.mrrefChr5 130205 7 + 294540 AACACAT +s mr.mrrefChr5 129955 7 + 294540 CTCACAT +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 278498 7 + 636262 CTCACAT +s simRat_chr6.simRat.chr6 267731 7 + 647215 TTCACAT +s simRat_chr6.simRat.chr6 267881 7 + 647215 AACACAT + +a +s simMouse_chr6.simMouse.chr6 278758 17 + 636262 GGAACTATAATTTCTTG +s Anc0.Anc0refChr3 221617 17 - 222631 GAAACAAAACTGTCTTA +s Anc1.Anc1refChr5 3142 17 - 6477 GAAACAAAACTGTCTTA +s Anc2.Anc2refChr13 93351 17 - 96486 GAAACAAAACTGTCTTA +s mr.mrrefChr5 130212 17 + 294540 GGAACTATAATTTCTTA +s mr.mrrefChr5 129962 17 + 294540 GAAGCAATACCTTATTA +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 278505 17 + 636262 GAAGCAATACCTTATTA +s simRat_chr6.simRat.chr6 267738 17 + 647215 GAAACAATACTTTCTTA +s simRat_chr6.simRat.chr6 267888 17 + 647215 GGAACTATAATTTCTCA + +a +s simMouse_chr6.simMouse.chr6 278775 14 + 636262 TAACAAGCAAGTAG +s Anc0.Anc0refChr3 221634 14 - 222631 TAACAAGCAGGCAG +s Anc1.Anc1refChr5 3159 14 - 6477 TAACAAGCAGGCAG +s Anc2.Anc2refChr13 93368 14 - 96486 TAACAAGCAGGCAG +s mr.mrrefChr5 130229 14 + 294540 TAACAAGCAGGCAG +s mr.mrrefChr5 129979 14 + 294540 TAACAAGCAGGTGG +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 278522 14 + 636262 TAACAAGCAGGCGG +s simRat_chr6.simRat.chr6 267755 14 + 647215 TAACAAGCAGGTGG +s simRat_chr6.simRat.chr6 267905 14 + 647215 TACTACGCAGGCAG + +a +s simMouse_chr6.simMouse.chr6 278789 21 + 636262 TCCATAATGTGGCCTACAATC +s Anc0.Anc0refChr3 221648 18 - 222631 TCTATCATG-GCCCTAC--TG +s Anc1.Anc1refChr5 3173 21 - 6477 TCTATCATGTGCCCTACAATG +s Anc2.Anc2refChr13 93382 18 - 96486 TGTCTCATA-GCCCTAC--TG +s mr.mrrefChr5 130243 21 + 294540 TCCATAATGTGGCCTACAATC +s mr.mrrefChr5 129993 21 + 294540 TCTATATGGTACCCTACAATT +s simCow_chr6.simCow.chr6 244027 18 - 602619 TGTCTCATA-GCCCTAC--TG +s simHuman_chr6.simHuman.chr6 354483 20 - 601863 TCTAGCATG-ACCTTACAATG +s simMouse_chr6.simMouse.chr6 278536 21 + 636262 TCTCTATGGTACCCTACAATT +s simRat_chr6.simRat.chr6 267769 21 + 647215 TCTATAAGGGACCCTACAATT +s simRat_chr6.simRat.chr6 267919 16 + 647215 TC-----TGTGGTCTATGATC + +a +s simMouse_chr6.simMouse.chr6 278810 9 + 636262 CTCCATACC +s Anc0.Anc0refChr3 221666 9 - 222631 CTACATAAT +s Anc1.Anc1refChr5 3194 9 - 6477 CTACATAAT +s Anc2.Anc2refChr13 93400 9 - 96486 CCAAATAAT +s mr.mrrefChr5 130264 9 + 294540 CTCCATACT +s mr.mrrefChr5 130014 9 + 294540 CAAGATAGT +s simCow_chr6.simCow.chr6 244045 9 - 602619 CCAAATAAT +s simHuman_chr6.simHuman.chr6 354503 9 - 601863 CTACATGAT +s simMouse_chr6.simMouse.chr6 278557 9 + 636262 CAAGATAGT +s simRat_chr6.simRat.chr6 267935 9 + 647215 CACCATACT + +a +s simMouse_chr6.simMouse.chr6 278819 46 + 636262 CTCCAATCATTTGGTTGGCATTAAGCGGCAACTGGATTCATTGTAC +s Anc0.Anc0refChr3 221675 6 - 222631 CTCCGA---------------------------------------- +s Anc1.Anc1refChr5 3203 45 - 6477 CTCCGATTATCTGGATGGTGCTA-GCAGCAAATGTGTACATTGTAT +s Anc2.Anc2refChr13 93409 6 - 96486 TTCCGA---------------------------------------- +s mr.mrrefChr5 130273 46 + 294540 CTCCAATCATTTGGTTGGCACTAAGCAGCAACTGGATTCATTGTAC +s mr.mrrefChr5 130023 6 + 294540 CTCCAA---------------------------------------- +s simCow_chr6.simCow.chr6 244056 6 - 602619 TTCCGA---------------------------------------- +s simHuman_chr6.simHuman.chr6 354512 45 - 601863 CTCAGATTATCTGGATGGTGCTA-GCAGCAAATGTGTACATTGTAT +s simMouse_chr6.simMouse.chr6 278566 6 + 636262 CTCCAA---------------------------------------- +s simRat_chr6.simRat.chr6 267944 46 + 647215 CTCCAATCATTTGGTTGGCACTAAGCAGCAATTGAATTCATTATAC a s simMouse_chr6.simMouse.chr6 278865 41 + 636262 CACAGGGGGGGTTATTGGAAGTAATGTTTCACCACAGCCTC @@ -115859,6 +119258,17 @@ s simRat_chr6.simRat.chr6 280614 23 + 647215 CTTAGGTTCCTCTGGTAGCTCTT a +s simMouse_chr6.simMouse.chr6 291946 5 + 636262 GTCCT +s Anc0.Anc0refChr8 2364 5 - 17196 GTTCT +s Anc1.Anc1refChr8 45812 5 - 57822 GTTCT +s Anc2.Anc2refChr5 8083 5 - 8386 GTTCT +s mr.mrrefChr5 142792 5 + 294540 GTCCT +s simDog_chr6.simDog.chr6 55989 5 + 593897 GTTCT +s simHuman_chr6.simHuman.chr6 360544 5 - 601863 GCTCT +s simMouse_chr6.simMouse.chr6 569456 5 - 636262 TAACT +s simRat_chr6.simRat.chr6 280637 5 + 647215 GTCAT + +a s simMouse_chr6.simMouse.chr6 291951 8 + 636262 TGGCCTGA s Anc0.Anc0refChr8 2370 8 - 17196 TGTCTTGA s Anc1.Anc1refChr8 45818 8 - 57822 TGTCTTGA @@ -115869,18 +119279,190 @@ 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 +s simMouse_chr6.simMouse.chr6 291959 4 + 636262 AGTC +s Anc0.Anc0refChr8 2378 4 - 17196 AATT +s Anc1.Anc1refChr8 45826 4 - 57822 AATT +s Anc2.Anc2refChr5 8097 4 - 8386 AATT +s mr.mrrefChr5 142806 4 + 294540 AGTC +s simDog_chr6.simDog.chr6 56004 4 + 593897 AATT +s simHuman_chr6.simHuman.chr6 360558 4 - 601863 AACT +s simMouse_chr6.simMouse.chr6 569461 4 - 636262 AGTC +s simRat_chr6.simRat.chr6 280651 4 + 647215 AGTC + +a +s simMouse_chr6.simMouse.chr6 291963 1 + 636262 T +s Anc0.Anc0refChr8 2384 1 - 17196 T +s Anc1.Anc1refChr8 45832 1 - 57822 T +s Anc2.Anc2refChr5 8103 1 - 8386 T +s mr.mrrefChr5 142810 1 + 294540 T +s simDog_chr6.simDog.chr6 56010 1 + 593897 T +s simHuman_chr6.simHuman.chr6 360564 1 - 601863 C +s simMouse_chr6.simMouse.chr6 569465 1 - 636262 T +s simRat_chr6.simRat.chr6 280655 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 291964 3 + 636262 GAG +s Anc0.Anc0refChr8 2408 3 - 17196 GAA +s Anc1.Anc1refChr8 45856 3 - 57822 GAA +s Anc2.Anc2refChr10 15 3 - 1800 GAA +s mr.mrrefChr5 142834 3 + 294540 GAT +s simCow_chr6.simCow.chr6 331149 3 - 602619 GAT +s simDog_chr6.simDog.chr6 260287 3 + 593897 GAA +s simHuman_chr6.simHuman.chr6 360588 3 - 601863 GAA +s simMouse_chr6.simMouse.chr6 569489 3 - 636262 GAT +s simRat_chr6.simRat.chr6 280679 3 + 647215 GAT + +a +s simMouse_chr6.simMouse.chr6 291967 4 + 636262 ATTG +s Anc0.Anc0refChr8 2411 4 - 17196 AATG +s Anc1.Anc1refChr8 45859 4 - 57822 AATG +s Anc2.Anc2refChr5 8118 4 - 8386 aatg +s Anc2.Anc2refChr10 18 4 - 1800 AATG +s mr.mrrefChr5 142837 4 + 294540 ATTG +s simCow_chr6.simCow.chr6 331152 4 - 602619 AAGA +s simCow_chr6.simCow.chr6 330867 4 - 602619 AACA +s simDog_chr6.simDog.chr6 260290 4 + 593897 AATG +s simDog_chr6.simDog.chr6 259965 4 + 593897 aatg +s simHuman_chr6.simHuman.chr6 360591 4 - 601863 AATG +s simMouse_chr6.simMouse.chr6 569492 4 - 636262 ATTG +s simRat_chr6.simRat.chr6 280682 4 + 647215 AATA + +a +s simMouse_chr6.simMouse.chr6 291971 8 + 636262 ATGTGTTT +s Anc0.Anc0refChr8 2416 7 - 17196 ATGTGTT- +s Anc1.Anc1refChr8 45864 7 - 57822 ATGTGTT- +s Anc2.Anc2refChr5 8123 7 - 8386 gtgtgtc- +s Anc2.Anc2refChr10 23 7 - 1800 ATGAATT- +s mr.mrrefChr5 142841 8 + 294540 ATGTGTTT +s simCow_chr6.simCow.chr6 331157 7 - 602619 ATGAATT- +s simCow_chr6.simCow.chr6 330872 7 - 602619 TGGTATC- +s simDog_chr6.simDog.chr6 259970 7 + 593897 gtgtgtc- +s simHuman_chr6.simHuman.chr6 360596 7 - 601863 ATGTGTT- +s simMouse_chr6.simMouse.chr6 569496 8 - 636262 ATGTGTTT +s simRat_chr6.simRat.chr6 280686 8 + 647215 ATGTGTTT + +a +s simMouse_chr6.simMouse.chr6 291979 36 + 636262 GCAGATATAATTAGTGAGCATGTGCATTTGATATTC +s Anc0.Anc0refChr8 2423 29 - 17196 GGAGA------AAATTAGCGAGCCCATT-gACATTC +s Anc1.Anc1refChr8 45871 32 - 57822 GGAGAt----tAAATTAGCGAGCCCATTTgACATTC +s Anc2.Anc2refChr5 8130 7 - 8386 ---ga------agatt-------------------- +s Anc2.Anc2refChr10 30 29 - 1800 GGTGA------AAATTAATGAGCCCACT-AACATTC +s mr.mrrefChr5 142849 36 + 294540 GCAAATATAATTAATAAGCATGTGCATTTGATATTC +s simCow_chr6.simCow.chr6 331164 29 - 602619 GGTGA------TAATTAATAAGCTCACT-AGTATTT +s simCow_chr6.simCow.chr6 330879 7 - 602619 ---TG------AAATC-------------------- +s simDog_chr6.simDog.chr6 260295 29 + 593897 GGTGA------AAATTAATGATCCCACT-AACATTC +s simDog_chr6.simDog.chr6 259977 7 + 593897 ---ga------agatt-------------------- +s simHuman_chr6.simHuman.chr6 360603 29 - 601863 GGAGA------AAATTAGCGAGCCCATTT-ACATTC +s simMouse_chr6.simMouse.chr6 569504 36 - 636262 GCAAATATAATTAATAAGCATGTGCATTTGATATTC +s simRat_chr6.simRat.chr6 280694 36 + 647215 GCAAAGATAATTAACAAACGTACGCATTTGATATTC + +a +s simMouse_chr6.simMouse.chr6 292015 26 + 636262 ATATTGTTGTGTTTAACTTTAAAGTG +s Anc0.Anc0refChr8 2454 25 - 17196 ACACTGTTATGTGCAGCTTTTGAAT- +s Anc1.Anc1refChr8 45905 25 - 57822 ACACTGTTATGTGCAGCTTTTGAAT- +s Anc2.Anc2refChr10 61 25 - 1800 ATATTGTTATGTGCAGCTTATGAAT- +s mr.mrrefChr5 142885 26 + 294540 ATATTGTTATGTTCAACTTTAAAGTG +s simCow_chr6.simCow.chr6 331200 24 - 602619 ATATTGTTATGTGCAGCTTA-GAAT- +s simDog_chr6.simDog.chr6 260326 13 + 593897 ----TGTAGTGT--------TGAAT- +s simHuman_chr6.simHuman.chr6 360634 25 - 601863 ACACTGTTATGTGAAGCTTTTGAAC- +s simMouse_chr6.simMouse.chr6 569540 26 - 636262 ATATTGTTATGTCCAACTTTAAAGTG +s simRat_chr6.simRat.chr6 280730 26 + 647215 ATATTCTTATGTTCAACTTTCAAGTG + +a +s simMouse_chr6.simMouse.chr6 292041 68 + 636262 CACGTTCAACACATCTTGGGGGATAAGTTGCATTGATGTAATAACGTTTTATAGGGGGCCATGGCATC +s Anc0.Anc0refChr8 2487 53 - 17196 TATGCT-------TCTGGTGGAATATATTGTATTGATGT--------CTCACAGGGAATCGTGGCATT +s Anc1.Anc1refChr8 45938 53 - 57822 TATGCT-------TCTGGTGGAATATATTGTATTGATGT--------CTCACAGGGAATCGTGGCATT +s Anc2.Anc2refChr10 94 53 - 1800 TAAACT-------TCTGGTGTAATATATTGTATTGATGT--------CTCACAGGGAATCGTGGCATT +s mr.mrrefChr5 142933 68 + 294540 CATGTTCAACACATCTTGGGGGATAAGTTGCATTGATGTAATAACGTTTTATAGGGGGCCATAGCATC +s simCow_chr6.simCow.chr6 331232 46 - 602619 TCAC--------------TGTGATATATTGTATTGATGT--------CTAACAGGAAATCAGGACATT +s simDog_chr6.simDog.chr6 260347 53 + 593897 AAAACT-------TCTGGGGTACTATAGTATATTGATGT--------CTCACAGGGACTTGTAGCATT +s simHuman_chr6.simHuman.chr6 360667 52 - 601863 TATGCT-------TCTGGTGGAATATATTGT-TTGATGT--------CTCACAGGGAATCTTGGCATT +s simMouse_chr6.simMouse.chr6 569566 68 - 636262 CATGTTCAACACATCTTGGGGGATAAGTTGCATTGATGTAATAACGTTTTATAGGGGGCCATAGCATC +s simRat_chr6.simRat.chr6 280778 67 + 647215 CGTGTTCAACACATCTT-GAGGATAAATTGCATTGATGTGATAATGTTTTATAGGGGGCCACAGCATC + +a +s simMouse_chr6.simMouse.chr6 292109 120 + 636262 ACCCATTCCTCATCTAGGACTCTTCTGGGATAAGTGGGCATCTTGCACAGGCGGAATTGTGCTTAAGGCAGAGGAGTTCTGAGGCTGTTTCATCCCGCATCATGATCATTCTGAGGGGCA +s Anc0.Anc0refChr8 2540 106 - 17196 GCCCCTTAC----CTGGGACTCTTCTGAGCCAAATGGGCATATTGCGCATGAGAAAT-ATTGTATAGATATATCAGT---AAGAC------ATGGTATATCAGTATCTACCCAGGGGGCA +s Anc1.Anc1refChr8 45991 109 - 57822 GCCCCTTACTC--CTGGGACTCTTCTGAGCCAAATGGGCATATTGCGCATGAGAAATTATTGTATAGATATATCAGT---AAGAC------ATGGTATATCAGTATCTACCCAGGGGGCA +s Anc2.Anc2refChr10 147 106 - 1800 GCACCTTAT----CTGGGTCTCTCCTGAGCCAAATGGAGATATCGCGTGTGAGAGAT-ATTGTATAGATATCTCAGG---AAGAC------ATGGTATATCAGTGTGTACTCAGGGGGAA +s mr.mrrefChr5 143001 120 + 294540 ACCCATTCCTCACCTAGGACTCTTCTGGGATAAGTGGGCATCTTGCACAGGGGGAATTGTGCTTAAGGCAGAGGAGTTCTGAGGCTGTTTCATCCCACATCATGATCATTCTGAGGGGCA +s simCow_chr6.simCow.chr6 331278 42 - 602619 GCAA----------------------------------------GTGGTTAGGAGAT-ATTGTATAGATGACTCAGG---AAGAC------A---------------------------- +s simDog_chr6.simDog.chr6 260400 106 + 593897 GCACCTTAT----CTGGGTCTCTCCTGAGCCAAATGGAGATATCGCATGTGAGAGAT-ATTGTATAGATATCTCAGG---GAGAC------ATGGTATATCAGTGTGTACTCAGGGGGAA +s simHuman_chr6.simHuman.chr6 360720 109 - 601863 GCCCCTTACTC--CTGGGACTCTTCTGTGCCAAATGGGCATGTTGCGCATGAGAAAATATTGTATAGATATATTAGT---AAGAC------ATTGTATATCAAAATCTGCCCAGGGGGCA +s simMouse_chr6.simMouse.chr6 569634 120 - 636262 ACCCATTCCTCACCTAGGACTCTTCTGGGATAAGTGGGCATCTTGCACAGGGGGAATTGTGCTTAAGGCAGAGGAGTTCTGAGGCTGTTTCATCCCACATCATGATCATTCTGAGGGGCA +s simRat_chr6.simRat.chr6 280845 120 + 647215 TCCCATTCCCCGCCTGGGGCTACTCTGGTACAAGTGGGCATCTTGCACAAAGAGTATTGTGCCTAAGGCCGAGGACTTCCGAGGCTGTTTCATCCCATGTCATGATCATCCTGAGAGGCA + +a +s simMouse_chr6.simMouse.chr6 292229 3 + 636262 GCA +s Anc0.Anc0refChr8 2646 3 - 17196 ACA +s Anc1.Anc1refChr8 46100 3 - 57822 ACA +s Anc2.Anc2refChr10 253 3 - 1800 ACA +s mr.mrrefChr5 143121 3 + 294540 GCA +s simCow_chr6.simCow.chr6 331320 3 - 602619 ACG +s simDog_chr6.simDog.chr6 260540 3 + 593897 ACA +s simMouse_chr6.simMouse.chr6 569754 3 - 636262 GCA +s simRat_chr6.simRat.chr6 280965 3 + 647215 GCA + +a +s simMouse_chr6.simMouse.chr6 292232 4 + 636262 TTCC +s Anc0.Anc0refChr8 2649 4 - 17196 TTCC +s Anc1.Anc1refChr8 46103 4 - 57822 TTCC +s Anc2.Anc2refChr10 265 4 - 1800 TTCC +s mr.mrrefChr5 143124 4 + 294540 TTCC +s simCow_chr6.simCow.chr6 331332 4 - 602619 TTTC +s simDog_chr6.simDog.chr6 260552 4 + 593897 TTCC +s simMouse_chr6.simMouse.chr6 569757 4 - 636262 TTCC +s simRat_chr6.simRat.chr6 280968 4 + 647215 CACA + +a +s simMouse_chr6.simMouse.chr6 292236 23 + 636262 TCTTGAACTGTATGGTTGTTGCT +s Anc0.Anc0refChr8 2653 22 - 17196 TATTGACCAGCATGGTTGTTGA- +s Anc1.Anc1refChr8 46107 22 - 57822 TATTGACCAGCATGGTTGTTGA- +s Anc2.Anc2refChr10 307 22 - 1800 TATTGACCAGCATGGTTGTTGA- +s mr.mrrefChr5 143128 23 + 294540 TCTTGAACTGTATGGTTGTTGCT +s simCow_chr6.simCow.chr6 331375 22 - 602619 TAATGACCTGTAAAGCTGTTGC- +s simDog_chr6.simDog.chr6 260594 22 + 593897 TATTGACCAGCATGGTTGTTGA- +s simMouse_chr6.simMouse.chr6 569761 23 - 636262 TCTTGAACTGTATGGTTGTTGCT +s simRat_chr6.simRat.chr6 280972 23 + 647215 TCTTGAACTGCATAATTGTTGCT + +a +s simMouse_chr6.simMouse.chr6 292259 96 + 636262 GAAGTGTTGCACATAATACAAGCACAATTGTTCATCTCAGAAATCCCTACTCAGTAGTTTCCAGCACACCCAATATAGGATTGCATAACAGATAAT +s Anc0.Anc0refChr8 2675 96 - 17196 GAAGTGTTGCAAATAGTAGAACTACAATTTCTTACCTTAAAAACCCCCACTTGGGATTTTCTGTAGCAAGGAATAAGAAATTGCACAACAGATTGT +s Anc1.Anc1refChr8 46129 96 - 57822 GAAGTGTTGCAAATAGTAGAACTACAATTTCTTACCTTAAAAACCCCCACTTGGGATTTTCTGTAGCAAGGAATAAGAAATTGCACAACAGATTGT +s Anc2.Anc2refChr10 329 96 - 1800 GAAGTGTTGCAAATAGTAGAACTACAATTTCTTACCTTAAAAACCCCCACTTGGGATTTTCTGTAGCAAGGAATAAGAAATTGCACAACAGATTGT +s mr.mrrefChr5 143151 96 + 294540 GAAGTGTTGCACATAATACAAGCACAATTGTTCATCTCAGAAATCCCTACTCAGTAGTTTCCAGCACACCCAATATAGGATTGCATAACAGATAAT +s simCow_chr6.simCow.chr6 331398 96 - 602619 GGCACGCTGTAAATAGAAGATATACAATTTCTTATCTCTAAAATCCCCACTCAGAATTTTCTGAAGCTATGAATAGAAAATCATACAAGAGACTAT +s simDog_chr6.simDog.chr6 260616 96 + 593897 GAAGTGTTGCAAATAGTAGAACTACAATTTCTTACCTTAAAAACCCCCACTTGGGATTTTCTGTAGCAAGGAATAAGAAACTGCACAGCGGATTGG +s simHuman_chr6.simHuman.chr6 360829 17 - 601863 -------------------------------------------------------------------------------ATTGCACAACAGATTGT +s simMouse_chr6.simMouse.chr6 569784 96 - 636262 GAAGTGTTGCACATAATACAAGCACAATTGTTCATCTCAGAAATCCCTACTCAGTAGTTTCCAGCACACCCAATATAGGATTGCATAACAGATAAT +s simRat_chr6.simRat.chr6 280995 81 + 647215 GAAGTGTTGCAAAT-------------CAA--TATTCCAGAAACCCCTACTCAGTAGTTTCCAGCATACCCAATATAGAATTGTGCAACAGACGAT + +a +s simMouse_chr6.simMouse.chr6 292355 14 + 636262 CCTTTGTTTACTTT +s Anc0.Anc0refChr8 2868 14 - 17196 ACTCCATTCATAAC +s Anc1.Anc1refChr8 46322 14 - 57822 ACTCCATTCATAAC +s Anc2.Anc2refChr10 532 14 - 1800 ACACCATTCATAAC +s mr.mrrefChr5 143247 14 + 294540 CCTTTGTTTACTTT +s simCow_chr6.simCow.chr6 331592 14 - 602619 ATACCGTTTATAAC +s simDog_chr6.simDog.chr6 260822 14 + 593897 ACACCAACCATAGT +s simHuman_chr6.simHuman.chr6 360943 14 - 601863 ACTCCATTCATAAC +s simMouse_chr6.simMouse.chr6 569880 14 - 636262 CCTTTGTTTACTCT +s simRat_chr6.simRat.chr6 281076 14 + 647215 CCTTGATTTGCCTT + +a +s simMouse_chr6.simMouse.chr6 292369 45 + 636262 GTGAAGTGAAATGATCCAACCATTTGAAGTGAAGAATCAGGTGAG +s Anc0.Anc0refChr8 2889 45 - 17196 GTCAGGCACAATGATTTGACCATCTAGTGTGTGGAGTCAGATGAG +s Anc1.Anc1refChr8 46343 45 - 57822 GTCAGGCACAATGATTTGACCATCTAGTGTGTGGAGTCAGATGAG +s Anc2.Anc2refChr5 7571 9 - 8386 ------------------------------------CCAGATGAG +s Anc2.Anc2refChr10 553 45 - 1800 GTCAGGCACAATGATTTGATCATCTAGTGTGTGGAGTCAGATGAG +s mr.mrrefChr5 143263 45 + 294540 GTGAAGCAAAATGATCTGACCATCTAATGTGAAGAATCAGGTGAG +s simCow_chr6.simCow.chr6 331613 44 - 602619 GTCAGA-ACAATGATTTGGTCTTTTACTGTGTGGAGCCAGATGAG +s simCow_chr6.simCow.chr6 330440 9 - 602619 ------------------------------------TCAGACAAG +s simDog_chr6.simDog.chr6 260843 42 + 593897 GTCAGGCACAAT---TTGATCATCTAGCATGTGGAATCAGATGTG +s simDog_chr6.simDog.chr6 259475 9 + 593897 ------------------------------------CCAGATGAG +s simHuman_chr6.simHuman.chr6 360964 45 - 601863 GTCAGGCACAATGATTTGACCATCTAGTGTGTGGAGGCACATGAG +s simMouse_chr6.simMouse.chr6 569896 5 - 636262 CTTGG---------------------------------------- +s simRat_chr6.simRat.chr6 281090 45 + 647215 GTGAAACAAAATGATCTGACCATCTAATATGAAGAATCAGGTGAG a s simMouse_chr6.simMouse.chr6 292414 22 + 636262 AAGAAGTTAGTAACCTCATTGT @@ -116270,52 +119852,84 @@ 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 +s simMouse_chr6.simMouse.chr6 293002 18 + 636262 GGTATAAACCTTCTTCAA +s Anc0.Anc0refChr8 3663 17 - 17196 GATATAA-CCCTCTCCAA +s Anc1.Anc1refChr5 4309 17 - 6477 GATATAT-AACTCTCCAC +s Anc1.Anc1refChr8 47192 17 - 57822 GATATAA-CCCTCTCCAA +s Anc2.Anc2refChr10 1327 17 - 1800 GATATAA-CCCTCTCCAA +s mr.mrrefChr5 143927 17 + 294540 GGTATAA-CCTTCTTCAA +s mr.mrrefChr5 131378 17 + 294540 GAGACAT-GGCCCTCTGT +s simCow_chr6.simCow.chr6 332213 17 - 602619 GACATAA-CTCTCTTCAA +s simDog_chr6.simDog.chr6 261625 17 + 593897 GTTATAA-CCCTCTCCAA +s simHuman_chr6.simHuman.chr6 355669 17 - 601863 GATATAT-AACTCTCCAC +s simHuman_chr6.simHuman.chr6 361894 17 - 601863 GATATAA-CCCTCTCCAA +s simMouse_chr6.simMouse.chr6 280311 17 + 636262 AAGACAT-GGCCCTCTGT +s simRat_chr6.simRat.chr6 268976 17 + 647215 GAGACAT-GGCCTGCTTT +s simRat_chr6.simRat.chr6 281792 17 + 647215 GGTATAA-CCTTCTACAA + +a +s simMouse_chr6.simMouse.chr6 293020 4 + 636262 CACA +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 143944 4 + 294540 TACA +s mr.mrrefChr5 131396 4 + 294540 ATTG +s simCow_chr6.simCow.chr6 332230 4 - 602619 TCCA +s simDog_chr6.simDog.chr6 261642 4 + 593897 ACCA +s simHuman_chr6.simHuman.chr6 355686 4 - 601863 ATCA +s simHuman_chr6.simHuman.chr6 361911 4 - 601863 CTCA +s simMouse_chr6.simMouse.chr6 280329 4 + 636262 ATTG +s simRat_chr6.simRat.chr6 268994 4 + 647215 ATTG +s simRat_chr6.simRat.chr6 281809 4 + 647215 TACA + +a +s simMouse_chr6.simMouse.chr6 293024 14 + 636262 CTAAATTGGTGTAA +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 143948 14 + 294540 CTAAATTGGTGTAA +s mr.mrrefChr5 131404 14 + 294540 TCAATTCAATCTAG +s simCow_chr6.simCow.chr6 332238 12 - 602619 TTAATT--ACATAG +s simDog_chr6.simDog.chr6 261650 14 + 593897 TTAGTTTAACATGG +s simHuman_chr6.simHuman.chr6 355694 14 - 601863 TCAAATCAACATAG +s simHuman_chr6.simHuman.chr6 361919 14 - 601863 TGATCTCAACATAG +s simMouse_chr6.simMouse.chr6 280337 14 + 636262 TCAATTCAATCTAG +s simRat_chr6.simRat.chr6 269007 14 + 647215 TAAATTCGATCTAG +s simRat_chr6.simRat.chr6 281813 14 + 647215 CTAATTTCACGTAA + +a +s simMouse_chr6.simMouse.chr6 293038 41 + 636262 CCCCAAGATCAAGAAGTGCAGTGTGATAAGGTAGCCAAGTT +s Anc0.Anc0refChr8 3702 41 - 17196 AGCGAAGATCAAGGAGTGCATTGTGCTAAGGCAGCAAAATT +s Anc1.Anc1refChr5 4348 41 - 6477 AGCAAGGATCAAGGAGTGCATTGTGCTAAGGCGGCAAAATT +s Anc1.Anc1refChr8 47231 41 - 57822 CGCGAAGATCAAGGAGTGCATTGTGCTAAGGCAGCAAAGTT +s Anc2.Anc2refChr10 1366 41 - 1800 AGTGAAGATCAAGGAGTGCATTGTGCCAAGGCAGCAAAATT +s mr.mrrefChr5 143962 41 + 294540 CCCCAAGATCAAGAAGTGCAGTGTGATAAGGTAGCAAAGTT +s mr.mrrefChr5 131418 41 + 294540 AGCACAGAACAAGAATTACAGTTTGCCAAGGCGGCAAAGTT +s simCow_chr6.simCow.chr6 332250 41 - 602619 AGTGAAGCTCCAAGAGTGCATTGTGCCAAGGTGGCAAACTC +s simDog_chr6.simDog.chr6 261664 41 + 593897 AGTGAAGAACTAGGATCACATTGTGTCAAGGGAGCAAAATT +s simHuman_chr6.simHuman.chr6 355708 41 - 601863 AGCAAGGATCAAGGAGTGCATTGTGCTAAGGCGGCAAAATT +s simHuman_chr6.simHuman.chr6 361942 41 - 601863 CGCAAAGATCAAGCAGTGCATTGTGCTATTGCAACAAAGTT +s simMouse_chr6.simMouse.chr6 280351 36 + 636262 AC---ACAACAACAATTAC--TTTGCCAAGGCGGCAAAGTT +s simRat_chr6.simRat.chr6 269021 41 + 647215 AGCACAGAACAAGTATCACAGCTTGCCAAGGCAGCAAGGTT +s simRat_chr6.simRat.chr6 281827 41 + 647215 ACCAACGATCAAGAAGTGAAGTGTGATATGGTAGCAAAGTT + +a +s simMouse_chr6.simMouse.chr6 293079 9 + 636262 GAGGCCAGA +s Anc0.Anc0refChr8 3743 9 - 17196 GAGGCGAGA +s Anc1.Anc1refChr5 4389 9 - 6477 GGCCCGAGA +s Anc1.Anc1refChr8 47272 9 - 57822 GAGGCCAGA +s Anc2.Anc2refChr10 1407 9 - 1800 GAGGCGAGA +s mr.mrrefChr5 144003 9 + 294540 GAGGCCAGA +s mr.mrrefChr5 131459 9 + 294540 GGTCATAGA +s simCow_chr6.simCow.chr6 332291 9 - 602619 GAGGTGAGA +s simDog_chr6.simDog.chr6 261705 9 + 593897 GAGCCGAGA +s simHuman_chr6.simHuman.chr6 355751 9 - 601863 GGCCCGAGA +s simHuman_chr6.simHuman.chr6 361983 9 - 601863 GACGCCAGA +s simMouse_chr6.simMouse.chr6 280387 7 + 636262 G--TATAGA +s simRat_chr6.simRat.chr6 269062 9 + 647215 GGTCACAGA +s simRat_chr6.simRat.chr6 281868 9 + 647215 GAGGCCAGA a s simMouse_chr6.simMouse.chr6 293088 4 + 636262 GTTT @@ -116329,6 +119943,69 @@ s simRat_chr6.simRat.chr6 281877 4 + 647215 GATT a +s simMouse_chr6.simMouse.chr6 293092 3 + 636262 TTG +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 144016 3 + 294540 TTG +s mr.mrrefChr5 131468 3 + 294540 TTA +s simCow_chr6.simCow.chr6 332303 3 - 602619 TTA +s simDog_chr6.simDog.chr6 261718 3 + 593897 TTA +s simHuman_chr6.simHuman.chr6 355762 3 - 601863 TTA +s simHuman_chr6.simHuman.chr6 361996 3 - 601863 TCA +s simMouse_chr6.simMouse.chr6 280394 3 + 636262 TTA +s simRat_chr6.simRat.chr6 269071 3 + 647215 TTA +s simRat_chr6.simRat.chr6 281881 3 + 647215 TTG + +a +s simMouse_chr6.simMouse.chr6 293095 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 144019 1 + 294540 A +s mr.mrrefChr5 131482 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 355776 1 - 601863 A +s simHuman_chr6.simHuman.chr6 362010 1 - 601863 A +s simMouse_chr6.simMouse.chr6 280408 1 + 636262 A +s simRat_chr6.simRat.chr6 269085 1 + 647215 A +s simRat_chr6.simRat.chr6 281884 1 + 647215 G + +a +s simMouse_chr6.simMouse.chr6 293096 4 + 636262 TCCC +s Anc0.Anc0refChr8 3771 4 - 17196 TCCA +s Anc1.Anc1refChr5 4413 4 - 6477 TCCA +s Anc1.Anc1refChr8 47300 4 - 57822 TCCA +s Anc2.Anc2refChr10 1435 4 - 1800 TCCA +s mr.mrrefChr5 144020 4 + 294540 TCCC +s mr.mrrefChr5 131483 4 + 294540 CCCA +s simCow_chr6.simCow.chr6 332391 4 - 602619 TCTA +s simDog_chr6.simDog.chr6 261733 4 + 593897 CCCA +s simHuman_chr6.simHuman.chr6 355777 4 - 601863 TCCA +s simHuman_chr6.simHuman.chr6 362011 4 - 601863 TCCA +s simMouse_chr6.simMouse.chr6 280409 4 + 636262 CTCC +s simRat_chr6.simRat.chr6 269086 4 + 647215 CCCA +s simRat_chr6.simRat.chr6 281895 4 + 647215 TCCC + +a +s simMouse_chr6.simMouse.chr6 293100 2 + 636262 TT +s Anc0.Anc0refChr8 3775 2 - 17196 TG +s Anc1.Anc1refChr5 4417 2 - 6477 TG +s Anc1.Anc1refChr8 47304 2 - 57822 TG +s Anc2.Anc2refChr10 1439 2 - 1800 TG +s mr.mrrefChr5 144024 2 + 294540 TT +s mr.mrrefChr5 131487 2 + 294540 TG +s simCow_chr6.simCow.chr6 332395 2 - 602619 GG +s simDog_chr6.simDog.chr6 261737 2 + 593897 TG +s simHuman_chr6.simHuman.chr6 355781 2 - 601863 TG +s simHuman_chr6.simHuman.chr6 362015 2 - 601863 TG +s simMouse_chr6.simMouse.chr6 280413 2 + 636262 TG +s simRat_chr6.simRat.chr6 281899 2 + 647215 TT + +a s simMouse_chr6.simMouse.chr6 293102 3 + 636262 TCC s Anc0.Anc0refChr8 3777 3 - 17196 TCC s Anc1.Anc1refChr5 4419 3 - 6477 CCC @@ -116355,18 +120032,100 @@ 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 +s simMouse_chr6.simMouse.chr6 293116 2 + 636262 TC +s Anc0.Anc0refChr8 3788 2 - 17196 TC +s Anc1.Anc1refChr5 4422 2 - 6477 TG +s Anc1.Anc1refChr8 47317 2 - 57822 TC +s Anc2.Anc2refChr10 1452 2 - 1800 TC +s mr.mrrefChr5 144040 2 + 294540 TC +s mr.mrrefChr5 131492 2 + 294540 TG +s simCow_chr6.simCow.chr6 332408 1 - 602619 -C +s simDog_chr6.simDog.chr6 261750 2 + 593897 TC +s simHuman_chr6.simHuman.chr6 355787 2 - 601863 TG +s simHuman_chr6.simHuman.chr6 362028 2 - 601863 TC +s simMouse_chr6.simMouse.chr6 280415 1 + 636262 -G +s simRat_chr6.simRat.chr6 269093 2 + 647215 TG +s simRat_chr6.simRat.chr6 281915 2 + 647215 TA + +a +s simMouse_chr6.simMouse.chr6 293118 6 + 636262 ATGGAC +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 144042 6 + 294540 ATGGAC +s mr.mrrefChr5 131494 6 + 294540 CTGGGG +s simCow_chr6.simCow.chr6 332409 6 - 602619 TTGGAG +s simDog_chr6.simDog.chr6 261752 6 + 593897 TCGGGG +s simHuman_chr6.simHuman.chr6 355789 6 - 601863 CTGGAG +s simHuman_chr6.simHuman.chr6 362030 6 - 601863 TTGAAG +s simMouse_chr6.simMouse.chr6 280416 6 + 636262 TAGGGG +s simRat_chr6.simRat.chr6 269101 6 + 647215 CTGGGG +s simRat_chr6.simRat.chr6 281917 6 + 647215 TTGGAC + +a +s simMouse_chr6.simMouse.chr6 293124 4 + 636262 TTCG +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 144048 4 + 294540 TTCG +s mr.mrrefChr5 131501 4 + 294540 TTTA +s simCow_chr6.simCow.chr6 332415 4 - 602619 TTTA +s simDog_chr6.simDog.chr6 261758 4 + 593897 TATA +s simHuman_chr6.simHuman.chr6 355795 4 - 601863 TTTA +s simHuman_chr6.simHuman.chr6 362036 4 - 601863 TTTA +s simMouse_chr6.simMouse.chr6 280423 4 + 636262 CTTA +s simRat_chr6.simRat.chr6 269108 4 + 647215 TTTA +s simRat_chr6.simRat.chr6 281923 4 + 647215 TCCA + +a +s simMouse_chr6.simMouse.chr6 293128 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 144052 1 + 294540 T +s mr.mrrefChr5 131505 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 355799 1 - 601863 T +s simHuman_chr6.simHuman.chr6 362040 1 - 601863 T +s simMouse_chr6.simMouse.chr6 280427 1 + 636262 T +s simRat_chr6.simRat.chr6 269112 1 + 647215 T +s simRat_chr6.simRat.chr6 281927 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 293129 7 + 636262 TAGGCTA +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 144053 7 + 294540 TAGGCTA +s mr.mrrefChr5 131507 7 + 294540 TAGGTTA +s simCow_chr6.simCow.chr6 332421 7 - 602619 TAGACTA +s simDog_chr6.simDog.chr6 261793 7 + 593897 TAGGTTA +s simHuman_chr6.simHuman.chr6 355801 7 - 601863 TAGGTTA +s simHuman_chr6.simHuman.chr6 362042 7 - 601863 TAGGCTA +s simMouse_chr6.simMouse.chr6 280429 7 + 636262 TAGGTTA +s simRat_chr6.simRat.chr6 269114 7 + 647215 TAGGTTA +s simRat_chr6.simRat.chr6 281928 7 + 647215 TAGGTTA + +a +s simMouse_chr6.simMouse.chr6 293136 14 + 636262 ATTTGGTCAGGTAG +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 144060 14 + 294540 ATTTGGTCAGGTAG +s mr.mrrefChr5 131515 14 + 294540 AATTGCTCATTCAG +s simCow_chr6.simCow.chr6 332429 14 - 602619 AATTGTTCAGTCAG +s simDog_chr6.simDog.chr6 261801 14 + 593897 AATTGTTCAGTTGG +s simHuman_chr6.simHuman.chr6 355809 14 - 601863 AAGTGTTTAATCAG +s simHuman_chr6.simHuman.chr6 362050 14 - 601863 ATTTGTTCAATTAG +s simMouse_chr6.simMouse.chr6 280437 14 + 636262 AATTGCTCATTCAG +s simRat_chr6.simRat.chr6 269122 14 + 647215 AATTGCTCATTCAG +s simRat_chr6.simRat.chr6 281935 14 + 647215 ACTTGGTCAGATAA a s simMouse_chr6.simMouse.chr6 293150 122 + 636262 CATCTATGTTGTTTCCTGATCCACACCTGTCGAGTTCATAGAGAAGATAGTTTTTGAGACAAAGGGAACTCCTCTGTACTAGTGGCATGGACTGAGTTGCAAAGTGGGACAATGTCAGCCAG @@ -116374,19 +120133,20 @@ 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 +s simMouse_chr6.simMouse.chr6 293272 5 + 636262 ACTGA +s Anc0.Anc0refChr8 3824 5 - 17196 AAACA +s Anc1.Anc1refChr5 4458 5 - 6477 AAACA +s Anc1.Anc1refChr8 47353 5 - 57822 AATGA +s Anc2.Anc2refChr10 1488 5 - 1800 AAACC +s mr.mrrefChr5 144195 5 + 294540 AATGA +s mr.mrrefChr5 131529 5 + 294540 AACTA +s simCow_chr6.simCow.chr6 332443 5 - 602619 AAACC +s simDog_chr6.simDog.chr6 261815 5 + 593897 AAACC +s simHuman_chr6.simHuman.chr6 355823 5 - 601863 AAACA +s simHuman_chr6.simHuman.chr6 362064 5 - 601863 AATGA +s simMouse_chr6.simMouse.chr6 280451 4 + 636262 AA-TA +s simRat_chr6.simRat.chr6 269136 5 + 647215 AACTT +s simRat_chr6.simRat.chr6 282070 5 + 647215 AAAAA a s simMouse_chr6.simMouse.chr6 293277 8 + 636262 AAAACCCT @@ -116400,6 +120160,100 @@ s simRat_chr6.simRat.chr6 282075 8 + 647215 AAAACCCC a +s simMouse_chr6.simMouse.chr6 293285 1 + 636262 A +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 144208 1 + 294540 A +s mr.mrrefChr5 131534 1 + 294540 G +s simCow_chr6.simCow.chr6 332456 1 - 602619 A +s simDog_chr6.simDog.chr6 261828 1 + 593897 A +s simHuman_chr6.simHuman.chr6 355828 1 - 601863 G +s simHuman_chr6.simHuman.chr6 362077 1 - 601863 A +s simMouse_chr6.simMouse.chr6 280455 1 + 636262 G +s simRat_chr6.simRat.chr6 269141 1 + 647215 G +s simRat_chr6.simRat.chr6 282083 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 293286 6 + 636262 GAAGGC +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 144209 6 + 294540 GAAGGC +s mr.mrrefChr5 131535 6 + 294540 GAACAT +s simCow_chr6.simCow.chr6 332457 6 - 602619 GAAAGG +s simDog_chr6.simDog.chr6 261829 6 + 593897 GAAAGT +s simHuman_chr6.simHuman.chr6 355837 6 - 601863 GAAAAT +s simHuman_chr6.simHuman.chr6 362078 6 - 601863 AAAAGT +s simMouse_chr6.simMouse.chr6 280456 6 + 636262 CAACCT +s simRat_chr6.simRat.chr6 269142 6 + 647215 GAGCAT +s simRat_chr6.simRat.chr6 282084 6 + 647215 GAAGGC + +a +s simMouse_chr6.simMouse.chr6 293292 14 + 636262 ATTGAAAAATCTGA +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 144215 14 + 294540 ATTGAAAAATCTGA +s mr.mrrefChr5 131543 14 + 294540 ATTGTAAAATTTGA +s simCow_chr6.simCow.chr6 332465 14 - 602619 ATTGAAAAATCTGA +s simDog_chr6.simDog.chr6 261837 14 + 593897 ATTGAAAAATCTGA +s simHuman_chr6.simHuman.chr6 355845 14 - 601863 ATTGAAAAATCTGA +s simHuman_chr6.simHuman.chr6 362086 14 - 601863 ATCAAAAAATCTGA +s simMouse_chr6.simMouse.chr6 280464 14 + 636262 ATTGTAAAATTTGA +s simRat_chr6.simRat.chr6 269150 14 + 647215 ATAGGAAAATTTGA +s simRat_chr6.simRat.chr6 282090 14 + 647215 ATTGAAAAATCTGA + +a +s simMouse_chr6.simMouse.chr6 293306 21 + 636262 CACTATAGTATTGACGTATAA +s Anc0.Anc0refChr8 3860 21 - 17196 CACCATTGTGTTCATGTACAC +s Anc1.Anc1refChr5 4486 21 - 6477 CACCACTGTGTTGATGTACAC +s Anc1.Anc1refChr8 47389 21 - 57822 CACCATTGTGTCCACGTACAC +s Anc2.Anc2refChr10 1524 21 - 1800 CACCATTGTGTTCATGTACAC +s mr.mrrefChr5 144229 21 + 294540 CACTATTGTGTCGACGTATAA +s mr.mrrefChr5 131557 21 + 294540 CACTATTGGGTTCATGAGCAC +s simCow_chr6.simCow.chr6 332479 21 - 602619 CACCATTTTGTTCATGGACGC +s simDog_chr6.simDog.chr6 261851 21 + 593897 CACCATTGTGTTCATGCACAC +s simHuman_chr6.simHuman.chr6 355859 21 - 601863 CACCACTGTGTTGATGTACAC +s simHuman_chr6.simHuman.chr6 362106 21 - 601863 CATCATTGTGTCCACGTACAC +s simMouse_chr6.simMouse.chr6 280478 21 + 636262 CACTATTGGGTTCATGAGAAC +s simRat_chr6.simRat.chr6 269164 21 + 647215 CACTATTGAGTTCATGAGCAC +s simRat_chr6.simRat.chr6 282104 21 + 647215 CACTATTGTGTCAATGTATAA + +a +s simMouse_chr6.simMouse.chr6 293327 3 + 636262 GTA +s Anc0.Anc0refChr8 3881 3 - 17196 CTA +s Anc1.Anc1refChr5 4507 3 - 6477 CCA +s Anc1.Anc1refChr8 47410 3 - 57822 CTA +s Anc2.Anc2refChr10 1545 3 - 1800 CTA +s mr.mrrefChr5 144250 3 + 294540 CTA +s mr.mrrefChr5 131578 3 + 294540 CCG +s simCow_chr6.simCow.chr6 332500 3 - 602619 CTA +s simDog_chr6.simDog.chr6 261872 3 + 593897 CTA +s simHuman_chr6.simHuman.chr6 355880 3 - 601863 CCA +s simHuman_chr6.simHuman.chr6 362127 3 - 601863 CTA +s simMouse_chr6.simMouse.chr6 280499 3 + 636262 CCG +s simRat_chr6.simRat.chr6 282125 3 + 647215 CTA + +a +s simMouse_chr6.simMouse.chr6 293330 3 + 636262 CCT +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 144253 3 + 294540 CCT +s mr.mrrefChr5 131581 3 + 294540 TCA +s simCow_chr6.simCow.chr6 332503 3 - 602619 CCT +s simDog_chr6.simDog.chr6 261875 3 + 593897 CAT +s simHuman_chr6.simHuman.chr6 355885 3 - 601863 TCT +s simHuman_chr6.simHuman.chr6 362130 3 - 601863 CCT +s simMouse_chr6.simMouse.chr6 280502 3 + 636262 TCA +s simRat_chr6.simRat.chr6 282128 3 + 647215 CCT + +a s simMouse_chr6.simMouse.chr6 293333 3 + 636262 CCA s Anc0.Anc0refChr8 3887 3 - 17196 CCA s Anc1.Anc1refChr8 47416 3 - 57822 CCA @@ -116411,6 +120265,36 @@ s simRat_chr6.simRat.chr6 282131 3 + 647215 CCA a +s simMouse_chr6.simMouse.chr6 293336 1 + 636262 A +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 144259 1 + 294540 A +s mr.mrrefChr5 131584 1 + 294540 G +s simCow_chr6.simCow.chr6 332509 1 - 602619 A +s simDog_chr6.simDog.chr6 261881 1 + 593897 G +s simHuman_chr6.simHuman.chr6 355888 1 - 601863 G +s simHuman_chr6.simHuman.chr6 362136 1 - 601863 A +s simMouse_chr6.simMouse.chr6 280505 1 + 636262 G +s simRat_chr6.simRat.chr6 282134 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 293337 20 + 636262 ACATGATGTAAGTGCACTAA +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 144260 20 + 294540 ACATGATGTAAGTGCACTAA +s mr.mrrefChr5 131585 20 + 294540 ATGTGGTCCAAGAGTGCTAT +s simCow_chr6.simCow.chr6 332510 20 - 602619 ACGTGCTGTGAGTACACTAG +s simDog_chr6.simDog.chr6 261882 15 + 593897 ATGTGATGCAAGTG-----G +s simHuman_chr6.simHuman.chr6 355890 20 - 601863 ATGTGATGCAAGTGCACTAG +s simHuman_chr6.simHuman.chr6 362137 20 - 601863 ATATGAGACAAGTGCATTAG +s simMouse_chr6.simMouse.chr6 280506 20 + 636262 ATGTGGTCCAAGAGTGCTAT +s simRat_chr6.simRat.chr6 282135 20 + 647215 ACAGGATGTAAGTGCACCAA + +a s simMouse_chr6.simMouse.chr6 293357 1 + 636262 A s Anc0.Anc0refChr8 3911 1 - 17196 A s Anc1.Anc1refChr8 47440 1 - 57822 A @@ -116422,11 +120306,89 @@ s simRat_chr6.simRat.chr6 282155 1 + 647215 A a +s simMouse_chr6.simMouse.chr6 293358 3 + 636262 ACC +s Anc0.Anc0refChr8 3912 3 - 17196 AGC +s Anc1.Anc1refChr5 4534 3 - 6477 AGC +s Anc1.Anc1refChr8 47441 3 - 57822 AGC +s Anc2.Anc2refChr10 1576 3 - 1800 AGC +s mr.mrrefChr5 144281 3 + 294540 ACC +s mr.mrrefChr5 131605 3 + 294540 AAC +s simCow_chr6.simCow.chr6 332531 2 - 602619 -GC +s simDog_chr6.simDog.chr6 261898 3 + 593897 AGC +s simHuman_chr6.simHuman.chr6 355910 3 - 601863 AGC +s simHuman_chr6.simHuman.chr6 362158 3 - 601863 GGC +s simMouse_chr6.simMouse.chr6 280526 3 + 636262 AAC +s simRat_chr6.simRat.chr6 282156 3 + 647215 ACC + +a +s simMouse_chr6.simMouse.chr6 293361 8 + 636262 GAGCCATG +s Anc0.Anc0refChr8 3934 8 - 17196 GAGTTACA +s Anc1.Anc1refChr5 4556 8 - 6477 GAATTACA +s Anc1.Anc1refChr8 47463 8 - 57822 GAGTTATA +s Anc2.Anc2refChr10 1598 8 - 1800 GAGTTACA +s mr.mrrefChr5 144303 8 + 294540 GAGCCATA +s mr.mrrefChr5 131627 8 + 294540 GAGTTAGA +s simCow_chr6.simCow.chr6 332552 8 - 602619 GAATTACA +s simDog_chr6.simDog.chr6 261920 8 + 593897 GAGTTACA +s simHuman_chr6.simHuman.chr6 355932 8 - 601863 GAATTACA +s simHuman_chr6.simHuman.chr6 362180 8 - 601863 GAGTTATA +s simMouse_chr6.simMouse.chr6 280548 8 + 636262 GAGTTAGA +s simRat_chr6.simRat.chr6 282178 8 + 647215 GAGCCATA + +a +s simMouse_chr6.simMouse.chr6 293369 7 + 636262 TCTCTGT +s Anc0.Anc0refChr8 3942 7 - 17196 TCCCTGT +s Anc1.Anc1refChr5 4564 7 - 6477 TCCCTGT +s Anc1.Anc1refChr8 47471 7 - 57822 TCCCTGT +s Anc2.Anc2refChr10 1606 7 - 1800 TCCCTGT +s mr.mrrefChr5 144311 7 + 294540 TCTCTGT +s mr.mrrefChr5 131635 7 + 294540 TCCCAGT +s simCow_chr6.simCow.chr6 332560 7 - 602619 TCTTAGT +s simDog_chr6.simDog.chr6 261928 7 + 593897 TCCCTGT +s simHuman_chr6.simHuman.chr6 355940 7 - 601863 TCCCTGT +s simHuman_chr6.simHuman.chr6 362188 7 - 601863 TTCATGT +s simMouse_chr6.simMouse.chr6 280556 7 + 636262 TCCCAGT +s simRat_chr6.simRat.chr6 269185 7 + 647215 TCCCAGT +s simRat_chr6.simRat.chr6 282186 7 + 647215 TCTCTGT + +a +s simMouse_chr6.simMouse.chr6 293376 5 + 636262 ACACT +s Anc0.Anc0refChr8 3949 5 - 17196 ACACT +s Anc1.Anc1refChr5 4571 5 - 6477 ATACT +s Anc1.Anc1refChr8 47478 5 - 57822 ACACT +s Anc2.Anc2refChr10 1613 5 - 1800 ACACT +s mr.mrrefChr5 144318 5 + 294540 ACACT +s mr.mrrefChr5 131642 5 + 294540 AGACT +s simCow_chr6.simCow.chr6 332567 5 - 602619 ACACC +s simDog_chr6.simDog.chr6 261935 5 + 593897 ACACT +s simHuman_chr6.simHuman.chr6 355947 5 - 601863 ACACT +s simHuman_chr6.simHuman.chr6 362195 5 - 601863 ACACT +s simMouse_chr6.simMouse.chr6 280564 5 + 636262 AGACT +s simRat_chr6.simRat.chr6 269192 5 + 647215 AGACT +s simRat_chr6.simRat.chr6 282193 5 + 647215 ACACT + +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 293401 2 + 636262 GT +s Anc0.Anc0refChr8 3955 2 - 17196 AC +s Anc1.Anc1refChr5 4577 2 - 6477 AC +s Anc1.Anc1refChr8 47484 2 - 57822 GT +s Anc2.Anc2refChr10 1619 2 - 1800 AC +s mr.mrrefChr5 144344 2 + 294540 GT +s mr.mrrefChr5 131648 2 + 294540 AC +s simCow_chr6.simCow.chr6 332573 2 - 602619 AA +s simDog_chr6.simDog.chr6 261941 2 + 593897 AC +s simHuman_chr6.simHuman.chr6 355953 2 - 601863 AC +s simHuman_chr6.simHuman.chr6 362201 2 - 601863 GT +s simMouse_chr6.simMouse.chr6 280570 2 + 636262 AC +s simRat_chr6.simRat.chr6 269198 2 + 647215 AC +s simRat_chr6.simRat.chr6 282219 2 + 647215 GT + +a s simMouse_chr6.simMouse.chr6 293403 8 + 636262 GTGACTGT s Anc0.Anc0refChr8 3957 8 - 17196 TGGACTCT s Anc1.Anc1refChr8 47486 8 - 57822 TGGACTCT @@ -116438,6 +120400,38 @@ s simRat_chr6.simRat.chr6 282221 8 + 647215 GTGACTCT a +s simMouse_chr6.simMouse.chr6 293411 1 + 636262 T +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 144354 1 + 294540 T +s mr.mrrefChr5 131650 1 + 294540 C +s simCow_chr6.simCow.chr6 332583 1 - 602619 A +s simDog_chr6.simDog.chr6 261951 1 + 593897 G +s simHuman_chr6.simHuman.chr6 355955 1 - 601863 A +s simHuman_chr6.simHuman.chr6 362211 1 - 601863 G +s simMouse_chr6.simMouse.chr6 280572 1 + 636262 C +s simRat_chr6.simRat.chr6 269200 1 + 647215 T +s simRat_chr6.simRat.chr6 282229 1 + 647215 C + +a +s simMouse_chr6.simMouse.chr6 293412 5 + 636262 CCATG +s Anc0.Anc0refChr8 3967 5 - 17196 TCCAC +s Anc1.Anc1refChr5 4581 5 - 6477 TCAAG +s Anc1.Anc1refChr8 47495 5 - 57822 CCCAC +s Anc2.Anc2refChr10 1631 5 - 1800 TCCAC +s mr.mrrefChr5 144355 5 + 294540 CCATG +s mr.mrrefChr5 131652 5 + 294540 TGAAG +s simCow_chr6.simCow.chr6 332585 5 - 602619 ACGAC +s simDog_chr6.simDog.chr6 261953 5 + 593897 TCCAC +s simHuman_chr6.simHuman.chr6 355957 5 - 601863 TCAAG +s simHuman_chr6.simHuman.chr6 362212 5 - 601863 CCCAC +s simMouse_chr6.simMouse.chr6 280574 5 + 636262 TGAAG +s simRat_chr6.simRat.chr6 269202 5 + 647215 TGAAG +s simRat_chr6.simRat.chr6 282230 3 + 647215 C--TG + +a s simMouse_chr6.simMouse.chr6 293417 7 + 636262 GATTCAT s Anc0.Anc0refChr8 3972 7 - 17196 CCTGCAG s Anc1.Anc1refChr8 47500 7 - 57822 CCTGCAG @@ -122866,12 +126860,148 @@ s simRat_chr6.simRat.chr6 302051 7 + 647215 TGCACCT a +s simMouse_chr6.simMouse.chr6 310367 3 + 636262 GGA +s Anc0.Anc0refChr8 24 3 + 17196 GAA +s Anc1.Anc1refChr3 24 3 + 3661 GAA +s Anc2.Anc2refChr8 36 3 + 12804 GAT +s mr.mrrefChr5 160750 3 + 294540 GGA +s mr.mrrefChr5 157626 3 + 294540 GAG +s simCow_chr6.simCow.chr6 322912 3 - 602619 AAT +s simDog_chr6.simDog.chr6 316280 3 - 593897 GAT +s simHuman_chr6.simHuman.chr6 226373 3 + 601863 GAA +s simMouse_chr6.simMouse.chr6 307235 3 + 636262 GAG +s simRat_chr6.simRat.chr6 298852 3 + 647215 GAG +s simRat_chr6.simRat.chr6 302058 3 + 647215 AGA + +a +s simMouse_chr6.simMouse.chr6 310370 11 + 636262 TTGTGTCTGGC +s Anc0.Anc0refChr8 27 11 + 17196 TTTAGAGTGGC +s Anc1.Anc1refChr3 27 11 + 3661 TTTAGAGTGGC +s Anc2.Anc2refChr8 39 11 + 12804 TTTAGAGTCGC +s mr.mrrefChr5 160753 11 + 294540 TTGTGTCTGGC +s mr.mrrefChr5 157629 11 + 294540 TTTTGAGTTGC +s simCow_chr6.simCow.chr6 322915 11 - 602619 GTTTGAGTCTC +s simDog_chr6.simDog.chr6 316283 10 - 593897 TCTAGAGTCG- +s simHuman_chr6.simHuman.chr6 226376 11 + 601863 TTTAGTGTGGC +s simMouse_chr6.simMouse.chr6 307240 11 + 636262 TTTTGAGTTTC +s simRat_chr6.simRat.chr6 298855 11 + 647215 TTTTGAGTTGC +s simRat_chr6.simRat.chr6 302061 11 + 647215 TCATGCCTGGC + +a +s simMouse_chr6.simMouse.chr6 310381 1 + 636262 T +s Anc0.Anc0refChr8 38 1 + 17196 T +s Anc1.Anc1refChr3 38 1 + 3661 T +s Anc2.Anc2refChr8 50 1 + 12804 T +s mr.mrrefChr5 160764 1 + 294540 T +s mr.mrrefChr5 157640 1 + 294540 T +s simCow_chr6.simCow.chr6 322926 1 - 602619 T +s simDog_chr6.simDog.chr6 316293 1 - 593897 T +s simHuman_chr6.simHuman.chr6 226387 1 + 601863 T +s simMouse_chr6.simMouse.chr6 307252 1 + 636262 T +s simRat_chr6.simRat.chr6 298866 1 + 647215 T +s simRat_chr6.simRat.chr6 302072 1 + 647215 T + +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 +s simMouse_chr6.simMouse.chr6 310383 17 + 636262 AATTTCTTACCACCCTA +s Anc0.Anc0refChr8 39 17 + 17196 ATTTGCTTGCTCATCTC +s Anc1.Anc1refChr3 39 17 + 3661 ATTTGCTTGCTCATCTC +s Anc2.Anc2refChr8 51 17 + 12804 ATTTGCTTGCTCGTCTC +s mr.mrrefChr5 160766 17 + 294540 AATTTCTTACCACCCTA +s mr.mrrefChr5 157641 17 + 294540 ATTTGCTTGCTCATCTA +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 307253 17 + 636262 ATTTGCTTGCTCATCTA +s simRat_chr6.simRat.chr6 298867 17 + 647215 ATTTGCTTGCTCATCTG +s simRat_chr6.simRat.chr6 302074 17 + 647215 AATTTCTTACTATTCTA + +a +s simMouse_chr6.simMouse.chr6 310400 5 + 636262 TCCCC +s Anc0.Anc0refChr8 59 5 + 17196 TCCCC +s Anc1.Anc1refChr3 59 5 + 3661 TCCCC +s Anc2.Anc2refChr8 71 5 + 12804 TGCCC +s mr.mrrefChr5 160783 5 + 294540 TCCCC +s mr.mrrefChr5 157661 5 + 294540 TTCCG +s simCow_chr6.simCow.chr6 322947 5 - 602619 CGCCC +s simDog_chr6.simDog.chr6 316314 5 - 593897 TGCCT +s simHuman_chr6.simHuman.chr6 226408 5 + 601863 TCCCC +s simMouse_chr6.simMouse.chr6 307273 5 + 636262 TTCCG +s simRat_chr6.simRat.chr6 298887 5 + 647215 TTCTG +s simRat_chr6.simRat.chr6 302091 5 + 647215 TCCCC + +a +s simMouse_chr6.simMouse.chr6 310405 1 + 636262 C +s Anc0.Anc0refChr8 64 1 + 17196 C +s Anc1.Anc1refChr3 64 1 + 3661 C +s Anc2.Anc2refChr8 76 1 + 12804 C +s mr.mrrefChr5 160788 1 + 294540 C +s mr.mrrefChr5 157666 1 + 294540 C +s simCow_chr6.simCow.chr6 322952 1 - 602619 C +s simDog_chr6.simDog.chr6 316319 1 - 593897 C +s simHuman_chr6.simHuman.chr6 226413 1 + 601863 T +s simMouse_chr6.simMouse.chr6 307278 1 + 636262 C +s simRat_chr6.simRat.chr6 302096 1 + 647215 C + +a +s simMouse_chr6.simMouse.chr6 310406 8 + 636262 TTTGCAGT +s Anc0.Anc0refChr8 65 8 + 17196 TGTGCTGT +s Anc1.Anc1refChr3 65 8 + 3661 TGTGCTGT +s Anc2.Anc2refChr8 77 8 + 12804 TGTGCTGT +s mr.mrrefChr5 160789 8 + 294540 TTTGCAGT +s mr.mrrefChr5 157667 8 + 294540 TGTGCTGT +s simCow_chr6.simCow.chr6 322953 8 - 602619 TGTGCTGT +s simDog_chr6.simDog.chr6 316320 8 - 593897 TGTGCTGC +s simHuman_chr6.simHuman.chr6 226414 8 + 601863 TGTGCTGT +s simMouse_chr6.simMouse.chr6 307279 8 + 636262 TGTGCTGT +s simRat_chr6.simRat.chr6 298892 8 + 647215 TGTGCCAT +s simRat_chr6.simRat.chr6 302097 8 + 647215 TGTGCAGT + +a +s simMouse_chr6.simMouse.chr6 310414 2 + 636262 AG +s Anc0.Anc0refChr8 73 2 + 17196 AA +s Anc1.Anc1refChr3 73 2 + 3661 AA +s Anc2.Anc2refChr8 85 2 + 12804 AA +s mr.mrrefChr5 160797 2 + 294540 AG +s mr.mrrefChr5 157676 2 + 294540 AA +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 307288 2 + 636262 AA +s simRat_chr6.simRat.chr6 298901 2 + 647215 AA +s simRat_chr6.simRat.chr6 302105 2 + 647215 AA + +a +s simMouse_chr6.simMouse.chr6 310416 65 + 636262 CCATACTTTGGGTTGGGCCTCTCATGGGTATAATGCAGAGATCCTAATGCCGAGATCTGTGAGAT +s Anc0.Anc0refChr8 75 51 + 17196 CCTTATTTTGGGTTGAGTCTCTGATGGATAT--------------AATGGTAATATTTGTAGGAT +s Anc1.Anc1refChr3 75 51 + 3661 CCTTATTTTGGGTTGAGTCTCTGATGGATAT--------------AATGGTAATATTTGTAGGAT +s Anc2.Anc2refChr8 87 51 + 12804 CCTTATATTGGGTCCAGTCTCTGCTGGATAT--------------AATGGTAATATTTGCAGGGT +s mr.mrrefChr5 160799 51 + 294540 CCATACTTTGGGTTGGGCCTCTCATGGGTAT--------------AATGCCGAGATCTGTGAGAT +s mr.mrrefChr5 157678 51 + 294540 TCTTATTTTGGGTTGAGTCTATGATTGATAT--------------AATGATAAGATTAGTAGGAT +s simCow_chr6.simCow.chr6 322965 51 - 602619 CTTTATCTTGGGTGCAGTCTCTGGTGGATAC--------------AATGATAATATCTTAAGGGT +s simDog_chr6.simDog.chr6 316330 49 - 593897 CCTTACATTGGGTCCAGTCTCCGCTGAATAT--------------ATTGGTAATATTTGCAGG-- +s simHuman_chr6.simHuman.chr6 226424 51 + 601863 CCTTATTTTGGGTTGAGTCTCTGATAGATAT--------------AATGGTAATATTTGTAGGAT +s simMouse_chr6.simMouse.chr6 307290 51 + 636262 TCTTATTTTGGGTTAAGTCTATGATTGGTAT--------------GATGATAAGATTAGTAGGAT +s simRat_chr6.simRat.chr6 298903 51 + 647215 TCTTATTTTGGGTTGAATCTATGATTGATAT--------------AATGATAAGATCAGTACGAT +s simRat_chr6.simRat.chr6 302107 51 + 647215 CCATACTTTGAGTTAGGCCTTTTATGGATAT--------------AATGGTGAGAACTGTGAGAT + +a +s simMouse_chr6.simMouse.chr6 310481 67 + 636262 TGAGTCAAGGCAAAAAACATTACCACATGAAACTGCACAATCTACTAGATGATTCATCATTCTTTTT +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 160850 67 + 294540 TGAGTCAAGGCAAAAAACATTACCACATGAAACTGCACAATCTACTAGATGATTCATCATTCTTTTT +s mr.mrrefChr5 157729 67 + 294540 GAATTGGGGGAAACAAACGCTGGCATGTAAAGACACTCCACCTTACAGTTGATTCCTTATTCTAGTT +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 307341 67 + 636262 GAATTGGGGGAAACAGATGCTGGCATGTAAAGACACTCCACTTTACAGTTTATGCCTTAGTCTAGTT +s simRat_chr6.simRat.chr6 298954 67 + 647215 TAATTGGGGGAAACAAACACTGGTGTCTAGAGACACTCCACCTTACAGTTGATTCCTTATTCTAGTT +s simRat_chr6.simRat.chr6 302158 67 + 647215 TGAGTCAAAGTAAACAACACTGGCACATGAAACTGCACAACCTAAGGGATTATTCATCATTCTTCTT a s simMouse_chr6.simMouse.chr6 310548 6 + 636262 CCCCTG @@ -122879,6 +127009,48 @@ s simRat_chr6.simRat.chr6 302225 6 + 647215 CCCCTG a +s simMouse_chr6.simMouse.chr6 310554 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 160923 1 + 294540 T +s mr.mrrefChr5 157796 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 307408 1 + 636262 T +s simRat_chr6.simRat.chr6 299021 1 + 647215 T +s simRat_chr6.simRat.chr6 302231 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 310555 27 + 636262 TAGTGTAGGACTGTTCTTTTTCTCTGC +s Anc0.Anc0refChr8 190 27 + 17196 GAATGCAGAACTCTTCTTTTACTCTGT +s Anc1.Anc1refChr3 195 27 + 3661 GAATGCAGAACTCTTCTTTTACTCTGT +s Anc2.Anc2refChr8 202 27 + 12804 GAATGCATAACTATTCTTTTACTCTGT +s mr.mrrefChr5 160924 27 + 294540 TAGTGTAGGACTGTTCTTTTTCTCTGC +s mr.mrrefChr5 157797 27 + 294540 GAATGGAATGTTCTTGTATAGTAGTGC +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 307409 27 + 636262 GAATGGAATGTTCTTGCATAGTGGTGC +s simRat_chr6.simRat.chr6 299022 27 + 647215 GAATGGAATGTTCTTGTATAGTAGTGC +s simRat_chr6.simRat.chr6 302232 27 + 647215 TAGTGTAGAACTGTTCTTTTTCTCTAC + +a +s simMouse_chr6.simMouse.chr6 310582 4 + 636262 CGTC +s Anc0.Anc0refChr8 217 4 + 17196 GGTG +s Anc1.Anc1refChr3 222 4 + 3661 GGTG +s Anc2.Anc2refChr8 229 4 + 12804 GGTG +s mr.mrrefChr5 160951 4 + 294540 CGTC +s mr.mrrefChr5 157824 4 + 294540 CATT +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 307436 4 + 636262 CATC +s simRat_chr6.simRat.chr6 299049 4 + 647215 CATT +s simRat_chr6.simRat.chr6 302259 4 + 647215 AGTC + +a s simMouse_chr6.simMouse.chr6 310586 6 + 636262 TGCAGT s Anc0.Anc0refChr8 221 6 + 17196 TGCAGT s Anc1.Anc1refChr3 226 6 + 3661 TGCAGT @@ -122901,6 +127073,48 @@ s simRat_chr6.simRat.chr6 302269 2 + 647215 TG a +s simMouse_chr6.simMouse.chr6 310594 14 + 636262 AGGTGAAGTTTACC +s Anc0.Anc0refChr8 235 14 + 17196 AAGTGATGTTTATC +s Anc1.Anc1refChr3 240 14 + 3661 AAGTGATGTTTATC +s Anc2.Anc2refChr8 248 14 + 12804 AAGTGATGTTTATC +s mr.mrrefChr5 160963 14 + 294540 AGGTGAAGTTTACC +s mr.mrrefChr5 157828 14 + 294540 AAGTGGTGTCTATT +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 307440 14 + 636262 AAGTGGTGTCTTTT +s simRat_chr6.simRat.chr6 299053 14 + 647215 AAGTGGTGTCTATT +s simRat_chr6.simRat.chr6 302271 14 + 647215 AGATGAAGTTTACC + +a +s simMouse_chr6.simMouse.chr6 310608 20 + 636262 TAAAAAATAGGCCTATTTCT +s Anc0.Anc0refChr8 250 20 + 17196 TCAAAGATAGGCCTATATGT +s Anc1.Anc1refChr3 255 20 + 3661 TCAAAGATAGGCCTATATGT +s Anc2.Anc2refChr8 263 20 + 12804 TCACAGATAGGCCTATATGC +s mr.mrrefChr5 160977 20 + 294540 TAAAAAATAGGCCTATTTCT +s mr.mrrefChr5 157843 20 + 294540 TCAAAGACAGGCCTCCATGA +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 307455 20 + 636262 TCAGAGACAGGCCTCCATGA +s simRat_chr6.simRat.chr6 299068 20 + 647215 TCAAAGGCAGGCCTCCATGA +s simRat_chr6.simRat.chr6 302285 20 + 647215 TATGAAATAGGCCCATTTTT + +a +s simMouse_chr6.simMouse.chr6 310628 9 + 636262 GCCCATCCA +s Anc0.Anc0refChr8 273 9 + 17196 ACCACTTCA +s Anc1.Anc1refChr3 278 9 + 3661 ACCACTTCA +s Anc2.Anc2refChr8 286 9 + 12804 ACCACTTCA +s mr.mrrefChr5 160997 9 + 294540 GCCCATCCA +s mr.mrrefChr5 157866 9 + 294540 GCTACTTCA +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 307478 9 + 636262 GCTACTTCA +s simRat_chr6.simRat.chr6 299091 9 + 647215 GCTACTTCA +s simRat_chr6.simRat.chr6 302305 9 + 647215 GCTAAACCA + +a s simMouse_chr6.simMouse.chr6 310637 1 + 636262 T s Anc0.Anc0refChr8 282 1 + 17196 T s Anc1.Anc1refChr3 287 1 + 3661 T @@ -122912,6 +127126,20 @@ s simRat_chr6.simRat.chr6 302314 1 + 647215 T a +s simMouse_chr6.simMouse.chr6 310638 10 + 636262 ACTGAGAAAT +s Anc0.Anc0refChr8 283 10 + 17196 GATGAGAAGT +s Anc1.Anc1refChr3 288 10 + 3661 GATGAGAAGT +s Anc2.Anc2refChr8 296 10 + 12804 GATGAGAAGT +s mr.mrrefChr5 161007 10 + 294540 ACTGAGAAAT +s mr.mrrefChr5 157875 10 + 294540 GTTGAGACTT +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 307487 10 + 636262 GTTGAGACTT +s simRat_chr6.simRat.chr6 299100 10 + 647215 GTTGAGACTG +s simRat_chr6.simRat.chr6 302315 10 + 647215 GCGGAGAAAT + +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 @@ -122922,11 +127150,109 @@ s simRat_chr6.simRat.chr6 302500 37 + 647215 GCAGGTTAAAAATCTAATGAATTGGGTAAGTGGTTCT a +s simMouse_chr6.simMouse.chr6 310896 20 + 636262 TCCGAAAAAAAAGAAGAAGA +s Anc0.Anc0refChr8 708 20 + 17196 TCTAAAGAAAAAGAACAAGA +s Anc1.Anc1refChr3 715 20 + 3661 TCTAAAGAAAAAGAACAAGA +s Anc2.Anc2refChr8 756 20 + 12804 TCTATAGAAAAAGAACATGA +s mr.mrrefChr5 161186 20 + 294540 TCCGAAAAAAAAGAAGAAGA +s mr.mrrefChr5 158294 20 + 294540 TCTAAAGAAATCGACCAAAA +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 307912 20 + 636262 TCTAAAGAAATCGACCAAAA +s simRat_chr6.simRat.chr6 299517 20 + 647215 TCTAAAGAAAAGGACCAAAA +s simRat_chr6.simRat.chr6 302537 20 + 647215 TCAGAAGCCAAAGGACACGA + +a +s simMouse_chr6.simMouse.chr6 310916 13 + 636262 TAGTCCATAGTTT +s Anc0.Anc0refChr8 728 13 + 17196 AAGCATAGAGTTT +s Anc1.Anc1refChr3 735 13 + 3661 AAGCATAGAGTTT +s Anc2.Anc2refChr8 776 13 + 12804 AAGCATAGAGTTT +s mr.mrrefChr5 161206 13 + 294540 TAGTCCATAGTTT +s mr.mrrefChr5 158314 13 + 294540 TAGCATAAAGTTC +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 307932 13 + 636262 TAGCATAAGTTTC +s simRat_chr6.simRat.chr6 299537 13 + 647215 TAGCACAAAGTTG +s simRat_chr6.simRat.chr6 302558 13 + 647215 CAGTATATAGTTT + +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 310934 3 + 636262 CTT +s Anc0.Anc0refChr8 741 3 + 17196 CTT +s Anc1.Anc1refChr3 748 3 + 3661 CTT +s Anc2.Anc2refChr8 789 3 + 12804 CTT +s mr.mrrefChr5 161224 3 + 294540 CTT +s mr.mrrefChr5 158327 3 + 294540 CTT +s simCow_chr6.simCow.chr6 280362 3 + 602619 TTT +s simDog_chr6.simDog.chr6 317004 3 - 593897 CTT +s simHuman_chr6.simHuman.chr6 227085 3 + 601863 CTT +s simMouse_chr6.simMouse.chr6 307945 3 + 636262 CTT +s simRat_chr6.simRat.chr6 299550 3 + 647215 CTT +s simRat_chr6.simRat.chr6 302576 3 + 647215 TTT + +a +s simMouse_chr6.simMouse.chr6 310937 32 + 636262 TATAACTATAGGTATATGAAGTATTTCATATG +s Anc0.Anc0refChr8 744 32 + 17196 TACTATAATAGCTATACGAAGTATTTCATATG +s Anc1.Anc1refChr3 751 32 + 3661 TACTATAATAGCTATACGAAGTATTTCATATG +s Anc2.Anc2refChr8 792 32 + 12804 TACTATAATAGCTTTACGAAGTATTTCATATG +s mr.mrrefChr5 161227 32 + 294540 TATAACTATAGGTATATGAAGTATTTCATATG +s mr.mrrefChr5 158330 32 + 294540 TACTACTACAGCTATACTAAGTATTTGAGATG +s simCow_chr6.simCow.chr6 280365 32 + 602619 TACTGTAATAGCTTCACGAAGTGTTTCATATG +s simDog_chr6.simDog.chr6 317007 32 - 593897 TACTATTATAGCTTTACGAAGTATTTCATGTG +s simHuman_chr6.simHuman.chr6 227088 32 + 601863 CATGATAATAGCTGTATGAAGTATTTCATATG +s simMouse_chr6.simMouse.chr6 307950 32 + 636262 TACTACTACAGCTATACTAAGTATTTGAGATG +s simRat_chr6.simRat.chr6 299553 32 + 647215 TACTACTGCAGCTATACTGAGTATTTGAGATG +s simRat_chr6.simRat.chr6 302579 32 + 647215 TGTTACTACAGTTATATGAAGTATTTCATATG + +a +s simMouse_chr6.simMouse.chr6 310969 24 + 636262 ACTTGTGTGGATTGCTTTCATGTT +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 161259 24 + 294540 ACTTGTGTGGATTGCTTTCATGTT +s mr.mrrefChr5 158362 24 + 294540 GCCAATTGGAATTGCCTTTCATCT +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 307982 24 + 636262 GCCAATTGGAATTGCCTTTCATCT +s simRat_chr6.simRat.chr6 299585 24 + 647215 GCCAATTGGAATTCCCTTTCATCT +s simRat_chr6.simRat.chr6 302612 24 + 647215 ACTCGTGTGAATTTCTTCCTTGTT + +a +s simMouse_chr6.simMouse.chr6 310993 16 + 636262 GTAAGTATTCAGACTA +s Anc0.Anc0refChr8 795 16 + 17196 GGCAGTTTTTAAACAA +s Anc1.Anc1refChr3 809 16 + 3661 GGCAGTTTTTAAACAA +s Anc2.Anc2refChr8 843 16 + 12804 GGCAGTTTTTAAACAA +s mr.mrrefChr5 161283 16 + 294540 GTAAGTATTCAGACTA +s mr.mrrefChr5 158386 16 + 294540 TCGCAGTTTAAAAAAC +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 308006 16 + 636262 TCGCAGTTTAAAAAAC +s simRat_chr6.simRat.chr6 299609 16 + 647215 TCACAGTTCAAAAATC +s simRat_chr6.simRat.chr6 302636 16 + 647215 GTAAGTATTCAGGCTA + +a +s simMouse_chr6.simMouse.chr6 311009 9 + 636262 TGTAACCTT +s Anc0.Anc0refChr8 811 7 + 17196 TGTAACC-- +s Anc1.Anc1refChr3 825 9 + 3661 TGTAACCTT +s Anc2.Anc2refChr8 859 7 + 12804 TGTAACC-- +s mr.mrrefChr5 161299 9 + 294540 TGTAACCTT +s mr.mrrefChr5 158402 9 + 294540 TGTGACCTT +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 308022 9 + 636262 TGTGACCTT +s simRat_chr6.simRat.chr6 299625 9 + 647215 TGTGACCTT +s simRat_chr6.simRat.chr6 302652 9 + 647215 TGTAACCCC + +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 @@ -123393,7 +127719,46 @@ s simRat_chr6.simRat.chr6 302995 3 + 647215 TAC a -s simMouse_chr6.simMouse.chr6 311354 16 + 636262 AATTTGGCAGATAATT +s simMouse_chr6.simMouse.chr6 311348 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 161632 3 + 294540 ACT +s mr.mrrefChr5 158643 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 308031 3 + 636262 ACT +s simRat_chr6.simRat.chr6 299904 3 + 647215 ACT +s simRat_chr6.simRat.chr6 302998 3 + 647215 ACT + +a +s simMouse_chr6.simMouse.chr6 311351 32 + 636262 AAAAATTTGGCAGATAATTGTCCTGTGCCCCA +s Anc0.Anc0refChr8 1109 16 + 17196 ATC----------------ATCCTGTGCTCTA +s Anc1.Anc1refChr3 1134 16 + 3661 ATC----------------ATCCTGTGCTCTA +s Anc2.Anc2refChr8 1159 16 + 12804 ATT----------------ATCCTGTGCTCTA +s mr.mrrefChr5 161635 16 + 294540 AAA----------------GTCCTGTGCCCCA +s mr.mrrefChr5 158655 16 + 294540 ATC----------------ATCCTGCACTCTA +s simCow_chr6.simCow.chr6 280703 16 + 602619 ATT----------------ATCCTGTCCTGGA +s simDog_chr6.simDog.chr6 590010 16 - 593897 ATT----------------ATCTTGTGCCCTA +s simHuman_chr6.simHuman.chr6 227439 16 + 601863 ATC----------------ATCCTGGGCTCCT +s simMouse_chr6.simMouse.chr6 308043 16 + 636262 GTC----------------ATCCTGCACTCTA +s simRat_chr6.simRat.chr6 299916 16 + 647215 ATC----------------ATCCTGCATTCTA +s simRat_chr6.simRat.chr6 303001 16 + 647215 AAA----------------GTCCTGTGCCCCA + +a +s simMouse_chr6.simMouse.chr6 311383 8 + 636262 ATTTGAAT +s Anc0.Anc0refChr8 1125 8 + 17196 AGTGGACT +s Anc1.Anc1refChr3 1150 8 + 3661 AGTGGACT +s Anc2.Anc2refChr8 1175 8 + 12804 AGTGGACT +s mr.mrrefChr5 161651 8 + 294540 ATTTGAAT +s mr.mrrefChr5 158671 8 + 294540 AGTGTACC +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 308059 8 + 636262 ATTGTACC +s simRat_chr6.simRat.chr6 299932 8 + 647215 AGTGTACA +s simRat_chr6.simRat.chr6 303029 8 + 647215 ATTTGAAT a s simMouse_chr6.simMouse.chr6 311391 3 + 636262 GGG @@ -123406,6 +127771,20 @@ s simRat_chr6.simRat.chr6 303037 3 + 647215 GGG a +s simMouse_chr6.simMouse.chr6 311394 22 + 636262 CAATTTCCTTTAACTAATGAAC +s Anc0.Anc0refChr8 1136 22 + 17196 CAGTATTCTTTAACTGGTGAAC +s Anc1.Anc1refChr3 1161 22 + 3661 CAGTATTCTTTAACTGGTGAAC +s Anc2.Anc2refChr8 1186 22 + 12804 CAGTATTCTTTAACAGGTGAAC +s mr.mrrefChr5 161662 22 + 294540 CAATTTCCTTTAACTAATGAAC +s mr.mrrefChr5 158679 22 + 294540 CAGTATTGTTCAACTAGCAAAC +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 308067 22 + 636262 CAGTATTGTTCAACCAGCAAAC +s simRat_chr6.simRat.chr6 299940 22 + 647215 CAGTATTCTTCAACTTCCAAAC +s simRat_chr6.simRat.chr6 303040 22 + 647215 CAGTGTCCTTTAACTAATGAAC + +a s simMouse_chr6.simMouse.chr6 311416 5 + 636262 TAGTC s Anc0.Anc0refChr8 1158 5 + 17196 TAGAC s Anc1.Anc1refChr3 1183 5 + 3661 TAGAC @@ -123417,49 +127796,206 @@ 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 +s simMouse_chr6.simMouse.chr6 311421 45 + 636262 CTTTCCCAGAGTAGAGTGGGAACAATATGTAGTCCCCTTCTCCAT +s Anc0.Anc0refChr8 1163 40 + 17196 CTTCCCCAGAGAA-----GCAATAACATACAAGCCCCTTCTTTAT +s Anc1.Anc1refChr3 1188 40 + 3661 CTTCCCCAGAGAA-----GCAATAACATACAAGCCCCTTCTTTAT +s Anc2.Anc2refChr8 1213 40 + 12804 CCTCCCCAGAGAA-----ACAATAACATAAATGCCCCTTCTTTAT +s mr.mrrefChr5 161689 40 + 294540 CTTTCCCAGAGTA-----GGAACAATATGTAGTCCCCTTCTCCAT +s mr.mrrefChr5 158701 40 + 294540 CTTCCCCAGAGAG-----GCAATAACATACAAGCCCATTCTCTAT +s simCow_chr6.simCow.chr6 280757 40 + 602619 CTTCCCCAGAGAA-----ACAATAACCTGAAGGCCCTTCCTTTAT +s simDog_chr6.simDog.chr6 590064 39 - 593897 CCTCCCCAAAGAA-----ATAATAACATAAATGCCCCTT-TTTAT +s simHuman_chr6.simHuman.chr6 227490 39 + 601863 CT-CTCCAGAGAA-----GCAATAACATACAAGCCCGTTCTTTAT +s simMouse_chr6.simMouse.chr6 308089 40 + 636262 CTCCCCCAGAGAG-----GCAATGACATACAAGCCCAGTCTCTGT +s simRat_chr6.simRat.chr6 299962 40 + 647215 CTTCCCCAGAGAG-----GCAATAACATACAAGCCCATGGTCTAT +s simRat_chr6.simRat.chr6 303067 40 + 647215 CTTCCCCAGAATA-----GGACTAATATGTAGTCCCCTTCTCCAT + +a +s simMouse_chr6.simMouse.chr6 311466 4 + 636262 AATG +s Anc0.Anc0refChr8 1203 2 + 17196 --TG +s Anc1.Anc1refChr3 1228 4 + 3661 AATG +s Anc2.Anc2refChr8 1253 2 + 12804 --TG +s mr.mrrefChr5 161729 4 + 294540 AATG +s mr.mrrefChr5 158741 4 + 294540 AACA +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 308129 4 + 636262 AACA +s simRat_chr6.simRat.chr6 608840 4 - 647215 AGCA +s simRat_chr6.simRat.chr6 300005 4 + 647215 ATCA +s simRat_chr6.simRat.chr6 303107 4 + 647215 AATG + +a +s simMouse_chr6.simMouse.chr6 311470 9 + 636262 CATCAATGA +s Anc0.Anc0refChr8 1205 7 + 17196 CAT--AGGA +s Anc1.Anc1refChr3 1232 9 + 3661 CATCAAGGA +s Anc2.Anc2refChr8 1255 7 + 12804 CAT--AGGA +s mr.mrrefChr5 161733 9 + 294540 CATCAATGA +s mr.mrrefChr5 158812 9 + 294540 CAGCAAGGA +s simCow_chr6.simCow.chr6 280799 7 + 602619 CAT--AGGA +s simDog_chr6.simDog.chr6 590105 7 - 593897 CAT--AGGA +s simHuman_chr6.simHuman.chr6 227533 7 + 601863 AAG--AGAA +s simMouse_chr6.simMouse.chr6 308194 3 + 636262 ------GGA +s simRat_chr6.simRat.chr6 608905 9 - 647215 CAGGAAGGC +s simRat_chr6.simRat.chr6 300076 9 + 647215 CAGCAAGAT +s simRat_chr6.simRat.chr6 303111 9 + 647215 CATCATTGA + +a +s simMouse_chr6.simMouse.chr6 311479 10 + 636262 GATCCCTAGT +s Anc0.Anc0refChr8 1212 8 + 17196 TTTCTA--TG +s Anc1.Anc1refChr3 1241 8 + 3661 TTTCTA--TG +s Anc2.Anc2refChr8 1268 8 + 12804 TTTCTA--TG +s mr.mrrefChr5 161742 8 + 294540 GATCCC--GT +s mr.mrrefChr5 158821 8 + 294540 GATGTC--AT +s simCow_chr6.simCow.chr6 280812 8 + 602619 CTTCTA--TG +s simDog_chr6.simDog.chr6 590118 8 - 593897 TTTCCA--TG +s simHuman_chr6.simHuman.chr6 227540 8 + 601863 TTTTTA--TG +s simMouse_chr6.simMouse.chr6 308197 8 + 636262 AATATC--AG +s simRat_chr6.simRat.chr6 608914 8 - 647215 GATGTG--AT +s simRat_chr6.simRat.chr6 300085 8 + 647215 GATGTC--GT +s simRat_chr6.simRat.chr6 303120 8 + 647215 AATTCC--AT + +a +s simMouse_chr6.simMouse.chr6 311489 39 + 636262 TTGGTGTACTCCATCTCAGGACAGTGTTTCAGGTCTGTA +s Anc0.Anc0refChr8 1220 25 + 17196 TTTGTGTACTCCATTTCAAAACATC-------------- +s Anc1.Anc1refChr3 1249 25 + 3661 TTTGTGTACTCCATTTCAAAACATC-------------- +s Anc2.Anc2refChr8 1276 25 + 12804 TTTGTGTACTCTATTTCAAAACATC-------------- +s mr.mrrefChr5 161750 25 + 294540 TTGGTGTACTCCATCTCAGGACAGT-------------- +s mr.mrrefChr5 158842 25 + 294540 TATGTGTATGCCATTTCAAAACAGC-------------- +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 308218 25 + 636262 TTTGTGTATGCGATTTCAAAACAGC-------------- +s simRat_chr6.simRat.chr6 608935 25 - 647215 TATGTGTGTGCCATTTCAACCCAAC-------------- +s simRat_chr6.simRat.chr6 300106 25 + 647215 TATGTGTATGCCATTTCAAAACAGC-------------- +s simRat_chr6.simRat.chr6 303128 25 + 647215 TTGGTGTACTTCAGCACAAGGTGGT-------------- + +a +s simMouse_chr6.simMouse.chr6 311528 15 + 636262 TGACATAGACCTATA +s Anc0.Anc0refChr8 1259 15 + 17196 TGGCATAAACCTATC +s Anc1.Anc1refChr3 1288 15 + 3661 TGGCATAAACCTATC +s Anc2.Anc2refChr8 1315 15 + 12804 TGGCATAAACCAATC +s mr.mrrefChr5 161775 15 + 294540 TGACATAGACCTATA +s mr.mrrefChr5 158879 15 + 294540 TGATATGAACCTATC +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 308255 15 + 636262 TGATATGAACCTATC +s simRat_chr6.simRat.chr6 608972 15 - 647215 TGTTATGAATCTATC +s simRat_chr6.simRat.chr6 300143 15 + 647215 AGATATGAGCCTACC +s simRat_chr6.simRat.chr6 303153 15 + 647215 TGGCATAGACCTATA + +a +s simMouse_chr6.simMouse.chr6 311543 21 + 636262 AGATAGTTGGTTATTATTTCT +s Anc0.Anc0refChr8 1274 21 + 17196 AGGCAGTGGGTTATTGTTTCT +s Anc1.Anc1refChr3 1303 21 + 3661 AGGCAGTGGGTTATTGTTTCT +s Anc2.Anc2refChr8 1330 21 + 12804 AAGCAATGGGTTATTGTTTCT +s mr.mrrefChr5 161790 21 + 294540 AGATAGTTGGTTATTATTTCT +s mr.mrrefChr5 158894 21 + 294540 AGAGAGTGGTTCATTGTTCCA +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 308270 21 + 636262 AGGGAGTGGTTCATTATTCCA +s simRat_chr6.simRat.chr6 608990 21 - 647215 CAATAGTGGTTAACTGGCAAA +s simRat_chr6.simRat.chr6 300158 21 + 647215 AGAGCGTGGTTCATTGTTCCA +s simRat_chr6.simRat.chr6 303168 21 + 647215 AGGTAGTTGGTTATTATTTCT + +a +s simMouse_chr6.simMouse.chr6 311564 7 + 636262 GTCTTCT +s Anc0.Anc0refChr8 1295 3 + 17196 GTC---- +s Anc1.Anc1refChr3 1324 7 + 3661 GTCTTTT +s Anc2.Anc2refChr8 1351 3 + 12804 GTC---- +s mr.mrrefChr5 161811 7 + 294540 GTCTTCT +s mr.mrrefChr5 158915 7 + 294540 GGGTTTT +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 308291 7 + 636262 GGGTTTT +s simRat_chr6.simRat.chr6 300179 7 + 647215 GTATTTT +s simRat_chr6.simRat.chr6 303189 7 + 647215 GTCTTCT + +a +s simMouse_chr6.simMouse.chr6 311571 4 + 636262 GTCC +s Anc0.Anc0refChr8 1298 4 + 17196 GTCC +s Anc1.Anc1refChr3 1331 4 + 3661 GTCC +s Anc2.Anc2refChr8 1354 4 + 12804 GTCC +s mr.mrrefChr5 161818 4 + 294540 GTCC +s mr.mrrefChr5 158922 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 308298 4 + 636262 GTCT +s simRat_chr6.simRat.chr6 300186 4 + 647215 ATCC +s simRat_chr6.simRat.chr6 303196 4 + 647215 GTCC + +a +s simMouse_chr6.simMouse.chr6 311575 39 + 636262 TTTGTAGCTATATAAACAGCCATTGCTCTGGTTACCTGG +s Anc0.Anc0refChr8 1308 35 + 17196 GCCT----CATATGAACAGCAGTTGTTCTAGTGATCTTA +s Anc1.Anc1refChr3 1341 35 + 3661 GCCT----CATATGAACAGCAGTTGTTCTAGTGATCTTA +s Anc2.Anc2refChr8 1364 35 + 12804 GCCT----CATAGGACCAGCAGTTGTTCTAGTGATCTTA +s mr.mrrefChr5 161822 35 + 294540 TTTG----TATATAAACAGCCATTGCTCTGGTTACCTGG +s mr.mrrefChr5 158932 35 + 294540 GACC----GATGTAAGCATTGGTTGTTCTAGTGGTATTA +s simCow_chr6.simCow.chr6 280899 26 + 602619 GCCT----TAGAA---------TTGTTCTAGTGATCCTA +s simDog_chr6.simDog.chr6 590216 34 - 593897 CCCT----CTTAGGACCAGCAGTTGTTGTAGTGAGCT-A +s simHuman_chr6.simHuman.chr6 227633 35 + 601863 GCCT----CATATGAACACCAGTTGCTCTAGTGGTTTTA +s simMouse_chr6.simMouse.chr6 308308 33 + 636262 GAC------ATGTAAGCATTGGTTGTTCTAGTGGTATTA +s simRat_chr6.simRat.chr6 300196 35 + 647215 GACC----GATGTAAGCATTGGATGTTCTGGTGATATTA +s simRat_chr6.simRat.chr6 303200 35 + 647215 CTTG----TATATAGACAGGCATTGCTCCGGTTAATTGG + +a +s simMouse_chr6.simMouse.chr6 311614 5 + 636262 TTATA +s Anc0.Anc0refChr8 1354 5 + 17196 TCATA +s Anc1.Anc1refChr3 1387 5 + 3661 TCATA +s Anc2.Anc2refChr8 1410 5 + 12804 TCATA +s mr.mrrefChr5 161857 5 + 294540 TTATA +s mr.mrrefChr5 158978 5 + 294540 TCATA +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 308352 5 + 636262 TCATA +s simRat_chr6.simRat.chr6 300242 5 + 647215 TCATA +s simRat_chr6.simRat.chr6 303235 5 + 647215 TTATT + +a +s simMouse_chr6.simMouse.chr6 311619 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 161862 1 + 294540 C +s mr.mrrefChr5 158986 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 308360 1 + 636262 C +s simRat_chr6.simRat.chr6 300250 1 + 647215 C +s simRat_chr6.simRat.chr6 303240 1 + 647215 C + +a +s simMouse_chr6.simMouse.chr6 311620 3 + 636262 CAA +s Anc0.Anc0refChr8 1363 2 + 17196 -AA +s Anc1.Anc1refChr3 1396 3 + 3661 CAA +s Anc2.Anc2refChr8 1419 2 + 12804 -AA +s mr.mrrefChr5 161863 3 + 294540 CAA +s mr.mrrefChr5 158987 3 + 294540 CAA +s simCow_chr6.simCow.chr6 280945 2 + 602619 -GA +s simDog_chr6.simDog.chr6 590270 2 - 593897 -AA +s simHuman_chr6.simHuman.chr6 227690 3 + 601863 CAA +s simMouse_chr6.simMouse.chr6 308361 2 + 636262 -AA +s simRat_chr6.simRat.chr6 300251 3 + 647215 CAA +s simRat_chr6.simRat.chr6 303241 3 + 647215 CAA + +a +s simMouse_chr6.simMouse.chr6 311623 17 + 636262 AGCTGGTTCATACCAGC +s Anc0.Anc0refChr8 1370 17 + 17196 AGTTGGGTTGTACCAGC +s Anc1.Anc1refChr3 1404 17 + 3661 AGTTGGGTTGTACCAGC +s Anc2.Anc2refChr8 1426 17 + 12804 AGTTTGGTTGTACCAGC +s mr.mrrefChr5 161866 17 + 294540 AGCTGGTTCATACCAGC +s mr.mrrefChr5 158995 17 + 294540 AGTAGATTTGTATCCGC +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 308368 17 + 636262 AGTATATTTGTATCCGC +s simRat_chr6.simRat.chr6 300259 17 + 647215 AGTAGATTTGTGTCTGC +s simRat_chr6.simRat.chr6 303245 17 + 647215 AGCTGGTTCCTACAAGC a s simMouse_chr6.simMouse.chr6 311640 2 + 636262 AA @@ -123467,6 +128003,90 @@ s simRat_chr6.simRat.chr6 303262 2 + 647215 AA a +s simMouse_chr6.simMouse.chr6 311642 6 + 636262 CTTATC +s Anc0.Anc0refChr8 1387 6 + 17196 CTTACC +s Anc1.Anc1refChr3 1421 6 + 3661 CTTACC +s Anc2.Anc2refChr8 1443 6 + 12804 CTTACG +s mr.mrrefChr5 161885 6 + 294540 CTTATC +s mr.mrrefChr5 159012 6 + 294540 CTGATC +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 308385 6 + 636262 CTGATC +s simRat_chr6.simRat.chr6 300276 6 + 647215 CTGATC +s simRat_chr6.simRat.chr6 303264 6 + 647215 CTTACC + +a +s simMouse_chr6.simMouse.chr6 311648 9 + 636262 CTCTCTTCC +s Anc0.Anc0refChr8 1397 9 + 17196 TTCTCTCCC +s Anc1.Anc1refChr3 1448 9 + 3661 TTCTCTCCC +s Anc2.Anc2refChr8 1453 9 + 12804 TTCTCTCCC +s mr.mrrefChr5 161891 9 + 294540 CTCTCTTCC +s mr.mrrefChr5 159039 9 + 294540 CATCATTTC +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 308412 9 + 636262 CATAATTTC +s simRat_chr6.simRat.chr6 300303 9 + 647215 CATCATTTC +s simRat_chr6.simRat.chr6 303270 9 + 647215 CTCTCTTCT + +a +s simMouse_chr6.simMouse.chr6 311657 16 + 636262 TCCTGAACATAAGTAG +s Anc0.Anc0refChr8 1406 16 + 17196 TCATGGATTTAAATAT +s Anc1.Anc1refChr3 1457 16 + 3661 TCATGGATTTAAATAT +s Anc2.Anc2refChr8 1462 16 + 12804 TCATGGATTTAAATCT +s mr.mrrefChr5 161900 16 + 294540 TCCTGAACATAAGTAG +s mr.mrrefChr5 159054 16 + 294540 CGATGCATTTAAATGA +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 308427 16 + 636262 CGATGCATTCATATGA +s simRat_chr6.simRat.chr6 300318 16 + 647215 CAATGCATTTAAATGA +s simRat_chr6.simRat.chr6 303279 16 + 647215 TCTTGAACATAAGTAC + +a +s simMouse_chr6.simMouse.chr6 311673 7 + 636262 ATTTGAT +s Anc0.Anc0refChr8 1422 7 + 17196 ATTGGAT +s Anc1.Anc1refChr3 1479 7 + 3661 ATTGGAT +s Anc2.Anc2refChr8 1478 7 + 12804 ATTGAAT +s mr.mrrefChr5 161916 7 + 294540 ATTTGAT +s mr.mrrefChr5 159076 7 + 294540 ATTGGAT +s simCow_chr6.simCow.chr6 281006 7 + 602619 ATTGAAT +s simDog_chr6.simDog.chr6 590327 7 - 593897 GTTGAAT +s simHuman_chr6.simHuman.chr6 227791 7 + 601863 ATTGTAT +s simMouse_chr6.simMouse.chr6 308449 7 + 636262 ATATGAT +s simRat_chr6.simRat.chr6 300340 7 + 647215 ACTGCAT +s simRat_chr6.simRat.chr6 303295 7 + 647215 ATTAGAC + +a +s simMouse_chr6.simMouse.chr6 311680 1 + 636262 A +s Anc0.Anc0refChr8 1429 1 + 17196 A +s Anc1.Anc1refChr3 1486 1 + 3661 A +s Anc2.Anc2refChr8 1485 1 + 12804 A +s mr.mrrefChr5 161923 1 + 294540 A +s mr.mrrefChr5 159083 1 + 294540 A +s simCow_chr6.simCow.chr6 281013 1 + 602619 A +s simDog_chr6.simDog.chr6 590334 1 - 593897 A +s simHuman_chr6.simHuman.chr6 227798 1 + 601863 A +s simMouse_chr6.simMouse.chr6 308461 1 + 636262 A +s simRat_chr6.simRat.chr6 300347 1 + 647215 A +s simRat_chr6.simRat.chr6 303302 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 311681 4 + 636262 GCCC +s Anc0.Anc0refChr8 1430 3 + 17196 GCC- +s Anc1.Anc1refChr3 1487 4 + 3661 GCCC +s Anc2.Anc2refChr8 1486 3 + 12804 GCC- +s mr.mrrefChr5 161924 4 + 294540 GCCC +s mr.mrrefChr5 159087 4 + 294540 GACA +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 308465 4 + 636262 GACA +s simRat_chr6.simRat.chr6 300351 4 + 647215 GACA +s simRat_chr6.simRat.chr6 303303 4 + 647215 GCCC + +a s simMouse_chr6.simMouse.chr6 311685 5 + 636262 CTTGC s Anc0.Anc0refChr8 1433 4 + 17196 -TTGC s Anc1.Anc1refChr3 1491 4 + 3661 -TTGC @@ -123478,11 +128098,94 @@ s simRat_chr6.simRat.chr6 303307 5 + 647215 CTTGC a +s simMouse_chr6.simMouse.chr6 311690 9 + 636262 ACCTTTTCA +s Anc0.Anc0refChr8 1437 9 + 17196 ACCCTTTCA +s Anc1.Anc1refChr3 1495 9 + 3661 ACCCTTTCA +s Anc2.Anc2refChr8 1493 9 + 12804 ACCCTGTCA +s mr.mrrefChr5 161933 9 + 294540 ACCTTTTCA +s mr.mrrefChr5 159091 9 + 294540 ATGCATTCA +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 308469 9 + 636262 ATGCATTCA +s simRat_chr6.simRat.chr6 300355 9 + 647215 ATGAATTCA +s simRat_chr6.simRat.chr6 303312 9 + 647215 ACCTTTCCA + +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 311702 7 + 636262 GGTCACA +s Anc0.Anc0refChr8 1446 7 + 17196 GGTGTCA +s Anc1.Anc1refChr3 1504 7 + 3661 GGTGTCA +s Anc2.Anc2refChr8 1502 7 + 12804 ATTGTCA +s mr.mrrefChr5 161945 7 + 294540 GGTCACA +s mr.mrrefChr5 159100 7 + 294540 GATGACA +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 308478 7 + 636262 GATGAGA +s simRat_chr6.simRat.chr6 300364 7 + 647215 GATGACA +s simRat_chr6.simRat.chr6 303324 7 + 647215 AGTCACA + +a +s simMouse_chr6.simMouse.chr6 311709 28 + 636262 TGACCTTATACCCCTGAAAGTAGGTCTG +s Anc0.Anc0refChr8 1505 28 + 17196 TGACCTTATACCCCTGAGATTAGCTCTG +s Anc1.Anc1refChr3 1563 28 + 3661 TGACCTTATACCCCTGAGATTAGCTCTG +s Anc2.Anc2refChr8 1561 28 + 12804 TGACCTTATACCCCTGAGATTAGCTCTG +s mr.mrrefChr5 161952 28 + 294540 TGACCTTATACCCCTGAAAGTAGGTCTG +s mr.mrrefChr5 159160 28 + 294540 TGTCCCTATACCTCTGAGACTGGCTCTG +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 308538 28 + 636262 TGTCCCTATACATGGGAGACTGACTCTG +s simRat_chr6.simRat.chr6 300424 28 + 647215 TGTCCCTATACCTCTGAGAATGGCTCTG +s simRat_chr6.simRat.chr6 303331 28 + 647215 TGACCTTATACCCCTGAGATAAGGTCTA + +a +s simMouse_chr6.simMouse.chr6 311737 21 + 636262 ACACTGGTAAGTACAATGGCA +s Anc0.Anc0refChr8 1533 21 + 17196 ATACTGGTAAGTACCATGGCA +s Anc1.Anc1refChr3 1591 21 + 3661 ATACTGGTAAGTACCATGGCA +s Anc2.Anc2refChr8 1589 21 + 12804 ATACTAGTAGGTACCATGGCC +s mr.mrrefChr5 161980 21 + 294540 ACACTGGTAAGTACAATGGCA +s mr.mrrefChr5 159190 21 + 294540 ACACTGGTAAGTACCATGGCA +s simCow_chr6.simCow.chr6 281117 21 + 602619 GTATTTGCAGTTACAAGGATG +s simDog_chr6.simDog.chr6 317460 21 - 593897 ATACCAGTAGGTACCATGGCC +s simHuman_chr6.simHuman.chr6 227901 21 + 601863 ATACTGGTCAGTATCATGGCA +s simMouse_chr6.simMouse.chr6 308568 21 + 636262 ACACTGGTAAGTACCACTGCA +s simRat_chr6.simRat.chr6 300454 21 + 647215 ACACAGTTGAGTACCATGGCA +s simRat_chr6.simRat.chr6 303359 21 + 647215 ATACTGGTGAGTACAATGGCA + +a +s simMouse_chr6.simMouse.chr6 311758 7 + 636262 CATATGA +s Anc0.Anc0refChr8 1554 7 + 17196 TGTATGA +s Anc1.Anc1refChr3 1612 7 + 3661 TGTATGA +s Anc2.Anc2refChr8 1610 7 + 12804 TGCATGA +s mr.mrrefChr5 162001 7 + 294540 CATATGA +s mr.mrrefChr5 159211 7 + 294540 CTTATGG +s simCow_chr6.simCow.chr6 281138 7 + 602619 TGAATGA +s simDog_chr6.simDog.chr6 317481 7 - 593897 TGCATGG +s simHuman_chr6.simHuman.chr6 227922 7 + 601863 TGTATGA +s simMouse_chr6.simMouse.chr6 308589 7 + 636262 CTTATGG +s simRat_chr6.simRat.chr6 303380 7 + 647215 CAAATGA + +a +s simMouse_chr6.simMouse.chr6 311765 15 + 636262 TCATGATAAAACAGA +s Anc0.Anc0refChr8 1561 15 + 17196 TCATAGTAAAACCAA +s Anc1.Anc1refChr3 1619 15 + 3661 TCATAGTAAAACCAA +s Anc2.Anc2refChr8 1617 15 + 12804 TCATACTAAAACTAA +s mr.mrrefChr5 162008 15 + 294540 TCATGATAAAACAGA +s mr.mrrefChr5 159218 15 + 294540 TTGTAGTATTAGCAA +s simCow_chr6.simCow.chr6 281145 15 + 602619 TCACATAAAAACGAA +s simDog_chr6.simDog.chr6 317488 15 - 593897 CCATGCTAGAACTAA +s simHuman_chr6.simHuman.chr6 227929 15 + 601863 TAATAGTAAAACCAA +s simMouse_chr6.simMouse.chr6 308596 15 + 636262 TTGTGATGTTAGCAA +s simRat_chr6.simRat.chr6 300475 15 + 647215 TTGCAGTACTAGCGA +s simRat_chr6.simRat.chr6 303387 15 + 647215 TCATGATAAAATGGA + +a s simMouse_chr6.simMouse.chr6 311780 2 + 636262 TT s Anc0.Anc0refChr8 1576 2 + 17196 AA s Anc1.Anc1refChr3 1634 2 + 3661 AA @@ -123494,17 +128197,74 @@ 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 +s simMouse_chr6.simMouse.chr6 311782 7 + 636262 GGGACCT +s Anc0.Anc0refChr8 1578 7 + 17196 GAGGACT +s Anc1.Anc1refChr3 1636 7 + 3661 GAGGACT +s Anc2.Anc2refChr8 1634 7 + 12804 GAGGATT +s mr.mrrefChr5 162025 7 + 294540 GGGACCT +s mr.mrrefChr5 159233 7 + 294540 GAGGACT +s simCow_chr6.simCow.chr6 281162 7 + 602619 GAGCATT +s simDog_chr6.simDog.chr6 317505 7 - 593897 GAGGATT +s simHuman_chr6.simHuman.chr6 227946 7 + 601863 GAGGACC +s simMouse_chr6.simMouse.chr6 308611 5 + 636262 GAG--TT +s simRat_chr6.simRat.chr6 300490 7 + 647215 GAGGACT +s simRat_chr6.simRat.chr6 303404 7 + 647215 GGGAACT + +a +s simMouse_chr6.simMouse.chr6 311789 22 + 636262 AGGACAAGACCAGCTAAGTTGA +s Anc0.Anc0refChr8 1585 22 + 17196 AGGACAAGAACAGCTAAGAATA +s Anc1.Anc1refChr3 1643 22 + 3661 AGGACAAGAACAGCTAAGAATA +s Anc2.Anc2refChr8 1642 22 + 12804 AGGGCAAGAACAGCTAAGAATA +s mr.mrrefChr5 162032 22 + 294540 AGGACAAGACCAGCTAAGTTGA +s mr.mrrefChr5 159240 22 + 294540 AGAACAGGATCCGCTAGGCAGA +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 308616 22 + 636262 AGAATAGGATCCGCTAGGCAGA +s simRat_chr6.simRat.chr6 300497 22 + 647215 AGAACAGGATGCCCTAGGCAGA +s simRat_chr6.simRat.chr6 303411 22 + 647215 AGGACAAGACCAGCTAAGTAGA + +a +s simMouse_chr6.simMouse.chr6 311811 8 + 636262 TTGATAAG +s Anc0.Anc0refChr8 1608 8 + 17196 CTATAAAG +s Anc1.Anc1refChr3 1666 8 + 3661 CTATAAAG +s Anc2.Anc2refChr8 1665 8 + 12804 CTAGGAAG +s mr.mrrefChr5 162054 8 + 294540 TTGATAAG +s mr.mrrefChr5 159263 8 + 294540 CTGTAAAG +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 308639 8 + 636262 CTGTAAAT +s simRat_chr6.simRat.chr6 300520 8 + 647215 CTGTAAAG +s simRat_chr6.simRat.chr6 303433 8 + 647215 TCTATAAG + +a +s simMouse_chr6.simMouse.chr6 311819 2 + 636262 CA +s Anc0.Anc0refChr8 1616 2 + 17196 CT +s Anc1.Anc1refChr3 1674 2 + 3661 CT +s Anc2.Anc2refChr8 1673 2 + 12804 CT +s mr.mrrefChr5 162062 2 + 294540 CA +s mr.mrrefChr5 159271 2 + 294540 CC +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 308647 2 + 636262 CC +s simRat_chr6.simRat.chr6 300528 2 + 647215 TC +s simRat_chr6.simRat.chr6 303442 2 + 647215 CA + +a +s simMouse_chr6.simMouse.chr6 311821 21 + 636262 ACCAGGATTAGGTCCAAAGCT +s Anc0.Anc0refChr8 1618 21 + 17196 ATGAAGATTAGGGTCAAAATT +s Anc1.Anc1refChr3 1676 21 + 3661 ATGAAGATTAGGGTCAAAATT +s Anc2.Anc2refChr8 1675 21 + 12804 ATGAAGATAAGGGTCAAAATC +s mr.mrrefChr5 162064 21 + 294540 ACCAGGATTAGGTCCAAAGCT +s mr.mrrefChr5 159274 21 + 294540 ATAAAGCTTAGGGTCAAAATT +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 308650 21 + 636262 ATAAAGCTTAGGGTCAAAATT +s simRat_chr6.simRat.chr6 300531 21 + 647215 ATATAGCTTGGGGTCAAAAAT +s simRat_chr6.simRat.chr6 303444 21 + 647215 ACCAGTAATAGGTCCAGGGCT a s simMouse_chr6.simMouse.chr6 311842 4 + 636262 GAAC @@ -123518,10 +128278,153 @@ 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 +s simMouse_chr6.simMouse.chr6 311846 6 + 636262 TAAGGC +s Anc0.Anc0refChr8 1643 6 + 17196 CAATGA +s Anc1.Anc1refChr3 1701 6 + 3661 CAATGA +s Anc2.Anc2refChr8 1700 6 + 12804 CAATGT +s mr.mrrefChr5 162089 6 + 294540 TAAGGC +s mr.mrrefChr5 159295 6 + 294540 CAATCA +s simCow_chr6.simCow.chr6 281228 6 + 602619 CAATAT +s simDog_chr6.simDog.chr6 317570 6 - 593897 CAATGT +s simHuman_chr6.simHuman.chr6 228011 6 + 601863 TAATCA +s simMouse_chr6.simMouse.chr6 308671 6 + 636262 CAATCA +s simRat_chr6.simRat.chr6 300552 6 + 647215 CAATCA +s simRat_chr6.simRat.chr6 303469 6 + 647215 CAATGT + +a +s simMouse_chr6.simMouse.chr6 311852 10 + 636262 ATGTCTAACT +s Anc0.Anc0refChr8 1649 10 + 17196 ATGTTTATCT +s Anc1.Anc1refChr3 1707 10 + 3661 ATGTTTATCT +s Anc2.Anc2refChr8 1706 10 + 12804 ATGTTTATCT +s mr.mrrefChr5 162095 10 + 294540 ATGTCTAACT +s mr.mrrefChr5 159301 10 + 294540 ATGTAGATTT +s simCow_chr6.simCow.chr6 281234 10 + 602619 ATGTTTATCT +s simDog_chr6.simDog.chr6 317576 10 - 593897 ATGTTTCTCT +s simHuman_chr6.simHuman.chr6 228017 10 + 601863 ATGTTTATTT +s simMouse_chr6.simMouse.chr6 308694 10 + 636262 ATGTAGATTT +s simRat_chr6.simRat.chr6 300558 10 + 647215 ATGTACATAT +s simRat_chr6.simRat.chr6 303475 10 + 647215 TTGTCTAACT + +a +s simMouse_chr6.simMouse.chr6 311862 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 162105 1 + 294540 A +s mr.mrrefChr5 159313 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 308706 1 + 636262 A +s simRat_chr6.simRat.chr6 300570 1 + 647215 A +s simRat_chr6.simRat.chr6 303485 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 311863 8 + 636262 CTGGGCAA +s Anc0.Anc0refChr8 1660 8 + 17196 CAGGGAAA +s Anc1.Anc1refChr3 1718 8 + 3661 CAGGGAAA +s Anc2.Anc2refChr8 1717 8 + 12804 CAGGGAAA +s mr.mrrefChr5 162106 8 + 294540 CTGGGCAA +s mr.mrrefChr5 159314 8 + 294540 CATGAAAA +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 308707 8 + 636262 CATGAAAA +s simRat_chr6.simRat.chr6 300571 8 + 647215 CATGAAAA +s simRat_chr6.simRat.chr6 303486 8 + 647215 CTGGGCAA + +a +s simMouse_chr6.simMouse.chr6 311871 3 + 636262 AAA +s Anc1.Anc1refChr3 1730 3 + 3661 AGA +s mr.mrrefChr5 162114 3 + 294540 AAA +s mr.mrrefChr5 159326 3 + 294540 GGT +s simHuman_chr6.simHuman.chr6 228040 3 + 601863 AGT +s simMouse_chr6.simMouse.chr6 308719 3 + 636262 GGT +s simRat_chr6.simRat.chr6 300583 3 + 647215 GGG +s simRat_chr6.simRat.chr6 303494 3 + 647215 AAA + +a +s simMouse_chr6.simMouse.chr6 311874 8 + 636262 CAAAACCA +s Anc0.Anc0refChr8 1671 8 + 17196 CAAAACCA +s Anc1.Anc1refChr3 1733 8 + 3661 CAAAACCA +s Anc2.Anc2refChr8 1728 8 + 12804 AAAAACCA +s mr.mrrefChr5 162117 8 + 294540 CAAAACCA +s mr.mrrefChr5 159329 8 + 294540 CAAAACAA +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 308722 8 + 636262 CAAGACAA +s simRat_chr6.simRat.chr6 300586 8 + 647215 CACAACAA +s simRat_chr6.simRat.chr6 303503 8 + 647215 CAAAACCA + +a +s simMouse_chr6.simMouse.chr6 311882 10 + 636262 TTGTTTTATC +s Anc0.Anc0refChr8 1687 10 + 17196 TTATTATGCT +s Anc1.Anc1refChr3 1749 10 + 3661 TTATTATGCT +s Anc2.Anc2refChr8 1744 10 + 12804 TTATTATGCT +s mr.mrrefChr5 162125 10 + 294540 TTGTTTTATC +s mr.mrrefChr5 159337 10 + 294540 ATATTATGCC +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 308730 10 + 636262 ATATTATACC +s simRat_chr6.simRat.chr6 300594 10 + 647215 ATATTATGAC +s simRat_chr6.simRat.chr6 303511 10 + 647215 TCACGTTAGC + +a +s simMouse_chr6.simMouse.chr6 311892 40 + 636262 TAGGATAATAACTTTATAAATCAGCACAAAATGCTCAGCA +s Anc0.Anc0refChr8 1707 39 + 17196 TG-GATGATAGCTTTACACATCAGTACAAGATGGCCAGCA +s Anc1.Anc1refChr3 1769 39 + 3661 TG-GATGATAGCTTTACACATCAGTACAAGATGGCCAGCA +s Anc2.Anc2refChr8 1764 39 + 12804 TG-GATGATAGGTCTACACATCAGTACAACATGGCCAGAA +s mr.mrrefChr5 162135 39 + 294540 TA-GATAATAACTTTATAAATCAGCACAAAATGCTCAGCA +s mr.mrrefChr5 159357 39 + 294540 TG-AATGATAGCTTTTCACATTGGTACAAGGTGGCCAGCA +s simCow_chr6.simCow.chr6 281294 39 + 602619 TG-GATGATAGATGTCTGCATCAGTGCAATGTGGACAGAA +s simDog_chr6.simDog.chr6 317634 39 - 593897 TG-AATGAGAGGGCTACACATCAGTACTACATGGCCAGAA +s simHuman_chr6.simHuman.chr6 228079 39 + 601863 TA-GATGATAGCTTTACACATCAGTACAAGATCGCAAGTA +s simMouse_chr6.simMouse.chr6 308750 39 + 636262 TG-AATGTTAGCTTTTCACTTTGGCACAAGGTGGCCAACA +s simRat_chr6.simRat.chr6 300614 39 + 647215 TG-AATCATAGCTTTCCACATTGATACAAGGTGGCCAGCA +s simRat_chr6.simRat.chr6 303521 39 + 647215 TA-GACGCTAACTTTATAGATCAGCACAAAATGTCCAGCA + +a +s simMouse_chr6.simMouse.chr6 311932 1 + 636262 A +s Anc0.Anc0refChr8 1746 1 + 17196 A +s Anc1.Anc1refChr3 1808 1 + 3661 A +s Anc2.Anc2refChr8 1803 1 + 12804 A +s mr.mrrefChr5 162174 1 + 294540 A +s mr.mrrefChr5 159396 1 + 294540 A +s simCow_chr6.simCow.chr6 281333 1 + 602619 A +s simDog_chr6.simDog.chr6 317673 1 - 593897 A +s simHuman_chr6.simHuman.chr6 228118 1 + 601863 A +s simMouse_chr6.simMouse.chr6 308789 1 + 636262 A +s simRat_chr6.simRat.chr6 303560 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 311933 17 + 636262 CTTGGAATACTCTTTCT +s Anc0.Anc0refChr8 1747 16 + 17196 TTTGGCAT-ATTGTTTT +s Anc1.Anc1refChr3 1809 16 + 3661 TTTGGCAT-ATTGTTTT +s Anc2.Anc2refChr8 1804 16 + 12804 TTTGGCAC-ACTGTTTT +s mr.mrrefChr5 162175 16 + 294540 CTTGGAAT-CTCTTTCT +s mr.mrrefChr5 159397 16 + 294540 TTTGACAT-GTTGTTTC +s simCow_chr6.simCow.chr6 281334 16 + 602619 TCTGGCAG-ACTGTTTT +s simDog_chr6.simDog.chr6 317674 16 - 593897 ATTGGCAC-ACCCTTTG +s simHuman_chr6.simHuman.chr6 228119 16 + 601863 TTTGGCTT-ATTGTTTT +s simMouse_chr6.simMouse.chr6 308790 16 + 636262 TTTGACAT-GTTGTTTC +s simRat_chr6.simRat.chr6 300653 16 + 647215 TTTGACGT-GTTGTTTA +s simRat_chr6.simRat.chr6 303561 16 + 647215 TTTGGAAT-CTCTTTTT + +a +s simMouse_chr6.simMouse.chr6 311950 17 + 636262 TCTACTGCCATGATTTT +s Anc0.Anc0refChr8 1764 17 + 17196 TCCTCTGATGAGATTTT +s Anc1.Anc1refChr3 1826 17 + 3661 TCCTCTGATGAGATTTT +s Anc2.Anc2refChr8 1821 17 + 12804 TCCTTTGATGAGAGCAT +s mr.mrrefChr5 162191 17 + 294540 TCTACTGCCATGATTTT +s mr.mrrefChr5 159413 17 + 294540 TCCTCTGATAAGATTTC +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 308808 17 + 636262 TCCTCTGACAAGATTTC +s simRat_chr6.simRat.chr6 300669 17 + 647215 TTCCCTAATAAGATTTT +s simRat_chr6.simRat.chr6 303577 17 + 647215 TCTACAGCCATGATTTT a s simMouse_chr6.simMouse.chr6 311967 1 + 636262 A @@ -123534,6 +128437,32 @@ s simRat_chr6.simRat.chr6 303594 1 + 647215 A a +s simMouse_chr6.simMouse.chr6 311968 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 162209 1 + 294540 T +s mr.mrrefChr5 159430 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 308825 1 + 636262 T +s simRat_chr6.simRat.chr6 300686 1 + 647215 T +s simRat_chr6.simRat.chr6 303595 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 311969 7 + 636262 CTTGTAC +s Anc0.Anc0refChr8 1783 7 + 17196 CTTGTAC +s Anc1.Anc1refChr3 1845 7 + 3661 CTTGTAC +s Anc2.Anc2refChr8 1840 7 + 12804 CTTCTAC +s mr.mrrefChr5 162210 7 + 294540 CTTGTAC +s mr.mrrefChr5 159431 7 + 294540 CTTGCAC +s simCow_chr6.simCow.chr6 281370 7 + 602619 CTCCCAC +s simDog_chr6.simDog.chr6 317752 7 - 593897 CTTCTAC +s simMouse_chr6.simMouse.chr6 308826 7 + 636262 CTTGCAC +s simRat_chr6.simRat.chr6 300687 7 + 647215 CTTGCAC +s simRat_chr6.simRat.chr6 303596 7 + 647215 CTTGTAC + +a s simMouse_chr6.simMouse.chr6 311976 3 + 636262 ATC s Anc0.Anc0refChr8 1790 3 + 17196 ACC s Anc1.Anc1refChr3 1852 3 + 3661 ACC @@ -123544,25 +128473,92 @@ s simRat_chr6.simRat.chr6 303604 3 + 647215 ACC a +s simMouse_chr6.simMouse.chr6 311979 1 + 636262 C +s Anc0.Anc0refChr8 1793 1 + 17196 C +s Anc1.Anc1refChr3 1855 1 + 3661 C +s Anc2.Anc2refChr8 1850 1 + 12804 C +s mr.mrrefChr5 162220 1 + 294540 C +s mr.mrrefChr5 159438 1 + 294540 T +s simCow_chr6.simCow.chr6 281380 1 + 602619 C +s simDog_chr6.simDog.chr6 317762 1 - 593897 C +s simMouse_chr6.simMouse.chr6 308833 1 + 636262 T +s simRat_chr6.simRat.chr6 300694 1 + 647215 T +s simRat_chr6.simRat.chr6 303607 1 + 647215 C + +a +s simMouse_chr6.simMouse.chr6 311980 24 + 636262 CCTGGCACACTTTAACCTCTAGCC +s Anc0.Anc0refChr8 1794 24 + 17196 CCTGATATTCTTCCACCTCTAGCC +s Anc1.Anc1refChr3 1856 24 + 3661 CCTGATATTCTTCCACCTCTAGCC +s Anc2.Anc2refChr8 1851 24 + 12804 CCTGATATTCCTCCACCTCTAGCC +s mr.mrrefChr5 162221 24 + 294540 CCTGGCACACTTTAACCTCTAGCC +s mr.mrrefChr5 159439 24 + 294540 CCTGATGTTCTTCTACCTCTAGCC +s simCow_chr6.simCow.chr6 281381 22 + 602619 TCTGATATCCCTCTAC--CTAGCC +s simDog_chr6.simDog.chr6 317763 24 - 593897 CCGGATATTCCTACACCTCCAGCC +s simHuman_chr6.simHuman.chr6 228153 24 + 601863 CCTGATGTTCTTCCACCTCTAGAC +s simMouse_chr6.simMouse.chr6 308835 24 + 636262 CCTGATGTTCATCTAACTCTAGCC +s simRat_chr6.simRat.chr6 300695 24 + 647215 CCTGATGTTCTTCTACATCTAGCA +s simRat_chr6.simRat.chr6 303608 24 + 647215 CCTGACATCCTTTAACCTCTGGCC + +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 +s simMouse_chr6.simMouse.chr6 312005 4 + 636262 TGTA +s Anc0.Anc0refChr8 1818 4 + 17196 TGTG +s Anc1.Anc1refChr3 1880 4 + 3661 TGTG +s Anc2.Anc2refChr8 1875 4 + 12804 TGTG +s mr.mrrefChr5 162246 4 + 294540 TGTA +s mr.mrrefChr5 159463 4 + 294540 TGTG +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 308859 4 + 636262 TGCG +s simRat_chr6.simRat.chr6 300719 4 + 647215 TATG +s simRat_chr6.simRat.chr6 303633 4 + 647215 TGTA + +a +s simMouse_chr6.simMouse.chr6 312009 15 + 636262 TCAGAGTGAACTCCA +s Anc0.Anc0refChr8 1825 13 + 17196 TCAGAATAAAAT--G +s Anc1.Anc1refChr3 1887 13 + 3661 TCAGAATAAAAT--G +s Anc2.Anc2refChr8 1882 13 + 12804 TCAGAATAAAAT--G +s mr.mrrefChr5 162250 13 + 294540 TCAGAGTGAACT--A +s mr.mrrefChr5 159470 13 + 294540 TCAGAATAAAAT--G +s simCow_chr6.simCow.chr6 281410 13 + 602619 TCAGAATATAAT--G +s simDog_chr6.simDog.chr6 317794 13 - 593897 TCAGAGTAAAAT--G +s simHuman_chr6.simHuman.chr6 228184 13 + 601863 TCAGAATAAACT--A +s simMouse_chr6.simMouse.chr6 308866 13 + 636262 TTAGAATAACAT--G +s simRat_chr6.simRat.chr6 300726 13 + 647215 TCAGAATAAAAT--G +s simRat_chr6.simRat.chr6 303637 13 + 647215 TCAGAATAAAGT--A + +a +s simMouse_chr6.simMouse.chr6 312024 9 + 636262 GCATTTGCC +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 162263 9 + 294540 GCATTTGCC +s mr.mrrefChr5 159483 9 + 294540 AGGGTGGCC +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 308879 9 + 636262 AGGGTGGCC +s simRat_chr6.simRat.chr6 300739 9 + 647215 AGGGTGGCC +s simRat_chr6.simRat.chr6 303650 9 + 647215 GCATTTGCC + +a +s simMouse_chr6.simMouse.chr6 312033 9 + 636262 TGGCTGTTT +s Anc0.Anc0refChr8 1845 9 + 17196 TTGCCCTTT +s Anc1.Anc1refChr3 1911 9 + 3661 TTGCCCTTT +s Anc2.Anc2refChr8 1902 9 + 12804 TTGCCCTTT +s mr.mrrefChr5 162272 9 + 294540 TGGCTGTTT +s mr.mrrefChr5 159495 9 + 294540 TGGCCCTTT +s simCow_chr6.simCow.chr6 281430 9 + 602619 TTGCCCTTT +s simDog_chr6.simDog.chr6 317814 9 - 593897 TTGCCCTTT +s simHuman_chr6.simHuman.chr6 228208 9 + 601863 TTTCCCTCT +s simMouse_chr6.simMouse.chr6 308891 6 + 636262 TG---CTTC +s simRat_chr6.simRat.chr6 300751 9 + 647215 TGGCCCTTT +s simRat_chr6.simRat.chr6 303659 9 + 647215 TTGCTGTTT a s simMouse_chr6.simMouse.chr6 312042 2 + 636262 CT @@ -123620,16 +128616,135 @@ s simRat_chr6.simRat.chr6 303712 64 + 647215 TCTGGCTTAAATGCAGTTTGAACAGCAATAATTTATAGTTACCCACCCTC---------TGATGTGGAGGCAG a +s simMouse_chr6.simMouse.chr6 312153 5 + 636262 GTAAT +s Anc0.Anc0refChr8 1913 5 + 17196 GTAAT +s Anc1.Anc1refChr3 1980 5 + 3661 GTAAT +s Anc2.Anc2refChr8 1970 5 + 12804 TTCAC +s mr.mrrefChr5 162383 5 + 294540 GTAAT +s mr.mrrefChr5 159504 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 308897 5 + 636262 GTAAC +s simRat_chr6.simRat.chr6 300760 5 + 647215 GTAAT +s simRat_chr6.simRat.chr6 303776 5 + 647215 GTAAT + +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 312166 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 162396 1 + 294540 C +s mr.mrrefChr5 159509 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 308902 1 + 636262 C +s simRat_chr6.simRat.chr6 300765 1 + 647215 C +s simRat_chr6.simRat.chr6 303789 1 + 647215 C + +a +s simMouse_chr6.simMouse.chr6 312167 1 + 636262 A +s Anc0.Anc0refChr8 1919 1 + 17196 A +s Anc1.Anc1refChr3 1986 1 + 3661 A +s Anc2.Anc2refChr8 1976 1 + 12804 T +s mr.mrrefChr5 162397 1 + 294540 A +s mr.mrrefChr5 159510 1 + 294540 A +s simCow_chr6.simCow.chr6 281502 1 + 602619 T +s simDog_chr6.simDog.chr6 317891 1 - 593897 T +s simMouse_chr6.simMouse.chr6 308903 1 + 636262 A +s simRat_chr6.simRat.chr6 300766 1 + 647215 A +s simRat_chr6.simRat.chr6 303790 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 312168 2 + 636262 CT +s Anc0.Anc0refChr8 1920 2 + 17196 CG +s Anc1.Anc1refChr3 1987 2 + 3661 CG +s Anc2.Anc2refChr8 1977 2 + 12804 AG +s mr.mrrefChr5 162398 2 + 294540 CT +s mr.mrrefChr5 159511 2 + 294540 TG +s simCow_chr6.simCow.chr6 281503 2 + 602619 TA +s simDog_chr6.simDog.chr6 317892 2 - 593897 AG +s simMouse_chr6.simMouse.chr6 308904 2 + 636262 TG +s simRat_chr6.simRat.chr6 303791 2 + 647215 CT + +a +s simMouse_chr6.simMouse.chr6 312170 4 + 636262 AGGT +s Anc0.Anc0refChr8 1922 4 + 17196 AGGT +s Anc1.Anc1refChr3 1989 4 + 3661 AGGT +s Anc2.Anc2refChr8 1979 4 + 12804 AGGG +s mr.mrrefChr5 162400 4 + 294540 AGGT +s mr.mrrefChr5 159513 4 + 294540 ACGT +s simCow_chr6.simCow.chr6 281505 4 + 602619 AGGG +s simDog_chr6.simDog.chr6 317894 4 - 593897 AGGG +s simMouse_chr6.simMouse.chr6 308906 4 + 636262 ACAT +s simRat_chr6.simRat.chr6 300767 4 + 647215 GCGT +s simRat_chr6.simRat.chr6 303793 4 + 647215 AGGT + +a +s simMouse_chr6.simMouse.chr6 312174 5 + 636262 ACTCC +s Anc0.Anc0refChr8 1926 5 + 17196 TGTCC +s Anc1.Anc1refChr3 1993 5 + 3661 TGTCC +s Anc2.Anc2refChr8 1983 5 + 12804 TACAC +s mr.mrrefChr5 162404 5 + 294540 ACTCC +s mr.mrrefChr5 159517 5 + 294540 TGTCC +s simCow_chr6.simCow.chr6 281509 5 + 602619 TACAC +s simDog_chr6.simDog.chr6 317898 5 - 593897 TACAC +s simMouse_chr6.simMouse.chr6 308911 5 + 636262 TGACC +s simRat_chr6.simRat.chr6 300771 5 + 647215 TGTCC +s simRat_chr6.simRat.chr6 303797 5 + 647215 ACTCC + +a +s simMouse_chr6.simMouse.chr6 312179 6 + 636262 ATGTTT +s Anc0.Anc0refChr8 1931 6 + 17196 ATATTT +s Anc1.Anc1refChr3 1998 6 + 3661 ATATTT +s Anc2.Anc2refChr8 2016 6 + 12804 ATATTT +s mr.mrrefChr5 162409 6 + 294540 ATGTTT +s mr.mrrefChr5 159522 6 + 294540 TTATTT +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 308916 6 + 636262 TTATTT +s simRat_chr6.simRat.chr6 300776 6 + 647215 TTATTT +s simRat_chr6.simRat.chr6 303802 6 + 647215 ACATTT + +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 312187 27 + 636262 ACTTGAAGGAAAAAGGTCTGACCCCTA +s Anc0.Anc0refChr8 1937 27 + 17196 ACTTGAAGGAAGAAGGTCTGACCTTGA +s Anc1.Anc1refChr3 2004 27 + 3661 ACTTGAAGGAAGAAGGTCTGACCTTGA +s Anc2.Anc2refChr8 2022 27 + 12804 ACTTGAAGGAAGAAGGTCTGACCTTGA +s mr.mrrefChr5 162417 27 + 294540 ACTTGAAGGAAAAAGGTCTGACCCCTA +s mr.mrrefChr5 159528 27 + 294540 ACCTGTAGGACAAAGGTCTGACCTTGG +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 308922 27 + 636262 ACCTGTAGAACAAAGGTTTGACCTTGG +s simRat_chr6.simRat.chr6 300782 27 + 647215 ACCTGTAGGACAAAAGTCTGACCTTGG +s simRat_chr6.simRat.chr6 303810 27 + 647215 ACCTGAAGGAAAAAGGTCTAACCCCAA + +a +s simMouse_chr6.simMouse.chr6 312214 18 + 636262 CTCCCATTTATGTCAACT +s Anc0.Anc0refChr8 1964 18 + 17196 TTTCCACTTATATCAACT +s Anc1.Anc1refChr3 2031 18 + 3661 TTTCCACTTATATCAACT +s Anc2.Anc2refChr8 2049 18 + 12804 TTTGCACTTATATCAATT +s mr.mrrefChr5 162444 18 + 294540 CTCCCATTTATGTCAACT +s mr.mrrefChr5 159555 18 + 294540 TTTCCACTGAAATCAACT +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 308949 18 + 636262 TTTCCACTGAATTCAGCC +s simRat_chr6.simRat.chr6 300809 18 + 647215 TTGCTGCCGAAATCAAct +s simRat_chr6.simRat.chr6 303837 18 + 647215 CTCCCATTTATGTCAGCA + +a s simMouse_chr6.simMouse.chr6 312232 1 + 636262 C s Anc0.Anc0refChr8 1982 1 + 17196 t s Anc1.Anc1refChr3 2049 1 + 3661 T @@ -123641,11 +128756,108 @@ s simRat_chr6.simRat.chr6 303855 1 + 647215 C a +s simMouse_chr6.simMouse.chr6 312233 11 + 636262 AGATTCAGTAC +s Anc0.Anc0refChr8 1983 11 + 17196 agattcaatat +s Anc1.Anc1refChr3 2050 11 + 3661 AGATtcaatat +s Anc2.Anc2refChr8 2068 11 + 12804 ggatccaatat +s mr.mrrefChr5 162463 11 + 294540 AGATTCAGTAC +s mr.mrrefChr5 159573 11 + 294540 AGTTtcaatat +s simCow_chr6.simCow.chr6 281593 11 + 602619 ggatcaaatac +s simDog_chr6.simDog.chr6 317994 11 - 593897 ggatccaatat +s simHuman_chr6.simHuman.chr6 228328 11 + 601863 ACGCtcaatat +s simMouse_chr6.simMouse.chr6 308967 11 + 636262 AGTTTTAATAT +s simRat_chr6.simRat.chr6 300827 11 + 647215 agtttcaatat +s simRat_chr6.simRat.chr6 303856 11 + 647215 AGATTCTATAT + +a +s simMouse_chr6.simMouse.chr6 312244 1 + 636262 C +s Anc0.Anc0refChr8 1994 1 + 17196 c +s Anc1.Anc1refChr3 2061 1 + 3661 c +s Anc2.Anc2refChr8 2079 1 + 12804 c +s mr.mrrefChr5 162474 1 + 294540 C +s mr.mrrefChr5 159584 1 + 294540 t +s simCow_chr6.simCow.chr6 281604 1 + 602619 c +s simDog_chr6.simDog.chr6 318005 1 - 593897 t +s simHuman_chr6.simHuman.chr6 228339 1 + 601863 c +s simMouse_chr6.simMouse.chr6 308978 1 + 636262 T +s simRat_chr6.simRat.chr6 303867 1 + 647215 C + +a +s simMouse_chr6.simMouse.chr6 312245 6 + 636262 ACTTTC +s Anc0.Anc0refChr8 1995 6 + 17196 gctctt +s Anc1.Anc1refChr3 2062 6 + 3661 gctctt +s Anc2.Anc2refChr8 2080 6 + 12804 gctctt +s mr.mrrefChr5 162475 6 + 294540 ACTTTC +s mr.mrrefChr5 159585 6 + 294540 gctctt +s simCow_chr6.simCow.chr6 281605 6 + 602619 gctcct +s simDog_chr6.simDog.chr6 318006 6 - 593897 gctctt +s simHuman_chr6.simHuman.chr6 228340 6 + 601863 actctc +s simMouse_chr6.simMouse.chr6 308979 6 + 636262 GCTCTT +s simRat_chr6.simRat.chr6 300838 6 + 647215 gttctt +s simRat_chr6.simRat.chr6 303868 6 + 647215 ACTTTC + +a +s simMouse_chr6.simMouse.chr6 312251 2 + 636262 CT +s Anc0.Anc0refChr8 2001 2 + 17196 ct +s Anc1.Anc1refChr3 2068 2 + 3661 ct +s Anc2.Anc2refChr8 2086 2 + 12804 ct +s mr.mrrefChr5 162481 2 + 294540 CT +s mr.mrrefChr5 159591 2 + 294540 gt +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 308985 2 + 636262 GT +s simRat_chr6.simRat.chr6 300844 2 + 647215 gt +s simRat_chr6.simRat.chr6 303874 2 + 647215 CT + +a +s simMouse_chr6.simMouse.chr6 312253 5 + 636262 GTCTG +s Anc0.Anc0refChr8 2004 5 + 17196 gtttg +s Anc1.Anc1refChr3 2071 5 + 3661 gtttg +s Anc2.Anc2refChr8 2089 5 + 12804 gttca +s mr.mrrefChr5 162483 5 + 294540 GTCTG +s mr.mrrefChr5 159594 5 + 294540 gtttg +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 308988 5 + 636262 GTTTG +s simRat_chr6.simRat.chr6 300847 5 + 647215 gtctg +s simRat_chr6.simRat.chr6 303877 5 + 647215 GTTTA + +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 312287 8 + 636262 GTCATGAC +s Anc0.Anc0refChr8 2009 8 + 17196 gttatgtg +s Anc1.Anc1refChr3 2076 8 + 3661 gttatgtg +s Anc2.Anc2refChr8 2094 8 + 12804 gttatgtg +s mr.mrrefChr5 162517 8 + 294540 GTCATGAC +s mr.mrrefChr5 159599 8 + 294540 gtcctaac +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 308993 8 + 636262 TTCCTAAC +s simRat_chr6.simRat.chr6 300852 8 + 647215 gtcctaac +s simRat_chr6.simRat.chr6 303911 8 + 647215 GTCATGGC + +a +s simMouse_chr6.simMouse.chr6 312295 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 162525 1 + 294540 A +s mr.mrrefChr5 159607 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 309001 1 + 636262 A +s simRat_chr6.simRat.chr6 300860 1 + 647215 a +s simRat_chr6.simRat.chr6 303919 1 + 647215 A + +a s simMouse_chr6.simMouse.chr6 312296 1 + 636262 G s Anc0.Anc0refChr8 2018 1 + 17196 g s Anc1.Anc1refChr3 2085 1 + 3661 g @@ -123668,6 +128880,20 @@ s simRat_chr6.simRat.chr6 303921 1 + 647215 T a +s simMouse_chr6.simMouse.chr6 312298 9 + 636262 GTGAGACAC +s Anc0.Anc0refChr8 2020 9 + 17196 gtgtgacac +s Anc1.Anc1refChr3 2087 9 + 3661 gtgtgacac +s Anc2.Anc2refChr8 2105 9 + 12804 gtgtgacac +s mr.mrrefChr5 162528 9 + 294540 GTGAGACAC +s mr.mrrefChr5 159608 9 + 294540 gtgcaacac +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 309002 9 + 636262 Gtgcaacac +s simRat_chr6.simRat.chr6 300861 9 + 647215 atgcaacac +s simRat_chr6.simRat.chr6 303922 9 + 647215 GTGAGATAC + +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 @@ -123678,7 +128904,60 @@ s simRat_chr6.simRat.chr6 303977 24 + 647215 CGGGcagtcatgacagtgcaagat a -s simMouse_chr6.simMouse.chr6 312408 3 + 636262 CCA +s simMouse_chr6.simMouse.chr6 312342 41 + 636262 AGTTGCAGGAGTCCCATGTTGACAGGATTCTGGTTCTGAGT +s Anc0.Anc0refChr8 2029 41 + 17196 agcttgaggggtcccattttcaaaagtttcaggttgcaatt +s Anc1.Anc1refChr3 2096 41 + 3661 agcttgaggggtcccattttcaaaagtttcaggttgcaatt +s Anc2.Anc2refChr8 2114 41 + 12804 cgctaaaggggtcccagttttaaaagtttcaggttgcaatt +s mr.mrrefChr5 162572 41 + 294540 agttgcaggagtcccatgttgacaggattctggttctgagt +s mr.mrrefChr5 159617 41 + 294540 agcttgagtggtcccactttcaaggcctccaggttgagaat +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 309011 41 + 636262 agcttgagtggtcccactttcaaggcctccaggttgagaAT +s simRat_chr6.simRat.chr6 300870 41 + 647215 agcttaagaggtcccactttcaaggcctccagtttgtgaat +s simRat_chr6.simRat.chr6 304001 41 + 647215 agctgcaagggtcccattttgacaggattctggttctgatt + +a +s simMouse_chr6.simMouse.chr6 312383 13 + 636262 ATGATGTGATACA +s Anc0.Anc0refChr8 2070 13 + 17196 aagatgtaataca +s Anc1.Anc1refChr3 2137 13 + 3661 aagatgtaataca +s Anc2.Anc2refChr8 2155 13 + 12804 aggagccaataca +s mr.mrrefChr5 162613 13 + 294540 atgatgtgataca +s mr.mrrefChr5 159659 13 + 294540 aagatgtgctgca +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 309053 13 + 636262 AAGATGTGATGCA +s simRat_chr6.simRat.chr6 300912 13 + 647215 aggatgtcctgca +s simRat_chr6.simRat.chr6 304042 13 + 647215 ataatgtgagaca + +a +s simMouse_chr6.simMouse.chr6 312396 21 + 636262 GCTTAAGAGATCCCAGTACTA +s Anc0.Anc0refChr8 2083 18 + 17196 gcttgagggacc---ccagtt +s Anc1.Anc1refChr3 2150 18 + 3661 gcttgagggacc---ccagtt +s Anc2.Anc2refChr8 2168 18 + 12804 gcttgagggacc---acagtt +s mr.mrrefChr5 162626 18 + 294540 gcttaagagatc---gtacta +s mr.mrrefChr5 159675 18 + 294540 actagagggttc---ccagtt +s simCow_chr6.simCow.chr6 281729 18 + 602619 ccatgagggatc---atagtt +s simDog_chr6.simDog.chr6 318088 18 - 593897 gcttgaggggcc---acagtc +s simHuman_chr6.simHuman.chr6 228424 18 + 601863 gcttgagggacc---ccagat +s simMouse_chr6.simMouse.chr6 309069 18 + 636262 ACTAGAGGGTTC---CCTGTT +s simRat_chr6.simRat.chr6 300928 18 + 647215 gttggagggttc---ccagtt +s simRat_chr6.simRat.chr6 304055 18 + 647215 gcttaatggatt---gtactt + +a +s simMouse_chr6.simMouse.chr6 312417 10 + 636262 AGATTTCCAG +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 162644 10 + 294540 agatttccag +s mr.mrrefChr5 159696 10 + 294540 ggacttacag +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 309090 10 + 636262 GGACTTACAG +s simRat_chr6.simRat.chr6 300949 10 + 647215 ggacttccag +s simRat_chr6.simRat.chr6 304073 10 + 647215 aggctgccag a s simMouse_chr6.simMouse.chr6 312427 10 + 636262 AGGTGGCAAG @@ -123692,7 +128971,46 @@ s simRat_chr6.simRat.chr6 304083 10 + 647215 gggtggcaag a -s simMouse_chr6.simMouse.chr6 312438 1 + 636262 G +s simMouse_chr6.simMouse.chr6 312437 2 + 636262 TG +s Anc0.Anc0refChr8 2122 1 + 17196 t- +s Anc1.Anc1refChr3 2192 1 + 3661 t- +s Anc2.Anc2refChr8 2207 1 + 12804 t- +s mr.mrrefChr5 162664 1 + 294540 t- +s mr.mrrefChr5 159706 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 309100 1 + 636262 T- +s simRat_chr6.simRat.chr6 300959 1 + 647215 T- +s simRat_chr6.simRat.chr6 304093 1 + 647215 c- + +a +s simMouse_chr6.simMouse.chr6 312439 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 162665 1 + 294540 c +s mr.mrrefChr5 159707 1 + 294540 T +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 309101 1 + 636262 C +s simRat_chr6.simRat.chr6 300960 1 + 647215 T +s simRat_chr6.simRat.chr6 304094 1 + 647215 c + +a +s simMouse_chr6.simMouse.chr6 312440 8 + 636262 TGGAGGAT +s Anc0.Anc0refChr8 2125 8 + 17196 tggggggt +s Anc1.Anc1refChr3 2195 8 + 3661 tggggggt +s Anc2.Anc2refChr8 2210 8 + 12804 tggggggt +s mr.mrrefChr5 162666 8 + 294540 tggaggat +s mr.mrrefChr5 159708 8 + 294540 TGGATGAT +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 309102 8 + 636262 TGGATGAT +s simRat_chr6.simRat.chr6 300961 8 + 647215 TGGATCAT +s simRat_chr6.simRat.chr6 304095 8 + 647215 tggaggat a s simMouse_chr6.simMouse.chr6 312448 3 + 636262 TAT @@ -123706,6 +129024,76 @@ s simRat_chr6.simRat.chr6 304103 3 + 647215 tgg a +s simMouse_chr6.simMouse.chr6 312451 10 + 636262 CAAACATACC +s Anc0.Anc0refChr8 2136 10 + 17196 caaataaatt +s Anc1.Anc1refChr3 2206 10 + 3661 caaataaatt +s Anc2.Anc2refChr8 2221 10 + 12804 cgaataaatt +s mr.mrrefChr5 162677 10 + 294540 caaacaTACC +s mr.mrrefChr5 159716 10 + 294540 CAAATAAAGC +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 309110 10 + 636262 CAAATAGAGC +s simRat_chr6.simRat.chr6 300969 10 + 647215 CAAATAAAAC +s simRat_chr6.simRat.chr6 304106 10 + 647215 caaataTATC + +a +s simMouse_chr6.simMouse.chr6 312461 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 162687 3 + 294540 ACA +s mr.mrrefChr5 159738 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 309132 3 + 636262 ACA +s simRat_chr6.simRat.chr6 300991 3 + 647215 ACA +s simRat_chr6.simRat.chr6 304116 3 + 647215 CCA + +a +s simMouse_chr6.simMouse.chr6 312464 14 + 636262 AGTTGGGAGGGACT +s Anc0.Anc0refChr8 2161 14 + 17196 aatcaagtactatt +s Anc1.Anc1refChr3 2231 14 + 3661 aatcaagtactatt +s Anc2.Anc2refChr8 2246 14 + 12804 aatcaagtactatt +s mr.mrrefChr5 162690 14 + 294540 AGTTGGGAGGGACT +s mr.mrrefChr5 159741 14 + 294540 TATGATGTACCATT +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 309135 14 + 636262 TATGATGTACCAAG +s simRat_chr6.simRat.chr6 300994 14 + 647215 TATGACATACAATT +s simRat_chr6.simRat.chr6 304202 14 + 647215 AGTTGGGAAGGACT + +a +s simMouse_chr6.simMouse.chr6 312478 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 162704 1 + 294540 G +s mr.mrrefChr5 159758 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 309152 1 + 636262 G +s simRat_chr6.simRat.chr6 301011 1 + 647215 G +s simRat_chr6.simRat.chr6 304216 1 + 647215 G + +a +s simMouse_chr6.simMouse.chr6 312479 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 162705 2 + 294540 AT +s mr.mrrefChr5 159759 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 309153 2 + 636262 AT +s simRat_chr6.simRat.chr6 301012 2 + 647215 AT +s simRat_chr6.simRat.chr6 304217 2 + 647215 AA + +a s simMouse_chr6.simMouse.chr6 312481 6 + 636262 CGCAGT s Anc0.Anc0refChr8 2216 6 + 17196 ctcagc s Anc1.Anc1refChr3 2286 6 + 3661 ctcagc @@ -123739,6 +129127,30 @@ s simRat_chr6.simRat.chr6 304311 129 + 647215 CTGGAATATGTGCCATTTTTGACAGGTGAGTAAGCAGAGGTGGCTAAGGGTATTGTACCAACGAGTAAGGTTAACAACAAAGCGCATCACAGATAGGCTAACATGGAATGTCACCAGTCTGATACGATG a +s simMouse_chr6.simMouse.chr6 312677 6 + 636262 TCTGTA +s Anc0.Anc0refChr8 2250 6 + 17196 tctcta +s Anc1.Anc1refChr3 2405 6 + 3661 TCTCTA +s Anc2.Anc2refChr8 2335 6 + 12804 tttctt +s mr.mrrefChr5 162903 6 + 294540 TCTGTA +s mr.mrrefChr5 159761 6 + 294540 TCTCTA +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 309155 6 + 636262 TCTCTA +s simRat_chr6.simRat.chr6 301014 6 + 647215 TCACTA +s simRat_chr6.simRat.chr6 304440 6 + 647215 TCTCTA + +a +s simMouse_chr6.simMouse.chr6 312683 12 + 636262 CCTGCTAACACA +s Anc1.Anc1refChr3 2412 12 + 3661 CATGCCAAGACA +s mr.mrrefChr5 162909 12 + 294540 CCTGCTAAGACA +s mr.mrrefChr5 159768 12 + 294540 CTTGCAAACACA +s simHuman_chr6.simHuman.chr6 228697 12 + 601863 cagcccaagaca +s simMouse_chr6.simMouse.chr6 309162 12 + 636262 CTTGCAAACACA +s simRat_chr6.simRat.chr6 301021 12 + 647215 CTAGGAAGCACA +s simRat_chr6.simRat.chr6 304446 12 + 647215 CTTGCTAAGACA + +a s simMouse_chr6.simMouse.chr6 312695 3 + 636262 AAT s Anc1.Anc1refChr3 2424 3 + 3661 gcc s mr.mrrefChr5 162921 3 + 294540 AAT @@ -123746,6 +129158,44 @@ s simRat_chr6.simRat.chr6 304458 3 + 647215 AGT a +s simMouse_chr6.simMouse.chr6 312698 3 + 636262 CAA +s Anc1.Anc1refChr3 2427 3 + 3661 CAA +s mr.mrrefChr5 162924 3 + 294540 CAA +s mr.mrrefChr5 159780 3 + 294540 CAG +s simHuman_chr6.simHuman.chr6 228712 3 + 601863 caa +s simMouse_chr6.simMouse.chr6 309174 3 + 636262 CAG +s simRat_chr6.simRat.chr6 301033 3 + 647215 CAG +s simRat_chr6.simRat.chr6 304461 3 + 647215 CAA + +a +s simMouse_chr6.simMouse.chr6 312701 2 + 636262 CT +s Anc0.Anc0refChr8 2293 2 + 17196 ct +s Anc1.Anc1refChr3 2467 2 + 3661 ct +s Anc2.Anc2refChr8 2378 2 + 12804 ct +s mr.mrrefChr5 162927 2 + 294540 CT +s mr.mrrefChr5 159783 2 + 294540 TT +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 309177 2 + 636262 TT +s simRat_chr6.simRat.chr6 301036 2 + 647215 TG +s simRat_chr6.simRat.chr6 304464 2 + 647215 TC + +a +s simMouse_chr6.simMouse.chr6 312703 30 + 636262 TCAGTGCCTGTAGCTCCTTGAGAATGATAC +s Anc0.Anc0refChr8 2302 30 + 17196 TCTGTGCCTGTAGTTCCTTGATTGTTGTAT +s Anc1.Anc1refChr3 2476 30 + 3661 TCTGTGCCTGTAGTTCCTTGATTGTTGTAT +s Anc2.Anc2refChr8 2387 30 + 12804 TCTGTGCCTGTAGTTCCTTGGTTGTTGTAT +s mr.mrrefChr5 162929 30 + 294540 TCAGTGCCTGTAGCTCCTTGAGAATGATAC +s mr.mrrefChr5 159792 30 + 294540 TCAGTACCTGCAGTTCTGTGACTGTCTTAT +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 309186 30 + 636262 TCAGTACCTGCAGTTCTGTGACTGTCTTAT +s simRat_chr6.simRat.chr6 301080 30 + 647215 TCAGTACCTGCAGTTCCGTGGCCGTTTAAT +s simRat_chr6.simRat.chr6 304466 30 + 647215 TCAGTGCCTGTAGGTCCTTGCGAATGATAC + +a s simMouse_chr6.simMouse.chr6 312733 2 + 636262 AG s Anc0.Anc0refChr8 2332 2 + 17196 GG s Anc1.Anc1refChr3 2506 2 + 3661 GG @@ -123757,6 +129207,48 @@ s simRat_chr6.simRat.chr6 304496 2 + 647215 AG a +s simMouse_chr6.simMouse.chr6 312735 3 + 636262 CAA +s Anc0.Anc0refChr8 2334 3 + 17196 CCA +s Anc1.Anc1refChr3 2508 3 + 3661 CCA +s Anc2.Anc2refChr8 2419 3 + 12804 CCA +s mr.mrrefChr5 162961 3 + 294540 CAA +s mr.mrrefChr5 159822 3 + 294540 CAA +s simCow_chr6.simCow.chr6 281975 3 + 602619 CCC +s simDog_chr6.simDog.chr6 318395 3 - 593897 TCA +s simHuman_chr6.simHuman.chr6 228799 3 + 601863 CCA +s simMouse_chr6.simMouse.chr6 309216 3 + 636262 CAA +s simRat_chr6.simRat.chr6 301110 3 + 647215 CAA +s simRat_chr6.simRat.chr6 304498 3 + 647215 CAA + +a +s simMouse_chr6.simMouse.chr6 312738 7 + 636262 ATTTTTT +s Anc0.Anc0refChr8 2337 7 + 17196 AGTTTTC +s Anc1.Anc1refChr3 2511 7 + 3661 AGTTTTC +s Anc2.Anc2refChr8 2422 7 + 12804 AGTTTTC +s mr.mrrefChr5 162964 7 + 294540 ATTTTTT +s mr.mrrefChr5 159825 7 + 294540 ATTTTTT +s simCow_chr6.simCow.chr6 281978 7 + 602619 AGCTTTC +s simDog_chr6.simDog.chr6 318398 3 - 593897 AGT---- +s simHuman_chr6.simHuman.chr6 228802 7 + 601863 AGTTTTC +s simMouse_chr6.simMouse.chr6 309221 7 + 636262 ATTTTTT +s simRat_chr6.simRat.chr6 301113 7 + 647215 ATGTTTT +s simRat_chr6.simRat.chr6 304501 7 + 647215 GTTTTTT + +a +s simMouse_chr6.simMouse.chr6 312745 16 + 636262 GCTGACATCAGAGGAG +s Anc0.Anc0refChr8 2344 16 + 17196 ATAGACATTGGTGGAG +s Anc1.Anc1refChr3 2518 16 + 3661 ATAGACATTGGTGGAG +s Anc2.Anc2refChr8 2429 16 + 12804 ATAGACATTGGTGGAG +s mr.mrrefChr5 162971 16 + 294540 ACTGACATCAGTGGAG +s mr.mrrefChr5 159833 16 + 294540 ATAAACACTTGTCAAG +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 309229 16 + 636262 ATAAACACTTGTCAAG +s simRat_chr6.simRat.chr6 301121 16 + 647215 ATAAGCACTGGTCAAG +s simRat_chr6.simRat.chr6 304508 16 + 647215 ACTGACATCAGTGGTG + +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 @@ -123768,6 +129260,48 @@ s simRat_chr6.simRat.chr6 304524 8 + 647215 ACAA---AAGC a +s simMouse_chr6.simMouse.chr6 312772 25 + 636262 CTTGCAGCTGGCCTTCCCTGACACT +s Anc0.Anc0refChr8 2368 25 + 17196 CTTGCAACTGGCTCTTCCTGACACT +s Anc1.Anc1refChr3 2542 25 + 3661 CTTGCAACTGGCTCTTCCTGACACT +s Anc2.Anc2refChr8 2453 25 + 12804 TTTGCAACTGGCTCTTCCTGACACT +s mr.mrrefChr5 162995 25 + 294540 CTTGCAGCTGGCCTTCCCTGACACT +s mr.mrrefChr5 159849 25 + 294540 CTTACTAGCGGCTCTCCTTGGCATT +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 309245 25 + 636262 CTTACTAGCGGCTCTCCTTGGCATT +s simRat_chr6.simRat.chr6 301141 25 + 647215 CTTACCCGCTGCTCTCCTTGGCACT +s simRat_chr6.simRat.chr6 304532 25 + 647215 CTTGTAGTTGGCCTTCCCTGACACT + +a +s simMouse_chr6.simMouse.chr6 312797 9 + 636262 AATGCATCA +s Anc0.Anc0refChr8 2394 9 + 17196 AATGCATTG +s Anc1.Anc1refChr3 2568 9 + 3661 AATGCATTG +s Anc2.Anc2refChr8 2479 9 + 12804 AATGCATTG +s mr.mrrefChr5 163020 9 + 294540 AATGCATCA +s mr.mrrefChr5 159875 9 + 294540 AATATATTG +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 309271 9 + 636262 AATATATTG +s simRat_chr6.simRat.chr6 301167 9 + 647215 AATGCATTG +s simRat_chr6.simRat.chr6 304557 9 + 647215 AATGCATCA + +a +s simMouse_chr6.simMouse.chr6 312806 28 + 636262 AGCACACCTCATCACTGGCAACTAGAGA +s Anc0.Anc0refChr8 2403 21 + 17196 AGCACACCACATCACTGGCAA------- +s Anc1.Anc1refChr3 2577 28 + 3661 AGCACACCACATCACTGGCAACTAGAAA +s Anc2.Anc2refChr8 2488 21 + 12804 AGCACACCACGTCACTAGCAA------- +s mr.mrrefChr5 163029 28 + 294540 AGCACACCTCATCACTGGCAACTAGAGA +s mr.mrrefChr5 159884 28 + 294540 ACTTTGCCATTTCACTGGCAGCTACACA +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 309280 28 + 636262 ACTTTGCCATTTCACTGGCAGCTACACA +s simRat_chr6.simRat.chr6 301176 28 + 647215 ACTTCGTCATTTCACTGGCAGCTACACA +s simRat_chr6.simRat.chr6 304566 28 + 647215 AGCACACCTCATCACTGGCAGCTAGAGA + +a s simMouse_chr6.simMouse.chr6 312834 12 + 636262 GACATTGGTGTG s Anc0.Anc0refChr8 2424 1 + 17196 -----------T s Anc1.Anc1refChr3 2605 12 + 3661 TATGATAATGTT @@ -130727,6 +136261,44 @@ s simRat_chr6.simRat.chr6 324774 38 + 647215 ACAGTACAAGAGGTTTTCTCACAAGAGTGTAGACTTTT a +s simMouse_chr6.simMouse.chr6 333749 1 + 636262 A +s Anc0.Anc0refChr4 13832 1 + 45765 G +s Anc1.Anc1refChr2 80706 1 - 144309 G +s Anc1.Anc1refChr4 0 1 - 17549 G +s Anc2.Anc2refChr2 27052 1 - 27695 G +s Anc2.Anc2refChr7 0 1 - 32194 G +s mr.mrrefChr0 44917 1 - 130230 G +s mr.mrrefChr5 181273 1 + 294540 G +s simCow_chr6.simCow.chr6 511931 1 - 602619 G +s simCow_chr6.simCow.chr6 511916 1 - 602619 G +s simCow_chr6.simCow.chr6 307940 1 + 602619 G +s simDog_chr6.simDog.chr6 402231 1 - 593897 G +s simDog_chr6.simDog.chr6 402216 1 - 593897 G +s simHuman_chr6.simHuman.chr6 517285 1 - 601863 A +s simHuman_chr6.simHuman.chr6 282165 1 - 601863 G +s simMouse_chr6.simMouse.chr6 546208 1 - 636262 G +s simRat_chr6.simRat.chr6 564833 1 - 647215 G +s simRat_chr6.simRat.chr6 324812 1 + 647215 G + +a +s simMouse_chr6.simMouse.chr6 333750 2 + 636262 AC +s Anc0.Anc0refChr4 13848 2 + 45765 AT +s Anc1.Anc1refChr2 80723 2 - 144309 AT +s Anc1.Anc1refChr4 1 2 - 17549 AA +s Anc2.Anc2refChr2 27068 2 - 27695 CT +s Anc2.Anc2refChr7 1 2 - 32194 AT +s mr.mrrefChr0 44934 2 - 130230 AT +s mr.mrrefChr5 181274 2 + 294540 AC +s simCow_chr6.simCow.chr6 511932 2 - 602619 TT +s simDog_chr6.simDog.chr6 402232 2 - 593897 AT +s simDog_chr6.simDog.chr6 287678 2 - 593897 CT +s simHuman_chr6.simHuman.chr6 517302 2 - 601863 AT +s simHuman_chr6.simHuman.chr6 282166 2 - 601863 AA +s simMouse_chr6.simMouse.chr6 546225 2 - 636262 AT +s simRat_chr6.simRat.chr6 564850 2 - 647215 AT +s simRat_chr6.simRat.chr6 324813 2 + 647215 AC + +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 @@ -130762,21 +136334,14 @@ 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 +s simMouse_chr6.simMouse.chr6 333838 18 + 636262 TCAAACATGTAGGAGTGA +s Anc0.Anc0refChr4 13850 8 + 45765 ----------ATCCATGA +s Anc1.Anc1refChr4 95 18 - 17549 TTAAGCACCAATCCATGA +s Anc2.Anc2refChr2 27070 8 - 27695 ----------ATCCATGA +s mr.mrrefChr5 181371 18 + 294540 TTAAGCATGAAGGAATGA +s simDog_chr6.simDog.chr6 287680 8 - 593897 ----------ATCCATGA +s simHuman_chr6.simHuman.chr6 282262 18 - 601863 TTAAGCACCAATCTATAA +s simRat_chr6.simRat.chr6 324910 18 + 647215 TTAAGCATGAAGGAATGA a s simMouse_chr6.simMouse.chr6 333856 10 + 636262 GTGCCTCAAT @@ -130789,20 +136354,127 @@ 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 +s simMouse_chr6.simMouse.chr6 333866 2 + 636262 AT +s Anc0.Anc0refChr4 13868 2 + 45765 TG +s Anc1.Anc1refChr2 80725 2 - 144309 TG +s Anc1.Anc1refChr4 123 2 - 17549 AT +s Anc2.Anc2refChr2 27088 2 - 27695 TG +s Anc2.Anc2refChr7 3 2 - 32194 TG +s mr.mrrefChr0 44936 2 - 130230 TC +s mr.mrrefChr5 181399 2 + 294540 AT +s simCow_chr6.simCow.chr6 511934 2 - 602619 TG +s simDog_chr6.simDog.chr6 402234 2 - 593897 TA +s simDog_chr6.simDog.chr6 287709 2 - 593897 TG +s simHuman_chr6.simHuman.chr6 517304 2 - 601863 TG +s simHuman_chr6.simHuman.chr6 282290 2 - 601863 AT +s simMouse_chr6.simMouse.chr6 546227 2 - 636262 TC +s simRat_chr6.simRat.chr6 564852 2 - 647215 TC +s simRat_chr6.simRat.chr6 324938 2 + 647215 AC + +a +s simMouse_chr6.simMouse.chr6 333868 1 + 636262 A +s Anc0.Anc0refChr4 13870 1 + 45765 A +s Anc1.Anc1refChr2 80727 1 - 144309 A +s Anc1.Anc1refChr4 125 1 - 17549 A +s Anc2.Anc2refChr2 27090 1 - 27695 A +s Anc2.Anc2refChr7 5 1 - 32194 A +s mr.mrrefChr0 44938 1 - 130230 A +s mr.mrrefChr5 181401 1 + 294540 A +s simCow_chr6.simCow.chr6 511936 1 - 602619 A +s simDog_chr6.simDog.chr6 287711 1 - 593897 A +s simHuman_chr6.simHuman.chr6 517306 1 - 601863 A +s simHuman_chr6.simHuman.chr6 282292 1 - 601863 A +s simMouse_chr6.simMouse.chr6 546229 1 - 636262 A +s simRat_chr6.simRat.chr6 564854 1 - 647215 A +s simRat_chr6.simRat.chr6 324940 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 333869 4 + 636262 CATC +s Anc0.Anc0refChr4 13871 4 + 45765 ATTA +s Anc1.Anc1refChr2 80728 4 - 144309 ATTA +s Anc1.Anc1refChr4 126 4 - 17549 CATT +s Anc2.Anc2refChr2 27091 4 - 27695 ATCT +s Anc2.Anc2refChr7 6 4 - 32194 ATTA +s mr.mrrefChr0 44939 4 - 130230 AATA +s mr.mrrefChr5 181402 4 + 294540 CATC +s simCow_chr6.simCow.chr6 511937 4 - 602619 ATGA +s simDog_chr6.simDog.chr6 402236 4 - 593897 ATTA +s simDog_chr6.simDog.chr6 287712 4 - 593897 ATCT +s simHuman_chr6.simHuman.chr6 517307 4 - 601863 ATTA +s simHuman_chr6.simHuman.chr6 282293 4 - 601863 CATT +s simMouse_chr6.simMouse.chr6 546230 4 - 636262 AATA +s simRat_chr6.simRat.chr6 564855 4 - 647215 AGTA +s simRat_chr6.simRat.chr6 324941 4 + 647215 CATC + +a +s simMouse_chr6.simMouse.chr6 333873 3 + 636262 CCT +s Anc0.Anc0refChr4 13875 3 + 45765 GGC +s Anc1.Anc1refChr2 80732 3 - 144309 AGC +s Anc1.Anc1refChr4 130 3 - 17549 GCC +s Anc2.Anc2refChr2 27095 3 - 27695 GCC +s Anc2.Anc2refChr7 10 3 - 32194 AGC +s mr.mrrefChr0 44943 3 - 130230 TGC +s mr.mrrefChr5 181406 3 + 294540 CCT +s simCow_chr6.simCow.chr6 511941 3 - 602619 CAC +s simDog_chr6.simDog.chr6 402240 3 - 593897 AGC +s simDog_chr6.simDog.chr6 287716 3 - 593897 GCC +s simHuman_chr6.simHuman.chr6 517311 3 - 601863 AGC +s simHuman_chr6.simHuman.chr6 282298 3 - 601863 TCC +s simMouse_chr6.simMouse.chr6 546234 3 - 636262 TGC +s simRat_chr6.simRat.chr6 564859 3 - 647215 TAC +s simRat_chr6.simRat.chr6 324945 3 + 647215 CCT + +a +s simMouse_chr6.simMouse.chr6 333876 12 + 636262 TATCTCAGTTTG +s Anc0.Anc0refChr4 13878 12 + 45765 TATATTAATTTG +s Anc1.Anc1refChr2 80735 12 - 144309 TGTATCCATTTT +s Anc1.Anc1refChr4 133 12 - 17549 TATCTTAGTTTG +s Anc2.Anc2refChr2 27098 12 - 27695 TATATTAATTTG +s Anc2.Anc2refChr7 13 12 - 32194 TGTATCCACCTT +s mr.mrrefChr0 44946 12 - 130230 TGCCTCTGTTTT +s mr.mrrefChr5 181409 12 + 294540 TATCTCAGTTTG +s simCow_chr6.simCow.chr6 511944 4 - 602619 TGCA-------- +s simDog_chr6.simDog.chr6 402247 12 - 593897 TGTATCCACCTT +s simDog_chr6.simDog.chr6 287719 12 - 593897 TATATTAATTTG +s simHuman_chr6.simHuman.chr6 517314 12 - 601863 TGTATCCATTTT +s simHuman_chr6.simHuman.chr6 282301 12 - 601863 TATCTTAGTTCG +s simMouse_chr6.simMouse.chr6 546237 12 - 636262 TGCCTCTGATTT +s simRat_chr6.simRat.chr6 564862 12 - 647215 TGCTTCTGTTTT +s simRat_chr6.simRat.chr6 324948 12 + 647215 TAGCTCAGGTTT + +a +s simMouse_chr6.simMouse.chr6 333888 6 + 636262 TATCGT +s Anc0.Anc0refChr4 13891 6 + 45765 TGGTGC +s Anc1.Anc1refChr2 80748 6 - 144309 TGGTGC +s Anc1.Anc1refChr4 145 6 - 17549 TGTTGT +s Anc2.Anc2refChr2 27110 6 - 27695 TGTTGT +s Anc2.Anc2refChr7 26 6 - 32194 TGGTGC +s mr.mrrefChr0 44959 6 - 130230 TGGTGC +s mr.mrrefChr5 181421 6 + 294540 TATCGT +s simDog_chr6.simDog.chr6 402260 6 - 593897 TGGTGC +s simDog_chr6.simDog.chr6 287731 6 - 593897 TGTTGT +s simHuman_chr6.simHuman.chr6 517327 6 - 601863 TGGTGT +s simHuman_chr6.simHuman.chr6 282313 6 - 601863 TGTGGT +s simMouse_chr6.simMouse.chr6 546250 6 - 636262 TGGTGC +s simRat_chr6.simRat.chr6 564875 6 - 647215 TGGTGC +s simRat_chr6.simRat.chr6 324960 6 + 647215 TATAGT + +a +s simMouse_chr6.simMouse.chr6 333894 5 + 636262 TCTGA +s Anc0.Anc0refChr4 13897 5 + 45765 TCTTA +s Anc1.Anc1refChr2 80754 5 - 144309 TCTTA +s Anc1.Anc1refChr4 151 5 - 17549 TCTTA +s Anc2.Anc2refChr2 27116 5 - 27695 TCTTA +s Anc2.Anc2refChr7 32 5 - 32194 TCTTA +s mr.mrrefChr0 44965 5 - 130230 TCTTA +s mr.mrrefChr5 181427 5 + 294540 TCTGA +s simDog_chr6.simDog.chr6 402266 5 - 593897 TCTTA +s simDog_chr6.simDog.chr6 287737 5 - 593897 TCTTA +s simHuman_chr6.simHuman.chr6 517333 5 - 601863 TCTTA +s simHuman_chr6.simHuman.chr6 282319 5 - 601863 TCTCA +s simMouse_chr6.simMouse.chr6 546256 2 - 636262 ---TA +s simRat_chr6.simRat.chr6 564882 5 - 647215 TCTTA +s simRat_chr6.simRat.chr6 324966 5 + 647215 TCTGA a s simMouse_chr6.simMouse.chr6 333899 56 + 636262 CTTTTAGGGTATGCTAGTTTTCAGATAGAGTCTTATACACGTTTAGGGCGTTGGCT @@ -136084,6 +141756,34 @@ s simRat_chr6.simRat.chr6 339521 7 + 647215 GATTAAG a +s simMouse_chr6.simMouse.chr6 348101 5 + 636262 CCTGG +s Anc0.Anc0refChr0 11484 5 + 26507 CCTAC +s Anc1.Anc1refChr6 11756 5 + 197743 CCTAC +s Anc2.Anc2refChr17 4761 5 + 28526 CCTAC +s mr.mrrefChr5 195411 5 + 294540 CCTGG +s mr.mrrefChr5 194946 5 + 294540 CTCAC +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 347637 5 + 636262 CTCAC +s simRat_chr6.simRat.chr6 339051 5 + 647215 CTCAC +s simRat_chr6.simRat.chr6 339528 5 + 647215 TCTGG + +a +s simMouse_chr6.simMouse.chr6 348106 8 + 636262 TGCCTTTG +s Anc0.Anc0refChr0 11491 8 + 26507 TACCTTCA +s Anc1.Anc1refChr6 11763 8 + 197743 TACCTTCA +s Anc2.Anc2refChr17 4768 8 + 28526 TACCTTCA +s mr.mrrefChr5 195416 8 + 294540 TGCCTTTG +s mr.mrrefChr5 194951 8 + 294540 TACCTTTG +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 347642 8 + 636262 TACCTTTG +s simRat_chr6.simRat.chr6 339056 8 + 647215 CACCTTTG +s simRat_chr6.simRat.chr6 339533 8 + 647215 TGCCTTTT + +a s simMouse_chr6.simMouse.chr6 348114 1 + 636262 C s Anc0.Anc0refChr0 11499 1 + 26507 C s Anc1.Anc1refChr6 11771 1 + 197743 C @@ -136095,11 +141795,95 @@ s simRat_chr6.simRat.chr6 339541 1 + 647215 C a +s simMouse_chr6.simMouse.chr6 348115 15 + 636262 TACTGATGGACAAAC +s Anc0.Anc0refChr0 11500 15 + 26507 TGCTGATGGACAAAC +s Anc1.Anc1refChr6 11772 15 + 197743 TGCTGATGGACAAAC +s Anc2.Anc2refChr17 4777 15 + 28526 TGCTGATGGACAAAC +s mr.mrrefChr5 195425 15 + 294540 TACTGATGGACAAAC +s mr.mrrefChr5 194959 15 + 294540 TACTTAGGGACAAAC +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 347650 15 + 636262 TACTTAGGGACAAAC +s simRat_chr6.simRat.chr6 339064 15 + 647215 TACTTAGGGACAAAT +s simRat_chr6.simRat.chr6 339542 15 + 647215 TACTGATGGACAAAC + +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 348141 15 + 636262 CTGGTGCACTTACTG +s Anc0.Anc0refChr0 11515 15 + 26507 TTGGCACAACTTCCA +s Anc1.Anc1refChr6 11787 15 + 197743 TTGGCACAACTTCCA +s Anc2.Anc2refChr17 4792 15 + 28526 TCGGCACAACTTCCA +s mr.mrrefChr5 195451 15 + 294540 CTGGTGCACCTACTA +s mr.mrrefChr5 194974 15 + 294540 TTGGTGTAACTTCTG +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 347665 15 + 636262 TTGATGTGACTTCTG +s simRat_chr6.simRat.chr6 339079 15 + 647215 TTGGTGCAACTTCTG +s simRat_chr6.simRat.chr6 339568 15 + 647215 CTGGGGCACCTACTA + +a +s simMouse_chr6.simMouse.chr6 348156 13 + 636262 TGGTAATCATTTT +s Anc0.Anc0refChr0 11530 13 + 26507 TGGTGAATTTTTT +s Anc1.Anc1refChr6 11802 13 + 197743 TGGTGAATTTTTT +s Anc2.Anc2refChr17 4807 13 + 28526 TGGTGAATTTTTT +s mr.mrrefChr5 195466 13 + 294540 TGGTAATCATTTT +s mr.mrrefChr5 195001 13 + 294540 TGGTGAAGTTTCT +s simCow_chr6.simCow.chr6 320099 13 + 602619 TGGTGAATTTTTT +s simDog_chr6.simDog.chr6 312233 13 + 593897 TGGGGATTTTTCT +s simHuman_chr6.simHuman.chr6 331899 13 + 601863 TGATAAATTTTTA +s simMouse_chr6.simMouse.chr6 347692 13 + 636262 CAGTGAAGTTCCT +s simRat_chr6.simRat.chr6 339106 13 + 647215 TGGTGAGGTTTCT +s simRat_chr6.simRat.chr6 339583 12 + 647215 TGGTAATCCTTT- + +a +s simMouse_chr6.simMouse.chr6 348169 21 + 636262 GTGTTGCTTTCAGTATAACGA +s Anc0.Anc0refChr0 11544 21 + 26507 ATATTGCTGTCAGTAGAAGCA +s Anc1.Anc1refChr6 11816 21 + 197743 ATATTGCTGTCAGTAGAAGCA +s Anc2.Anc2refChr17 4821 21 + 28526 ATCTTTCTGTCAGTAGAAGCA +s mr.mrrefChr5 195479 21 + 294540 GTGTTGCTTTCAGTATAACGA +s mr.mrrefChr5 195015 21 + 294540 ATATTCCTGTGTGTGTAACCA +s simCow_chr6.simCow.chr6 320113 21 + 602619 GTCTTCCTGTTAGTGGAAGCA +s simDog_chr6.simDog.chr6 312247 21 + 593897 AACTCTTTGTCAATAGAAGCA +s simHuman_chr6.simHuman.chr6 331913 21 + 601863 TTACTGCTGTCAGCAGGAGCA +s simMouse_chr6.simMouse.chr6 347706 21 + 636262 ATATTCCTGTGTGTGTAACCA +s simRat_chr6.simRat.chr6 339120 21 + 647215 ATATTCCGTTATGTGTAACCA +s simRat_chr6.simRat.chr6 339595 16 + 647215 -----GTTATCAGTATAAATA + +a +s simMouse_chr6.simMouse.chr6 348190 46 + 636262 TGATAACATAACTCTCAGTTCCAGTTCCTTCGTGGTAGTCTAGTCT +s Anc0.Anc0refChr0 11584 46 + 26507 GAAAGACGCAGCTCTATGTTCAGGTTCCTTGGTGGTAATTTGGTCA +s Anc1.Anc1refChr6 11856 46 + 197743 GAAAGACGCAGCTCTATGTTCAGGTTCCTTGGTGGTAATTTGGTCA +s Anc2.Anc2refChr17 4861 46 + 28526 GAAAGACGCAGGCCCATGTTCAGGTTCCTTGGTGGTAATTTGGTGA +s mr.mrrefChr5 195500 46 + 294540 TGATGACACAACTCTCAGTTCAGGTTCCTTGGTGGTAGTTTAGTCA +s mr.mrrefChr5 195055 46 + 294540 TAAAGAAACAGCTCTACATTCACGCTCTTCCGTGGTAGATTAGTTA +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 347746 46 + 636262 TAAAGAAACAGCTCTACATTCACCCTCTTCCAGGGTAGTTTAGTTA +s simRat_chr6.simRat.chr6 339160 46 + 647215 TGAAAAAACAGCACTACATGCATGCTCATCTGTGTTAGATTAATTA +s simRat_chr6.simRat.chr6 339611 46 + 647215 TGATGACACAACTCTGAGTTCAGGTCCCTTGGTGGTAGCTTAGTCA + +a +s simMouse_chr6.simMouse.chr6 348236 6 + 636262 ACTAAC +s Anc0.Anc0refChr0 11630 6 + 26507 ACTAAC +s Anc1.Anc1refChr6 11902 6 + 197743 ACTAAC +s Anc2.Anc2refChr17 4907 6 + 28526 ACTAAC +s mr.mrrefChr5 195546 6 + 294540 ACTAAC +s mr.mrrefChr5 195101 6 + 294540 ACTAGC +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 347792 6 + 636262 ACTAGC +s simRat_chr6.simRat.chr6 339206 6 + 647215 ACTAGC +s simRat_chr6.simRat.chr6 339657 6 + 647215 ACTAAC + +a s simMouse_chr6.simMouse.chr6 348242 2 + 636262 CC s Anc1.Anc1refChr6 11908 2 + 197743 GA s mr.mrrefChr5 195552 2 + 294540 CC @@ -136107,11 +141891,76 @@ s simRat_chr6.simRat.chr6 339663 2 + 647215 CC a +s simMouse_chr6.simMouse.chr6 348244 6 + 636262 GGTTAT +s Anc0.Anc0refChr0 11636 6 + 26507 TGTCAC +s Anc1.Anc1refChr6 11910 6 + 197743 TGTCAC +s Anc2.Anc2refChr17 4913 6 + 28526 TGTCTC +s mr.mrrefChr5 195554 6 + 294540 TGTTAT +s mr.mrrefChr5 195107 6 + 294540 TGTCAC +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 347798 6 + 636262 TGTCAC +s simRat_chr6.simRat.chr6 339212 6 + 647215 TGTCAC +s simRat_chr6.simRat.chr6 339665 6 + 647215 TGTTAT + +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 348251 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 195561 1 + 294540 C +s mr.mrrefChr5 195113 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 347804 1 + 636262 C +s simRat_chr6.simRat.chr6 339218 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 348252 6 + 636262 ACCAAT +s Anc0.Anc0refChr0 11643 6 + 26507 AACTAT +s Anc1.Anc1refChr6 11917 6 + 197743 AACTAT +s Anc2.Anc2refChr17 4933 6 + 28526 AACTTT +s mr.mrrefChr5 195562 6 + 294540 ACCAAT +s mr.mrrefChr5 195114 6 + 294540 AGTAAT +s simDog_chr6.simDog.chr6 312376 6 + 593897 AACTTT +s simHuman_chr6.simHuman.chr6 332014 6 + 601863 AACTAT +s simMouse_chr6.simMouse.chr6 347805 6 + 636262 AGTAAT +s simRat_chr6.simRat.chr6 339219 6 + 647215 AGTAAT + +a +s simMouse_chr6.simMouse.chr6 348258 2 + 636262 TG +s Anc0.Anc0refChr0 11657 2 + 26507 TG +s Anc1.Anc1refChr6 11931 2 + 197743 TG +s Anc2.Anc2refChr17 4947 2 + 28526 TG +s mr.mrrefChr5 195568 2 + 294540 TG +s mr.mrrefChr5 195120 2 + 294540 TA +s simDog_chr6.simDog.chr6 312390 2 + 593897 TG +s simHuman_chr6.simHuman.chr6 332028 2 + 601863 TG +s simMouse_chr6.simMouse.chr6 347811 2 + 636262 TA +s simRat_chr6.simRat.chr6 339225 2 + 647215 TA + +a +s simMouse_chr6.simMouse.chr6 348260 8 + 636262 ATGTATAA +s Anc0.Anc0refChr0 11659 8 + 26507 ATTTATTT +s Anc1.Anc1refChr6 11933 8 + 197743 ATTTATTT +s Anc2.Anc2refChr17 4949 8 + 28526 ACTAATTT +s mr.mrrefChr5 195570 8 + 294540 ATGTATAA +s mr.mrrefChr5 195122 8 + 294540 ATTTTAAA +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 347813 8 + 636262 ATTTTAAA +s simRat_chr6.simRat.chr6 339227 8 + 647215 ATTTTAAA +s simRat_chr6.simRat.chr6 339672 8 + 647215 ATGTATAT + +a s simMouse_chr6.simMouse.chr6 348268 5 + 636262 TGATG s Anc0.Anc0refChr0 11667 5 + 26507 TGATG s Anc1.Anc1refChr6 11941 5 + 197743 TGATG @@ -136123,27 +141972,139 @@ s simRat_chr6.simRat.chr6 339680 5 + 647215 CGATG a +s simMouse_chr6.simMouse.chr6 348273 2 + 636262 CA +s Anc0.Anc0refChr0 11672 1 + 26507 -T +s Anc1.Anc1refChr6 11946 2 + 197743 CT +s Anc2.Anc2refChr17 4962 1 + 28526 -T +s mr.mrrefChr5 195583 2 + 294540 CA +s mr.mrrefChr5 195130 2 + 294540 CT +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 347821 2 + 636262 CT +s simRat_chr6.simRat.chr6 339235 2 + 647215 CT +s simRat_chr6.simRat.chr6 339685 2 + 647215 GA + +a +s simMouse_chr6.simMouse.chr6 348275 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 195585 4 + 294540 AGAA +s mr.mrrefChr5 195132 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 347823 4 + 636262 AGAA +s simRat_chr6.simRat.chr6 339245 4 + 647215 AGAA +s simRat_chr6.simRat.chr6 339687 4 + 647215 AAAA + +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 348285 7 + 636262 TGTAATG +s Anc0.Anc0refChr0 11677 7 + 26507 TCTAATA +s Anc1.Anc1refChr6 11952 7 + 197743 TCTAATA +s Anc2.Anc2refChr17 4967 7 + 28526 TTCAATA +s mr.mrrefChr5 195595 7 + 294540 TGTAATG +s mr.mrrefChr5 195136 7 + 294540 TCTAATA +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 347827 7 + 636262 TCTAATA +s simRat_chr6.simRat.chr6 339249 7 + 647215 TTTAATA +s simRat_chr6.simRat.chr6 339697 7 + 647215 TGTAGTG + +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 +s simMouse_chr6.simMouse.chr6 348308 5 + 636262 ATACA +s Anc0.Anc0refChr0 11684 5 + 26507 ATTCA +s Anc1.Anc1refChr6 11959 5 + 197743 ATTCA +s Anc2.Anc2refChr17 4974 5 + 28526 ATTCA +s mr.mrrefChr5 195618 5 + 294540 ATACA +s mr.mrrefChr5 195143 5 + 294540 ATTCA +s simCow_chr6.simCow.chr6 320236 5 + 602619 ATTCA +s simDog_chr6.simDog.chr6 312420 4 + 593897 ATT-A +s simHuman_chr6.simHuman.chr6 332054 5 + 601863 ATTCA +s simMouse_chr6.simMouse.chr6 347834 5 + 636262 ATTCA +s simRat_chr6.simRat.chr6 339256 5 + 647215 ATTCA +s simRat_chr6.simRat.chr6 339720 5 + 647215 ATACA + +a +s simMouse_chr6.simMouse.chr6 348313 2 + 636262 AG +s Anc0.Anc0refChr0 11689 2 + 26507 AG +s Anc1.Anc1refChr6 11964 2 + 197743 AG +s Anc2.Anc2refChr17 4979 2 + 28526 AG +s mr.mrrefChr5 195623 2 + 294540 AG +s mr.mrrefChr5 195148 2 + 294540 AG +s simCow_chr6.simCow.chr6 320241 2 + 602619 GG +s simDog_chr6.simDog.chr6 312424 2 + 593897 AG +s simHuman_chr6.simHuman.chr6 332059 2 + 601863 AG +s simMouse_chr6.simMouse.chr6 347839 2 + 636262 AG +s simRat_chr6.simRat.chr6 339725 2 + 647215 AG + +a +s simMouse_chr6.simMouse.chr6 348315 11 + 636262 AGAGCTGAGAG +s Anc0.Anc0refChr0 11691 11 + 26507 AGAGCTGAGAG +s Anc1.Anc1refChr6 11966 11 + 197743 AGAGCTGAGAG +s Anc2.Anc2refChr17 4981 11 + 28526 AGAGCTGAGAG +s mr.mrrefChr5 195625 11 + 294540 AGAGCTGAGAG +s mr.mrrefChr5 195150 11 + 294540 AGAGCTAGGAA +s simCow_chr6.simCow.chr6 320243 11 + 602619 AGAGCTGAAAG +s simDog_chr6.simDog.chr6 312426 11 + 593897 AGAGCTGAGAG +s simHuman_chr6.simHuman.chr6 332061 11 + 601863 AGAGCTGACGG +s simMouse_chr6.simMouse.chr6 347841 11 + 636262 AGAGCTAGGAA +s simRat_chr6.simRat.chr6 339261 11 + 647215 AGAGCCAGGAA +s simRat_chr6.simRat.chr6 339727 11 + 647215 AGAGCTGAGAG + +a +s simMouse_chr6.simMouse.chr6 348326 20 + 636262 GTTATAATGCTAATGCCCAG +s Anc0.Anc0refChr0 11702 20 + 26507 GTCATAATGCTTAGACACAT +s Anc1.Anc1refChr6 11977 20 + 197743 GTCATAATGCTTAGACACAT +s Anc2.Anc2refChr17 4992 20 + 28526 GACATAATGCTTTGACACAT +s mr.mrrefChr5 195636 20 + 294540 GTTATAATGCTAATGCCCAG +s mr.mrrefChr5 195161 20 + 294540 GTCATAATGTTTAGTTGCAT +s simCow_chr6.simCow.chr6 320254 20 + 602619 GCCATAATGCTTTGACACAT +s simDog_chr6.simDog.chr6 312437 19 + 593897 GACATAATGCTT-GAGACAT +s simHuman_chr6.simHuman.chr6 332072 18 + 601863 ATCA--ATGCTTAGACACAT +s simMouse_chr6.simMouse.chr6 347852 19 + 636262 GTC-TAATGTTTAGTTGCAT +s simRat_chr6.simRat.chr6 339272 20 + 647215 GTCATAATGTTTAGTGGGAT +s simRat_chr6.simRat.chr6 339742 20 + 647215 GTTATAACACTAATGCTCAC + +a +s simMouse_chr6.simMouse.chr6 348346 18 + 636262 TGGTGTTTCCCTAAGACA +s Anc0.Anc0refChr0 11731 18 + 26507 TGGTGTATCCTTAAGATG +s Anc1.Anc1refChr6 12006 18 + 197743 TGGTGTATCCTTAAGATG +s Anc2.Anc2refChr17 5021 18 + 28526 TGATGTATCCTTAAGATG +s mr.mrrefChr5 195656 18 + 294540 TGGTGTTTCCCTAAGACA +s mr.mrrefChr5 195197 18 + 294540 TGGTTTACTCTTTAGATG +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 347887 18 + 636262 TGGTTTACTCTTTAGATG +s simRat_chr6.simRat.chr6 339308 18 + 647215 TGGTTTACTCTTTAGATG +s simRat_chr6.simRat.chr6 339762 18 + 647215 TGGTGTTTCCCTAAGGCA + +a +s simMouse_chr6.simMouse.chr6 348364 7 + 636262 CTGGCAC +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 195674 7 + 294540 CTGGCAC +s mr.mrrefChr5 195216 7 + 294540 CTGGAAC +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 347906 7 + 636262 CTGGAAC +s simRat_chr6.simRat.chr6 339327 7 + 647215 CTGGAAC +s simRat_chr6.simRat.chr6 339780 7 + 647215 TTGCTAA a s simMouse_chr6.simMouse.chr6 348371 18 + 636262 AGCCTGCAATGTCCAGAT @@ -136151,6 +142112,62 @@ s simRat_chr6.simRat.chr6 339787 16 + 647215 TGCCTACAAA--TCAGAT a +s simMouse_chr6.simMouse.chr6 348389 26 + 636262 TGTTTTTTGCTGTTCTATTCCCGTTA +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 195697 26 + 294540 TGTTTTTTGCTGTTCTATTCCTGGTA +s mr.mrrefChr5 195223 26 + 294540 TGTTTTTTGCTGGTATATTTCAGGTA +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 347913 26 + 636262 TGTTTTTTGTTGGTATATTTCAGGTA +s simRat_chr6.simRat.chr6 339334 26 + 647215 TGTTTTTTGCTGGTTAAGTTCAGGTA +s simRat_chr6.simRat.chr6 339803 26 + 647215 TGTTTTTTGCTGTTCTATTCCTGGTA + +a +s simMouse_chr6.simMouse.chr6 348415 37 + 636262 TCGGACACCTATTGGCCTTTGGTCCATTGCAAGTACC +s Anc0.Anc0refChr0 11780 37 + 26507 CCTAAGATCTCTTGACCATTTGTCCATTGGAAGCACC +s Anc1.Anc1refChr6 12058 37 + 197743 CCTAAGATCTCTTGACCATTTGTCCATTGGAAGCACC +s Anc2.Anc2refChr17 5070 37 + 28526 CCTAAGATCTCTTGACCATTTGTCCATCAGAAGCACC +s mr.mrrefChr5 195723 37 + 294540 TCGGACACCTATTGGCCTTTGGTCCATTGGAAGTACC +s mr.mrrefChr5 195249 37 + 294540 CATATGGTATACCAGCCATTTGTGTATTGGGTATAAC +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 347939 37 + 636262 CATATGGTATACCAGCCATTTGTGTATTGGGTATAAC +s simRat_chr6.simRat.chr6 339360 37 + 647215 CATATGCTATACCAACCATTTGTGTATTGGTTATAAC +s simRat_chr6.simRat.chr6 339833 37 + 647215 TTGGACATTCATTGGTGTTTGATCCATTGGAATTACC + +a +s simMouse_chr6.simMouse.chr6 348452 10 + 636262 ACAAGTCAAG +s Anc0.Anc0refChr0 11817 10 + 26507 AGAAGTCAAA +s Anc1.Anc1refChr6 12095 10 + 197743 AGAAGTCAAA +s Anc2.Anc2refChr17 5107 10 + 28526 AGAAGTCAAA +s mr.mrrefChr5 195760 10 + 294540 ACAAGTCAAG +s mr.mrrefChr5 195286 10 + 294540 AGACATCAAG +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 347976 10 + 636262 AGACATCAAG +s simRat_chr6.simRat.chr6 339397 10 + 647215 AGACATCAAG +s simRat_chr6.simRat.chr6 339870 10 + 647215 ACAAGTCGAG + +a +s simMouse_chr6.simMouse.chr6 348462 7 + 636262 ACATACA +s Anc0.Anc0refChr0 11828 7 + 26507 ATACAGG +s Anc1.Anc1refChr6 12106 7 + 197743 ATACAGG +s Anc2.Anc2refChr17 5118 7 + 28526 ATACAGG +s mr.mrrefChr5 195770 7 + 294540 GTATAGG +s mr.mrrefChr5 195297 7 + 294540 GCATGGT +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 347987 7 + 636262 GCATGGT +s simRat_chr6.simRat.chr6 339408 7 + 647215 GCATAGT +s simRat_chr6.simRat.chr6 339880 7 + 647215 GTATGGG + +a s simMouse_chr6.simMouse.chr6 348469 4 + 636262 ATAA s Anc0.Anc0refChr0 11835 4 + 26507 ATAA s Anc1.Anc1refChr6 12113 4 + 197743 ATAA @@ -136173,6 +142190,89 @@ s simRat_chr6.simRat.chr6 339891 3 + 647215 AGA a +s simMouse_chr6.simMouse.chr6 348476 7 + 636262 GTTAGGA +s Anc0.Anc0refChr0 11848 7 + 26507 GTTTGGA +s Anc1.Anc1refChr6 12126 7 + 197743 GTTTGGA +s Anc2.Anc2refChr17 5138 7 + 28526 GTGTGGA +s mr.mrrefChr5 195784 7 + 294540 GTTAGGA +s mr.mrrefChr5 195304 7 + 294540 GTTAGGA +s simCow_chr6.simCow.chr6 320401 7 + 602619 GTGTGAA +s simDog_chr6.simDog.chr6 312582 7 + 593897 GTGTGGA +s simHuman_chr6.simHuman.chr6 332209 7 + 601863 GTTTGGG +s simMouse_chr6.simMouse.chr6 347994 7 + 636262 GTTAGGA +s simRat_chr6.simRat.chr6 339415 7 + 647215 GTTAGGA +s simRat_chr6.simRat.chr6 339894 7 + 647215 GTTGGGA + +a +s simMouse_chr6.simMouse.chr6 348483 1 + 636262 T +s Anc0.Anc0refChr0 11855 1 + 26507 T +s Anc1.Anc1refChr6 12133 1 + 197743 T +s Anc2.Anc2refChr17 5145 1 + 28526 T +s mr.mrrefChr5 195791 1 + 294540 T +s mr.mrrefChr5 195311 1 + 294540 T +s simCow_chr6.simCow.chr6 320408 1 + 602619 T +s simDog_chr6.simDog.chr6 312589 1 + 593897 T +s simHuman_chr6.simHuman.chr6 332216 1 + 601863 T +s simMouse_chr6.simMouse.chr6 348001 1 + 636262 T +s simRat_chr6.simRat.chr6 339901 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 348484 13 + 636262 CAACTGGGCATTA +s Anc0.Anc0refChr0 11856 13 + 26507 CAACTAGGCATTA +s Anc1.Anc1refChr6 12134 13 + 197743 CAACTAGGCATTA +s Anc2.Anc2refChr17 5146 13 + 28526 CAACTAGGCATTA +s mr.mrrefChr5 195792 13 + 294540 CAACTGGGCATTA +s mr.mrrefChr5 195312 13 + 294540 CAACTGGACATTA +s simCow_chr6.simCow.chr6 320409 13 + 602619 CAACTAGGCATTA +s simDog_chr6.simDog.chr6 312590 12 + 593897 TAACTGAGCAAT- +s simHuman_chr6.simHuman.chr6 332217 13 + 601863 CAATTAGACATTA +s simMouse_chr6.simMouse.chr6 348002 13 + 636262 CAACTGGACATTA +s simRat_chr6.simRat.chr6 339422 13 + 647215 CAACTGGACATTA +s simRat_chr6.simRat.chr6 339902 13 + 647215 CAACTGGGTATTA + +a +s simMouse_chr6.simMouse.chr6 348497 9 + 636262 AAGATAACA +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 195805 9 + 294540 AAGATAACA +s mr.mrrefChr5 195325 9 + 294540 TAAATTCTA +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 348015 9 + 636262 TAAATTCTA +s simRat_chr6.simRat.chr6 339435 9 + 647215 TAGATTCTA +s simRat_chr6.simRat.chr6 339915 9 + 647215 CAGATTACA + +a +s simMouse_chr6.simMouse.chr6 348506 6 + 636262 TTGGGG +s Anc0.Anc0refChr0 11876 6 + 26507 CCAGGG +s Anc1.Anc1refChr6 12156 6 + 197743 CCAGGG +s Anc2.Anc2refChr17 5166 6 + 28526 CCTTGG +s mr.mrrefChr5 195814 6 + 294540 TTGGGG +s mr.mrrefChr5 195334 6 + 294540 TCAGGG +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 348024 6 + 636262 TCAGGG +s simRat_chr6.simRat.chr6 339444 6 + 647215 TACGGG +s simRat_chr6.simRat.chr6 339924 6 + 647215 TTGGGG + +a +s simMouse_chr6.simMouse.chr6 348512 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 195820 1 + 294540 C +s mr.mrrefChr5 195340 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 348030 1 + 636262 C +s simRat_chr6.simRat.chr6 339450 1 + 647215 C +s simRat_chr6.simRat.chr6 339930 1 + 647215 C + +a s simMouse_chr6.simMouse.chr6 348513 1 + 636262 T s Anc0.Anc0refChr0 11883 1 + 26507 T s Anc1.Anc1refChr6 12163 1 + 197743 T @@ -136184,6 +142284,48 @@ s simRat_chr6.simRat.chr6 339931 1 + 647215 T a +s simMouse_chr6.simMouse.chr6 348514 30 + 636262 GCAACAGTGTGAACAGATGCTCTGGCCCTG +s Anc0.Anc0refChr0 11884 30 + 26507 ACAGCAATGTGGACTACAGGTCTGGACCTG +s Anc1.Anc1refChr6 12164 30 + 197743 ACAGCAATGTGGACTACAGGTCTGGACCTG +s Anc2.Anc2refChr17 5180 30 + 28526 ACACCAATGTGGACTACAGGTCTGGACCTG +s mr.mrrefChr5 195822 30 + 294540 GCAACAGTGTGAACAGTTGGTCTGGACCTG +s mr.mrrefChr5 195341 30 + 294540 ACAGCAGCGTTTACAACTGGTCTGGGCCTG +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 348031 30 + 636262 ACAGCAGCGTTTACAACTGGTCTGGGCCTG +s simRat_chr6.simRat.chr6 339451 30 + 647215 ATTACAATGTGTACAACAGGTCTGGGCCTG +s simRat_chr6.simRat.chr6 339932 30 + 647215 GCAACAGTGTGAACACTGTGTCTGGACCTG + +a +s simMouse_chr6.simMouse.chr6 348544 7 + 636262 TACCATT +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 195852 7 + 294540 TACCATT +s mr.mrrefChr5 195379 7 + 294540 TACCAAT +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 348069 7 + 636262 TACCAAT +s simRat_chr6.simRat.chr6 339496 7 + 647215 TACCAGT +s simRat_chr6.simRat.chr6 339962 7 + 647215 TACCATT + +a +s simMouse_chr6.simMouse.chr6 348551 7 + 636262 TACTGCA +s Anc0.Anc0refChr0 11920 7 + 26507 GGCTGTA +s Anc1.Anc1refChr6 12201 7 + 197743 GGCTGTA +s Anc2.Anc2refChr17 5216 7 + 28526 GGCTGTA +s mr.mrrefChr5 195859 7 + 294540 TACTGCA +s mr.mrrefChr5 195404 7 + 294540 GATTGAG +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 348094 7 + 636262 GATTGAG +s simRat_chr6.simRat.chr6 339521 7 + 647215 GATTAAG +s simRat_chr6.simRat.chr6 339969 7 + 647215 CACTGCA + +a s simMouse_chr6.simMouse.chr6 348558 3 + 636262 CCA s Anc0.Anc0refChr0 11927 3 + 26507 CCA s Anc1.Anc1refChr6 12208 3 + 197743 CCA @@ -142093,6 +148235,34 @@ s simRat_chr6.simRat.chr6 357806 2 + 647215 GT a +s simMouse_chr6.simMouse.chr6 365364 13 + 636262 CACTGTTGGCCGT +s Anc0.Anc0refChr0 361 13 - 26507 CACTGTTGGCACT +s Anc1.Anc1refChr6 170648 13 - 197743 CACTGTTGGCACT +s Anc2.Anc2refChr17 7604 13 - 28526 CACTGTTGGCACT +s mr.mrrefChr5 212446 13 + 294540 CACTGTTGGCCGT +s mr.mrrefChr5 82096 13 - 294540 CTCTGTTGGCAGT +s simCow_chr6.simCow.chr6 263545 13 - 602619 CACTGTTGGCACA +s simDog_chr6.simDog.chr6 265081 13 - 593897 CACTGTTGGCACT +s simHuman_chr6.simHuman.chr6 251014 13 - 601863 CACTGTTGGCACT +s simMouse_chr6.simMouse.chr6 270900 13 - 636262 CTCTGTTGGCAGT +s simRat_chr6.simRat.chr6 289409 13 - 647215 CTCTGTTGGCAGT +s simRat_chr6.simRat.chr6 357808 13 + 647215 CACTGTTGGCCTT + +a +s simMouse_chr6.simMouse.chr6 365377 31 + 636262 ATATGGTGACTCCCCTGGTTCACTGCACTCT +s Anc0.Anc0refChr0 374 31 - 26507 AAATGATAACTCCCCTAGTTCACTGTGCTCT +s Anc1.Anc1refChr6 170661 31 - 197743 AAATGATAACTCCCCTAGTTCACTGTGCTCT +s Anc2.Anc2refChr17 7617 31 - 28526 AAATGATAACTCCCCTAGTCCACTGAGCTCT +s mr.mrrefChr5 212459 31 + 294540 ATATGGTGACTCCCCTGGTTCACTGCACTCT +s mr.mrrefChr5 82109 31 - 294540 GTAGGATGACTCCCCTAGTTAACTGTGCTCT +s simCow_chr6.simCow.chr6 263558 31 - 602619 GAATTATATCTCACCTAGTCCACTGCTCTCT +s simDog_chr6.simDog.chr6 265095 31 - 593897 AAATGGTGACGCCCCTGGGCCACTGAGCTTT +s simHuman_chr6.simHuman.chr6 251027 31 - 601863 AAACGATAAATCCCCTAGTTCATTGTGATCT +s simMouse_chr6.simMouse.chr6 270913 31 - 636262 GTAGGATGACTCCCCTAGTTAACTGTGCTCT +s simRat_chr6.simRat.chr6 289422 31 - 647215 GTAGGATGACTTCCCTAGTTAACTGTGCTCT +s simRat_chr6.simRat.chr6 357821 31 + 647215 ATATGGTGACTCCCCTGGCTCACTGCACTCT + +a s simMouse_chr6.simMouse.chr6 365408 2 + 636262 TG s Anc0.Anc0refChr0 405 2 - 26507 TG s Anc1.Anc1refChr6 170692 2 - 197743 TG @@ -142104,7 +148274,32 @@ s simRat_chr6.simRat.chr6 357852 2 + 647215 TG a -s simMouse_chr6.simMouse.chr6 365426 6 + 636262 TATTAC +s simMouse_chr6.simMouse.chr6 365410 22 + 636262 ACCAATTAAGGAAGCCTATTAC +s Anc0.Anc0refChr0 407 16 - 26507 ACCAATTTAAAAAAAC------ +s Anc1.Anc1refChr6 170694 16 - 197743 ACCAATTTAAAAAAAC------ +s Anc2.Anc2refChr17 7650 16 - 28526 GCCAATTTAAAAAATC------ +s mr.mrrefChr5 212492 16 + 294540 ACCAATTAAGGAAGCC------ +s mr.mrrefChr5 82140 16 - 294540 ACCAGTCGGACAAAAC------ +s simCow_chr6.simCow.chr6 263591 16 - 602619 GCCAATTTAAAACACC------ +s simDog_chr6.simDog.chr6 265128 16 - 593897 GCCAATTTAAAGAATC------ +s simHuman_chr6.simHuman.chr6 251060 15 - 601863 ACCAATCTAAAAAAA------- +s simMouse_chr6.simMouse.chr6 270944 16 - 636262 TCCAGTAGGCCAAGAC------ +s simRat_chr6.simRat.chr6 289453 16 - 647215 ACCAGTCGGACAAAAC------ +s simRat_chr6.simRat.chr6 357854 16 + 647215 ACCAGCTTAGGAAACC------ + +a +s simMouse_chr6.simMouse.chr6 365432 11 + 636262 GATTGGGACTT +s Anc0.Anc0refChr0 432 11 - 26507 AATTGAGACTT +s Anc1.Anc1refChr6 170720 11 - 197743 AATTGAGACTT +s Anc2.Anc2refChr17 7675 11 - 28526 AATCCAGACTT +s mr.mrrefChr5 212508 11 + 294540 GATTGGGACTT +s mr.mrrefChr5 82163 11 - 294540 AATTGAAACTT +s simCow_chr6.simCow.chr6 263618 11 - 602619 AATAAAGACTT +s simDog_chr6.simDog.chr6 265150 11 - 593897 GATCCAGACTT +s simHuman_chr6.simHuman.chr6 251085 11 - 601863 AAGTGAGACTT +s simMouse_chr6.simMouse.chr6 270967 11 - 636262 AATTGAAATCT +s simRat_chr6.simRat.chr6 289476 11 - 647215 AATTGAAGCTT +s simRat_chr6.simRat.chr6 357870 11 + 647215 AATTGAGACTT a s simMouse_chr6.simMouse.chr6 365443 1 + 636262 A @@ -142118,6 +148313,20 @@ s simRat_chr6.simRat.chr6 357881 1 + 647215 G a +s simMouse_chr6.simMouse.chr6 365444 19 + 636262 CACCTACTTGGGGTTATCA +s Anc0.Anc0refChr0 444 18 - 26507 CATCCA-TTGGGGGAATAA +s Anc1.Anc1refChr6 170732 19 - 197743 CATCCACTTGGGGGAATAA +s Anc2.Anc2refChr17 7687 18 - 28526 CATCCA-TTGAGGGACTAG +s mr.mrrefChr5 212520 19 + 294540 CACCTACTTGGGGTTATCA +s mr.mrrefChr5 82174 19 - 294540 CATCTACCTGCGGGAATAA +s simCow_chr6.simCow.chr6 263630 17 - 602619 CATCCG-TC-ATGGACTAA +s simDog_chr6.simDog.chr6 265162 18 - 593897 CATACA-TTGAGGGACTAG +s simHuman_chr6.simHuman.chr6 251097 18 - 601863 CATCCACTTGGGGGAATA- +s simMouse_chr6.simMouse.chr6 270978 19 - 636262 CTTCTACCTGCGGGCATAA +s simRat_chr6.simRat.chr6 289487 19 - 647215 CATCTACCTACGGGAATAA +s simRat_chr6.simRat.chr6 357882 19 + 647215 CACCTGCTTCAGGTAGTAA + +a s simMouse_chr6.simMouse.chr6 365463 5 + 636262 TAGTG s Anc0.Anc0refChr0 462 1 - 26507 ----G s Anc1.Anc1refChr6 170751 2 - 197743 ---TG @@ -142129,11 +148338,150 @@ s simRat_chr6.simRat.chr6 357901 5 + 647215 TAGTG a +s simMouse_chr6.simMouse.chr6 365468 11 + 636262 GGTGTGGCTGC +s Anc0.Anc0refChr0 463 11 - 26507 GGTGGGGAAGC +s Anc1.Anc1refChr6 170753 11 - 197743 GGTGGGGAAGC +s Anc2.Anc2refChr17 7706 11 - 28526 GGTGGGGGAGC +s mr.mrrefChr5 212544 11 + 294540 GGTGTGGCTGC +s mr.mrrefChr5 82193 11 - 294540 GGTGTGGAAGC +s simCow_chr6.simCow.chr6 263648 11 - 602619 GGTGGGTGAGC +s simDog_chr6.simDog.chr6 265181 11 - 593897 GGTGGGGGAGC +s simHuman_chr6.simHuman.chr6 251117 11 - 601863 GATGGGGAAGC +s simMouse_chr6.simMouse.chr6 270997 11 - 636262 GGCGTGGAAGC +s simRat_chr6.simRat.chr6 289506 11 - 647215 GGTGTGGAAGC +s simRat_chr6.simRat.chr6 357906 11 + 647215 GGTGTGGCTGC + +a +s simMouse_chr6.simMouse.chr6 365479 18 + 636262 CTAAAAATATACATGTCT +s Anc0.Anc0refChr0 494 18 - 26507 CTAAAAATATAGGTGTCT +s Anc1.Anc1refChr6 170785 18 - 197743 CTAAAAATATAGGTGTCT +s Anc2.Anc2refChr17 7737 18 - 28526 ATAAAAATACAGGGGTCT +s mr.mrrefChr5 212555 18 + 294540 CTAAAAATATACATGTCT +s mr.mrrefChr5 82220 18 - 294540 CTAAAAATATCAGTGTCT +s simCow_chr6.simCow.chr6 263679 11 - 602619 ATA-------AGGGTTCT +s simDog_chr6.simDog.chr6 265212 18 - 593897 ATAAAAATACAGGGGTCT +s simHuman_chr6.simHuman.chr6 251149 17 - 601863 A-AAAAATGTAGGTGTCT +s simMouse_chr6.simMouse.chr6 271024 18 - 636262 CTAACAGTATCAATGTTT +s simRat_chr6.simRat.chr6 289533 18 - 647215 CTAAAAATATCAGTGTCT +s simRat_chr6.simRat.chr6 357917 18 + 647215 CTAAGAATATATGTGTCT + +a +s simMouse_chr6.simMouse.chr6 365497 3 + 636262 CAA +s Anc0.Anc0refChr0 513 3 - 26507 AAA +s Anc1.Anc1refChr6 170804 3 - 197743 AAA +s Anc2.Anc2refChr17 7756 3 - 28526 AAA +s mr.mrrefChr5 212573 3 + 294540 CAA +s mr.mrrefChr5 82239 3 - 294540 AAA +s simCow_chr6.simCow.chr6 263691 3 - 602619 AAA +s simDog_chr6.simDog.chr6 265231 3 - 593897 AAA +s simHuman_chr6.simHuman.chr6 251167 3 - 601863 AAA +s simMouse_chr6.simMouse.chr6 271043 3 - 636262 AAA +s simRat_chr6.simRat.chr6 289552 3 - 647215 GCA +s simRat_chr6.simRat.chr6 357935 3 + 647215 CAA + +a +s simMouse_chr6.simMouse.chr6 365500 10 + 636262 TAGCTATGTA +s Anc0.Anc0refChr0 516 10 - 26507 TAGCTCTATA +s Anc1.Anc1refChr6 170807 10 - 197743 TAGCTCTATA +s Anc2.Anc2refChr17 7759 10 - 28526 CAGCTCTATA +s mr.mrrefChr5 212576 10 + 294540 TAGCTATGTA +s mr.mrrefChr5 82242 10 - 294540 AAGCTTCATA +s simCow_chr6.simCow.chr6 263694 10 - 602619 CAGCTTTATG +s simDog_chr6.simDog.chr6 265234 10 - 593897 CAACTCTATA +s simHuman_chr6.simHuman.chr6 251170 10 - 601863 TAGCCCTATA +s simMouse_chr6.simMouse.chr6 271046 10 - 636262 AAGCTTCACA +s simRat_chr6.simRat.chr6 289555 10 - 647215 GCGCTTCATA +s simRat_chr6.simRat.chr6 357939 10 + 647215 TAGCCATATA + +a +s simMouse_chr6.simMouse.chr6 365510 2 + 636262 TT +s Anc0.Anc0refChr0 534 2 - 26507 TT +s Anc1.Anc1refChr6 170825 2 - 197743 TT +s Anc2.Anc2refChr17 7777 2 - 28526 CC +s mr.mrrefChr5 212586 2 + 294540 TT +s mr.mrrefChr5 82259 2 - 294540 TT +s simCow_chr6.simCow.chr6 263709 2 - 602619 CC +s simDog_chr6.simDog.chr6 265252 2 - 593897 CC +s simHuman_chr6.simHuman.chr6 251188 2 - 601863 TT +s simMouse_chr6.simMouse.chr6 271063 2 - 636262 TT +s simRat_chr6.simRat.chr6 289572 2 - 647215 TT +s simRat_chr6.simRat.chr6 357949 2 + 647215 TT + +a +s simMouse_chr6.simMouse.chr6 365512 2 + 636262 CT +s Anc0.Anc0refChr0 536 2 - 26507 CT +s Anc1.Anc1refChr6 170827 2 - 197743 CT +s Anc2.Anc2refChr17 7779 2 - 28526 CC +s mr.mrrefChr5 212588 2 + 294540 CT +s mr.mrrefChr5 82261 2 - 294540 TT +s simCow_chr6.simCow.chr6 263711 2 - 602619 CC +s simDog_chr6.simDog.chr6 265254 2 - 593897 CC +s simHuman_chr6.simHuman.chr6 251190 2 - 601863 TT +s simMouse_chr6.simMouse.chr6 271065 2 - 636262 CT +s simRat_chr6.simRat.chr6 289574 2 - 647215 TT +s simRat_chr6.simRat.chr6 357958 2 + 647215 CT + +a +s simMouse_chr6.simMouse.chr6 365514 35 + 636262 GTTGCTTTGAAAACATGTAATTCAAAGCATGTCAG +s Anc0.Anc0refChr0 538 35 - 26507 GTAACTTTGAGAACCCATAATTCAGAATGTGGCAT +s Anc1.Anc1refChr6 170829 35 - 197743 GTAACTTTGAGAACCCATAATTCAGAATGTGGCAT +s Anc2.Anc2refChr17 7782 35 - 28526 GTAACTTTGAGAACCCATAATTCAGAATGTGGCAT +s mr.mrrefChr5 212590 35 + 294540 GTTGCTTTGAAAACATGTAATTCAAAGCATGTCAG +s mr.mrrefChr5 82263 35 - 294540 GTAACTTTGAGAATCCACAATTTGGAATGTGTCAT +s simCow_chr6.simCow.chr6 263714 35 - 602619 GTAACTTTGAGAACCCATAATTCACAGTGTGGCAT +s simDog_chr6.simDog.chr6 265257 25 - 593897 GT----------ACCAATATTCCAGGATGTGACAT +s simHuman_chr6.simHuman.chr6 251192 35 - 601863 TTAACTTTGAGAACTCACAATTCAGATTCTGGCAT +s simMouse_chr6.simMouse.chr6 271067 35 - 636262 GTAACTCTGAGAATCCACGATTTGGAATGTCTCAT +s simRat_chr6.simRat.chr6 289576 35 - 647215 GTAAGTTTGAACATCCACAATTTGGAGTGTGTCAT +s simRat_chr6.simRat.chr6 357960 35 + 647215 GTTGCTTTGAAAACCTATAATTCAAAGCATGTCAG + +a +s simMouse_chr6.simMouse.chr6 365549 1 + 636262 T +s Anc0.Anc0refChr0 573 1 - 26507 G +s Anc1.Anc1refChr6 170864 1 - 197743 G +s Anc2.Anc2refChr17 7817 1 - 28526 G +s mr.mrrefChr5 212625 1 + 294540 T +s mr.mrrefChr5 82298 1 - 294540 G +s simCow_chr6.simCow.chr6 263749 1 - 602619 G +s simDog_chr6.simDog.chr6 265282 1 - 593897 G +s simHuman_chr6.simHuman.chr6 251227 1 - 601863 G +s simMouse_chr6.simMouse.chr6 271102 1 - 636262 G +s simRat_chr6.simRat.chr6 357995 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 365550 3 + 636262 GGC +s Anc0.Anc0refChr0 574 3 - 26507 GCC +s Anc1.Anc1refChr6 170865 3 - 197743 GCC +s Anc2.Anc2refChr17 7818 3 - 28526 GCC +s mr.mrrefChr5 212626 3 + 294540 GGC +s mr.mrrefChr5 82299 3 - 294540 GCC +s simCow_chr6.simCow.chr6 263750 3 - 602619 GCC +s simDog_chr6.simDog.chr6 265283 3 - 593897 GCC +s simHuman_chr6.simHuman.chr6 251228 3 - 601863 GAC +s simMouse_chr6.simMouse.chr6 271103 3 - 636262 GCC +s simRat_chr6.simRat.chr6 289611 3 - 647215 GCC +s simRat_chr6.simRat.chr6 357996 3 + 647215 GGC + +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 365556 3 + 636262 GGT +s Anc0.Anc0refChr0 577 3 - 26507 AGT +s Anc1.Anc1refChr6 170868 3 - 197743 AGT +s Anc2.Anc2refChr17 7821 3 - 28526 AGT +s mr.mrrefChr5 212632 3 + 294540 GGT +s mr.mrrefChr5 82302 3 - 294540 TGA +s simCow_chr6.simCow.chr6 263753 3 - 602619 ATT +s simDog_chr6.simDog.chr6 265286 3 - 593897 AGT +s simHuman_chr6.simHuman.chr6 251231 3 - 601863 AGT +s simMouse_chr6.simMouse.chr6 271106 3 - 636262 TGA +s simRat_chr6.simRat.chr6 289614 3 - 647215 TGA +s simRat_chr6.simRat.chr6 358002 3 + 647215 GGT + +a s simMouse_chr6.simMouse.chr6 365559 71 + 636262 CTCACAAATAATTCCACTGCATAGCTGGAGTATGAGCAATGAGCATCATTGACATCCTCGCTGACTTCCAC s Anc0.Anc0refChr0 26148 66 + 26507 CTTACAGTTAATTCCACTGCACAGCAGGAGAATGACTAATGAGTATCATTCACATCCCCATTGACT----- s Anc1.Anc1refChr6 27097 66 + 197743 CTTACAGTTAATTCCACTGCACAGCAGGAGAATGACTAATGAGTATCATTCACATCCCCATTGACT----- @@ -142244,6 +148592,77 @@ s simRat_chr6.simRat.chr6 358340 95 + 647215 GAGGCGGAATACTCATCATCCAATTGCAGCATATTACCTGGTACTATGGTCCTACTTTCTGCCTGATGAATGGTTCCTGGACAAGTGTGAGCATA a +s simMouse_chr6.simMouse.chr6 365977 2 + 636262 TC +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 213056 2 + 294540 TC +s mr.mrrefChr5 35359 2 + 294540 TT +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 436319 2 - 601863 TC +s simHuman_chr6.simHuman.chr6 351186 2 + 601863 TT +s simMouse_chr6.simMouse.chr6 180103 2 + 636262 TT +s simRat_chr6.simRat.chr6 170306 2 + 647215 TT +s simRat_chr6.simRat.chr6 358435 2 + 647215 TC + +a +s simMouse_chr6.simMouse.chr6 365979 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 213058 1 + 294540 T +s mr.mrrefChr5 35362 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 436322 1 - 601863 T +s simHuman_chr6.simHuman.chr6 351189 1 + 601863 T +s simMouse_chr6.simMouse.chr6 180106 1 + 636262 T +s simRat_chr6.simRat.chr6 170309 1 + 647215 T +s simRat_chr6.simRat.chr6 358437 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 365980 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 213059 2 + 294540 CT +s mr.mrrefChr5 35363 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 436323 2 - 601863 GT +s simHuman_chr6.simHuman.chr6 351190 2 + 601863 GT +s simMouse_chr6.simMouse.chr6 180107 2 + 636262 CT +s simRat_chr6.simRat.chr6 170310 2 + 647215 CT +s simRat_chr6.simRat.chr6 358438 2 + 647215 CT + +a +s simMouse_chr6.simMouse.chr6 365982 3 + 636262 TAA +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 213061 3 + 294540 TAA +s mr.mrrefChr5 35365 3 + 294540 TTG +s simCow_chr6.simCow.chr6 434998 3 - 602619 TAG +s simDog_chr6.simDog.chr6 143141 3 + 593897 TTG +s simHuman_chr6.simHuman.chr6 436325 3 - 601863 TTG +s simHuman_chr6.simHuman.chr6 351192 3 + 601863 TTG +s simMouse_chr6.simMouse.chr6 180109 3 + 636262 TTG +s simRat_chr6.simRat.chr6 170312 3 + 647215 TTG +s simRat_chr6.simRat.chr6 358440 3 + 647215 TAA + +a s simMouse_chr6.simMouse.chr6 365985 5 + 636262 GATCT s Anc1.Anc1refChr6 27465 5 + 197743 TATCT s mr.mrrefChr5 213064 5 + 294540 TATCT @@ -142251,6 +148670,41 @@ s simRat_chr6.simRat.chr6 358443 5 + 647215 TATCA a +s simMouse_chr6.simMouse.chr6 365990 1 + 636262 T +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 213069 1 + 294540 T +s mr.mrrefChr5 35368 1 + 294540 C +s simCow_chr6.simCow.chr6 435001 1 - 602619 C +s simDog_chr6.simDog.chr6 143144 1 + 593897 C +s simHuman_chr6.simHuman.chr6 436328 1 - 601863 C +s simHuman_chr6.simHuman.chr6 351200 1 + 601863 C +s simMouse_chr6.simMouse.chr6 180112 1 + 636262 C +s simRat_chr6.simRat.chr6 170315 1 + 647215 C +s simRat_chr6.simRat.chr6 358448 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 365991 9 + 636262 ATTTACATA +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 213070 9 + 294540 ATTTACATA +s mr.mrrefChr5 35369 9 + 294540 ATGTATATG +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 436329 9 - 601863 ATCTACATG +s simHuman_chr6.simHuman.chr6 351201 9 + 601863 ATCTACATA +s simMouse_chr6.simMouse.chr6 180113 9 + 636262 ATGTATATG +s simRat_chr6.simRat.chr6 170316 9 + 647215 ATATATATG +s simRat_chr6.simRat.chr6 358449 9 + 647215 ATTTGTATA + +a s simMouse_chr6.simMouse.chr6 366000 2 + 636262 CA s Anc0.Anc0refChr1 12836 2 + 62388 CA s Anc1.Anc1refChr6 27480 2 + 197743 CA @@ -142273,6 +148727,44 @@ s simRat_chr6.simRat.chr6 358460 2 + 647215 CA a +s simMouse_chr6.simMouse.chr6 366004 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 213083 1 + 294540 T +s mr.mrrefChr5 35378 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 436338 1 - 601863 T +s simHuman_chr6.simHuman.chr6 351215 1 + 601863 T +s simMouse_chr6.simMouse.chr6 180122 1 + 636262 T +s simRat_chr6.simRat.chr6 170325 1 + 647215 T +s simRat_chr6.simRat.chr6 358462 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 366005 6 + 636262 ATAAGG +s Anc0.Anc0refChr1 12841 6 + 62388 CTAAGC +s Anc1.Anc1refChr2 13643 6 - 144309 CTACAC +s Anc1.Anc1refChr6 27485 6 + 197743 CTAAGC +s Anc2.Anc2refChr3 14023 6 - 53186 CTAAGC +s Anc2.Anc2refChr17 21326 6 + 28526 CTAAGC +s mr.mrrefChr5 213084 6 + 294540 ATAAGG +s mr.mrrefChr5 35379 6 + 294540 CTACAC +s simCow_chr6.simCow.chr6 339462 6 + 602619 CTAAGC +s simCow_chr6.simCow.chr6 435012 3 - 602619 CT---C +s simDog_chr6.simDog.chr6 329212 6 + 593897 CTAAGC +s simDog_chr6.simDog.chr6 143155 6 + 593897 CTAAGC +s simHuman_chr6.simHuman.chr6 436349 6 - 601863 CTACAT +s simHuman_chr6.simHuman.chr6 351216 5 + 601863 CTAAG- +s simMouse_chr6.simMouse.chr6 180123 6 + 636262 CTACAC +s simRat_chr6.simRat.chr6 170326 6 + 647215 CTAAAC +s simRat_chr6.simRat.chr6 358463 6 + 647215 ATGAGT + +a s simMouse_chr6.simMouse.chr6 366011 2 + 636262 TT s Anc0.Anc0refChr1 12847 2 + 62388 TT s Anc1.Anc1refChr6 27491 2 + 197743 TT @@ -142287,6 +148779,25 @@ s simRat_chr6.simRat.chr6 358469 2 + 647215 TT a +s simMouse_chr6.simMouse.chr6 366013 2 + 636262 TG +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 213092 2 + 294540 TG +s mr.mrrefChr5 35385 2 + 294540 TC +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 436355 2 - 601863 TT +s simHuman_chr6.simHuman.chr6 351222 2 + 601863 TC +s simMouse_chr6.simMouse.chr6 180129 2 + 636262 TC +s simRat_chr6.simRat.chr6 170332 2 + 647215 TC +s simRat_chr6.simRat.chr6 358471 2 + 647215 TG + +a s simMouse_chr6.simMouse.chr6 366015 1 + 636262 A s Anc1.Anc1refChr6 27495 1 + 197743 A s mr.mrrefChr5 213094 1 + 294540 A @@ -142294,7 +148805,61 @@ s simRat_chr6.simRat.chr6 358473 1 + 647215 A a -s simMouse_chr6.simMouse.chr6 366025 2 + 636262 GT +s simMouse_chr6.simMouse.chr6 366016 1 + 636262 T +s Anc0.Anc0refChr1 12851 1 + 62388 T +s Anc1.Anc1refChr2 13651 1 - 144309 T +s Anc1.Anc1refChr6 27496 1 + 197743 T +s Anc2.Anc2refChr3 14033 1 - 53186 T +s Anc2.Anc2refChr17 21336 1 + 28526 T +s mr.mrrefChr5 213095 1 + 294540 T +s mr.mrrefChr5 35387 1 + 294540 T +s simCow_chr6.simCow.chr6 339472 1 + 602619 T +s simCow_chr6.simCow.chr6 435020 1 - 602619 T +s simDog_chr6.simDog.chr6 329222 1 + 593897 T +s simDog_chr6.simDog.chr6 143165 1 + 593897 T +s simHuman_chr6.simHuman.chr6 436357 1 - 601863 C +s simHuman_chr6.simHuman.chr6 351225 1 + 601863 T +s simMouse_chr6.simMouse.chr6 180131 1 + 636262 T +s simRat_chr6.simRat.chr6 170334 1 + 647215 T +s simRat_chr6.simRat.chr6 358474 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 366017 1 + 636262 C +s Anc0.Anc0refChr1 12852 1 + 62388 C +s Anc1.Anc1refChr2 13652 1 - 144309 T +s Anc1.Anc1refChr6 27497 1 + 197743 C +s Anc2.Anc2refChr3 14034 1 - 53186 T +s Anc2.Anc2refChr17 21337 1 + 28526 C +s mr.mrrefChr5 213096 1 + 294540 C +s mr.mrrefChr5 35388 1 + 294540 C +s simCow_chr6.simCow.chr6 339473 1 + 602619 T +s simCow_chr6.simCow.chr6 435021 1 - 602619 T +s simDog_chr6.simDog.chr6 329223 1 + 593897 C +s simDog_chr6.simDog.chr6 143166 1 + 593897 T +s simHuman_chr6.simHuman.chr6 436358 1 - 601863 T +s simHuman_chr6.simHuman.chr6 351226 1 + 601863 C +s simMouse_chr6.simMouse.chr6 180134 1 + 636262 C +s simRat_chr6.simRat.chr6 170335 1 + 647215 C +s simRat_chr6.simRat.chr6 358475 1 + 647215 C + +a +s simMouse_chr6.simMouse.chr6 366018 26 + 636262 ACTTGGTGTAGATAGATATGTTAGTT +s Anc0.Anc0refChr1 12854 24 + 62388 GTTCATT--AAACATATATCTTGGTT +s Anc1.Anc1refChr2 13654 24 - 144309 GTTCATC--AAACATATATCTTGGCT +s Anc1.Anc1refChr6 27499 24 + 197743 GTTTATT--AAATATATATCTTGGTT +s Anc2.Anc2refChr3 14036 24 - 53186 GTTCATC--AAACATATATCTTGGTT +s Anc2.Anc2refChr17 21339 24 + 28526 GTTCATT--AAACATATATCTTGGTT +s mr.mrrefChr5 213097 24 + 294540 ACTTGGT--AGATAGATATGTTAGTT +s mr.mrrefChr5 35390 24 + 294540 GATCATC--AAACACATATTTTGACT +s simCow_chr6.simCow.chr6 339475 24 + 602619 GTTCATA--AGACATATATCCTGGCT +s simCow_chr6.simCow.chr6 435023 24 - 602619 GTCTGTC--AAACATATGACTTGTTT +s simDog_chr6.simDog.chr6 329225 24 + 593897 GTTCATT--AAACATATATCTTGGTT +s simDog_chr6.simDog.chr6 143168 24 + 593897 GCTCATC--ACACCAATATCATAGTT +s simHuman_chr6.simHuman.chr6 436374 24 - 601863 CTTCATC--AAATATATATCTTGGCT +s simHuman_chr6.simHuman.chr6 351228 24 + 601863 GTTTATC--ACCTCCATATTTTGGTT +s simMouse_chr6.simMouse.chr6 180136 24 + 636262 GATCATC--AAACACATATTTTGACT +s simRat_chr6.simRat.chr6 170337 24 + 647215 GCTCACC--AAACACATATTTTGATT +s simRat_chr6.simRat.chr6 358476 24 + 647215 ACTAGGT--AGATAGATACCTCAGTT a s simMouse_chr6.simMouse.chr6 366044 6 + 636262 AATGAA @@ -142313,6 +148878,44 @@ s simRat_chr6.simRat.chr6 358500 6 + 647215 AGTGAA a +s simMouse_chr6.simMouse.chr6 366050 13 + 636262 ACAGTTATACAAA +s Anc0.Anc0refChr1 12884 13 + 62388 ACAGATATACAAA +s Anc1.Anc1refChr2 13684 13 - 144309 ACAGATATACAAA +s Anc1.Anc1refChr6 27529 13 + 197743 ACAGATATACAAA +s Anc2.Anc2refChr3 14066 13 - 53186 ACAGATATACAAA +s Anc2.Anc2refChr17 21369 13 + 28526 ACAGATATACTAA +s mr.mrrefChr5 213127 13 + 294540 ACAGTTATACAAA +s mr.mrrefChr5 35414 13 + 294540 CTACGTATACAAA +s simCow_chr6.simCow.chr6 339505 13 + 602619 ACAGATATACCAA +s simCow_chr6.simCow.chr6 435053 13 - 602619 ACAGATACACAAA +s simDog_chr6.simDog.chr6 329255 13 + 593897 ACAGATATATTAA +s simDog_chr6.simDog.chr6 143198 13 + 593897 ACTTATATACAAC +s simHuman_chr6.simHuman.chr6 436404 13 - 601863 TCAGCTATACAGA +s simHuman_chr6.simHuman.chr6 351257 13 + 601863 ACAGATATACAAA +s simMouse_chr6.simMouse.chr6 180160 13 + 636262 CTACGCATACAAA +s simRat_chr6.simRat.chr6 170361 13 + 647215 CTATGTATACAAA +s simRat_chr6.simRat.chr6 358506 11 + 647215 A--GGTATACAAA + +a +s simMouse_chr6.simMouse.chr6 366063 18 + 636262 GAGTGGTTAAGGTAACAG +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 213140 18 + 294540 GAGTGGTTAAGGTAGCAG +s mr.mrrefChr5 35427 18 + 294540 GAGAATTTGCAGAGTAAA +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 436417 18 - 601863 GGGTAGTTGAGGGAGCAG +s simHuman_chr6.simHuman.chr6 351270 18 + 601863 GAGTAGTTGGGGCAGGAG +s simMouse_chr6.simMouse.chr6 180173 18 + 636262 GAGAATTTGCAGAGTAAA +s simRat_chr6.simRat.chr6 170374 18 + 647215 GAGAATTTGCAGAGTAGA +s simRat_chr6.simRat.chr6 358517 18 + 647215 GAGTGAGTAAGATGGCAG + +a s simMouse_chr6.simMouse.chr6 366081 1 + 636262 A s Anc0.Anc0refChr1 12915 1 + 62388 A s Anc1.Anc1refChr6 27560 1 + 197743 A @@ -142324,6 +148927,118 @@ s simRat_chr6.simRat.chr6 358535 1 + 647215 A a +s simMouse_chr6.simMouse.chr6 366082 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 213159 2 + 294540 AA +s mr.mrrefChr5 35445 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 436435 2 - 601863 AA +s simHuman_chr6.simHuman.chr6 351289 2 + 601863 AA +s simMouse_chr6.simMouse.chr6 180191 2 + 636262 AA +s simRat_chr6.simRat.chr6 170392 2 + 647215 AA +s simRat_chr6.simRat.chr6 358536 2 + 647215 AA + +a +s simMouse_chr6.simMouse.chr6 366084 3 + 636262 CCT +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 213161 3 + 294540 CCT +s mr.mrrefChr5 35447 3 + 294540 TCT +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 436437 3 - 601863 TCT +s simHuman_chr6.simHuman.chr6 351291 3 + 601863 TCT +s simMouse_chr6.simMouse.chr6 180193 3 + 636262 TCT +s simRat_chr6.simRat.chr6 170394 3 + 647215 TCT +s simRat_chr6.simRat.chr6 358538 3 + 647215 CCT + +a +s simMouse_chr6.simMouse.chr6 366087 5 + 636262 CCAAC +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 213164 5 + 294540 CCAAC +s mr.mrrefChr5 35450 5 + 294540 CTCAA +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 436440 5 - 601863 CTCAA +s simHuman_chr6.simHuman.chr6 351294 5 + 601863 CTAAA +s simMouse_chr6.simMouse.chr6 180196 5 + 636262 ATAAA +s simRat_chr6.simRat.chr6 170397 5 + 647215 CTCAA +s simRat_chr6.simRat.chr6 358541 5 + 647215 CCAAT + +a +s simMouse_chr6.simMouse.chr6 366092 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 213169 4 + 294540 CATG +s mr.mrrefChr5 35455 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 436445 4 - 601863 CATG +s simHuman_chr6.simHuman.chr6 351299 4 + 601863 TCTG +s simMouse_chr6.simMouse.chr6 180201 4 + 636262 CATG +s simRat_chr6.simRat.chr6 170402 4 + 647215 CATG +s simRat_chr6.simRat.chr6 358546 4 + 647215 CATG + +a +s simMouse_chr6.simMouse.chr6 366096 15 + 636262 AAAGCAGTGCTTTCA +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 213173 15 + 294540 AAAGCAGTGCTTTCA +s mr.mrrefChr5 35459 15 + 294540 AAAGTGGAGCTCCCA +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 436449 15 - 601863 ACAGCAGTGCTCTCA +s simHuman_chr6.simHuman.chr6 351303 15 + 601863 AAAGCAGATCTCTCA +s simMouse_chr6.simMouse.chr6 180205 15 + 636262 AAAGTGGAGCTCCCA +s simRat_chr6.simRat.chr6 170406 15 + 647215 AAAGTGGAGCTCCCA +s simRat_chr6.simRat.chr6 358550 15 + 647215 AAAGCAGCGCTTTCC + +a +s simMouse_chr6.simMouse.chr6 366111 7 + 636262 GATGTGT +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 213188 7 + 294540 GATGTGT +s mr.mrrefChr5 35475 7 + 294540 GTTGTGC +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 436465 7 - 601863 ACTGGGC +s simHuman_chr6.simHuman.chr6 351319 7 + 601863 GCTGTGT +s simMouse_chr6.simMouse.chr6 180221 7 + 636262 GTTGTGC +s simRat_chr6.simRat.chr6 170422 7 + 647215 GTTGTGT +s simRat_chr6.simRat.chr6 358565 7 + 647215 AGTCTGT + +a s simMouse_chr6.simMouse.chr6 366118 1 + 636262 C s Anc0.Anc0refChr1 12953 1 + 62388 C s Anc1.Anc1refChr2 13752 1 - 144309 C @@ -142340,6 +149055,25 @@ s simRat_chr6.simRat.chr6 358572 1 + 647215 C a +s simMouse_chr6.simMouse.chr6 366119 6 + 636262 AGGGCT +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 213196 6 + 294540 ATGGCT +s mr.mrrefChr5 35482 6 + 294540 GTGGTG +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 436473 6 - 601863 ATAGTG +s simHuman_chr6.simHuman.chr6 351327 6 + 601863 ATGGTG +s simMouse_chr6.simMouse.chr6 180228 6 + 636262 GTGGTG +s simRat_chr6.simRat.chr6 170429 6 + 647215 GTGGTG +s simRat_chr6.simRat.chr6 358573 6 + 647215 ATGGCC + +a s simMouse_chr6.simMouse.chr6 366125 2 + 636262 GA s Anc0.Anc0refChr1 12960 2 + 62388 GA s Anc1.Anc1refChr6 27605 2 + 197743 GA @@ -142351,6 +149085,99 @@ s simRat_chr6.simRat.chr6 358579 2 + 647215 AG a +s simMouse_chr6.simMouse.chr6 366127 4 + 636262 GAGG +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 213204 4 + 294540 GAGG +s mr.mrrefChr5 35488 4 + 294540 CACT +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 436479 4 - 601863 TACT +s simHuman_chr6.simHuman.chr6 351335 4 + 601863 AACG +s simMouse_chr6.simMouse.chr6 180234 4 + 636262 CACT +s simRat_chr6.simRat.chr6 170435 4 + 647215 CACT +s simRat_chr6.simRat.chr6 358581 4 + 647215 GAGG + +a +s simMouse_chr6.simMouse.chr6 366131 3 + 636262 ACC +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 213208 3 + 294540 ACC +s mr.mrrefChr5 35492 3 + 294540 GTG +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 436483 3 - 601863 ATG +s simHuman_chr6.simHuman.chr6 351348 3 + 601863 ATC +s simMouse_chr6.simMouse.chr6 180238 3 + 636262 GTG +s simRat_chr6.simRat.chr6 170439 3 + 647215 GTG +s simRat_chr6.simRat.chr6 358585 3 + 647215 ACC + +a +s simMouse_chr6.simMouse.chr6 366134 3 + 636262 ACC +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 213211 3 + 294540 ACC +s mr.mrrefChr5 35495 3 + 294540 CAT +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 436489 3 - 601863 CAT +s simHuman_chr6.simHuman.chr6 351351 3 + 601863 AGT +s simMouse_chr6.simMouse.chr6 180241 3 + 636262 CAT +s simRat_chr6.simRat.chr6 170442 3 + 647215 CAT +s simRat_chr6.simRat.chr6 358588 3 + 647215 ACC + +a +s simMouse_chr6.simMouse.chr6 366137 8 + 636262 CAACCTAA +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 213214 8 + 294540 CAACCTAA +s mr.mrrefChr5 35517 8 + 294540 AGCGTAGT +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 436511 8 - 601863 AAAGTTAT +s simHuman_chr6.simHuman.chr6 351354 8 + 601863 CCACCTAT +s simMouse_chr6.simMouse.chr6 180263 8 + 636262 AGCGTAGT +s simRat_chr6.simRat.chr6 358591 8 + 647215 CAACCCTA + +a +s simMouse_chr6.simMouse.chr6 366145 4 + 636262 CTCC +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 213222 4 + 294540 CTCC +s mr.mrrefChr5 35529 4 + 294540 CTCT +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 436523 4 - 601863 CTTT +s simHuman_chr6.simHuman.chr6 351362 4 + 601863 CACT +s simMouse_chr6.simMouse.chr6 180275 4 + 636262 CTCT +s simRat_chr6.simRat.chr6 358599 4 + 647215 TTCA + +a s simMouse_chr6.simMouse.chr6 366149 4 + 636262 CTCT s Anc0.Anc0refChr2 0 1 + 17989 G--- s Anc1.Anc1refChr6 27629 4 + 197743 GTCT @@ -145269,22 +152096,22 @@ 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 +s simMouse_chr6.simMouse.chr6 373349 11 + 636262 GTATGATTGCA +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 7 + 294540 GGATGA----A +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 373190 7 + 636262 GGGTCA----G +s simRat_chr6.simRat.chr6 365452 7 + 647215 GGATGA----A + +a +s simMouse_chr6.simMouse.chr6 373360 162 + 636262 GGCCTGTAAGATTCTGACTCATTATTAGAGGTTTGATGCTCATTGTTACTTACCAAATTGTACCCCGGTGGGTCATGTCCTCCAGGAAGAGCCAGTACATGATCCAACCCAGTTCTGGAGCAGATCCAATCTACCCTTTCTCAGCTATATGAATCATTCTGC +s mr.mrrefChr5 219982 161 + 294540 GGCCTGTAACATTCTGACTCATTATTAGATGTTTGATTTTGATGTCCACTTACCAAATTGTACTCCTGTGGGTCATGTTCTCCAG-AAGAGCCAGTACATGATCCAACCCAGTTCTGGAGCAGATCCAATCTACCCTTTCTCAGCTATATGAATCATTCTGC +s simMouse_chr6.simMouse.chr6 373267 82 + 636262 GGCCTG-AACATTCTGTCTCATTATTTGATGTTTGAGTTTGATGTCCACTTA-CAAATTGTACTCCTGTGGGTCATGTTCTCCA------------------------------------------------------------------------------ +s simRat_chr6.simRat.chr6 365459 161 + 647215 GGCCTGTAAAATTCTGACTCATTATTAGATGTTTGATTTTTGTGTCCCTTTACAAAATAGTACTCCTGTGGGTCATGTTCCCCAA-ATTAACCTGTACATGATCCAACCCAGTGCTGGAGCAGATGCAATCTGCCCTTTATCAGGTATATGATTCCTTTTGC a s simMouse_chr6.simMouse.chr6 373522 126 + 636262 TATTAGCAAATTTCCTTTTCTATTAGGCTGTTATTACCCTAATACAACATTCTGAGCTGACAGCCTTAACCACTGGCAAACATGCTGGCATGGATGAAATACAGATCCTTACCTTTGGGCCTGCTA @@ -145292,12 +152119,492 @@ s simRat_chr6.simRat.chr6 365627 120 + 647215 TATTAGGTAATTTCCTTTTCCATTAGGCTGTTATTAAC-TAATACAACATTCTGAGCTGCCAGCCTTAACCACTGGCAAACATGCTGGCATAGAAAAGATAAAGAATCTCACCTTT-----TGCTA a +s simMouse_chr6.simMouse.chr6 373648 2 + 636262 GG +s Anc0.Anc0refChr2 6526 2 + 17989 GG +s Anc1.Anc1refChr6 34610 2 + 197743 GG +s Anc2.Anc2refChr17 28480 2 + 28526 TC +s mr.mrrefChr0 119577 2 - 130230 GG +s mr.mrrefChr5 220263 2 + 294540 GG +s simCow_chr6.simCow.chr6 346006 2 + 602619 GA +s simDog_chr6.simDog.chr6 336873 2 + 593897 TC +s simMouse_chr6.simMouse.chr6 624670 2 - 636262 GG +s simRat_chr6.simRat.chr6 636176 2 - 647215 GG +s simRat_chr6.simRat.chr6 365747 2 + 647215 GG + +a +s simMouse_chr6.simMouse.chr6 373650 5 + 636262 ATCTC +s Anc0.Anc0refChr2 6528 5 + 17989 ATCCC +s Anc1.Anc1refChr6 34612 5 + 197743 ATCCC +s Anc2.Anc2refChr17 28482 5 + 28526 ATACA +s mr.mrrefChr0 119688 5 - 130230 ATCCC +s mr.mrrefChr0 10664 5 + 130230 ATCCC +s mr.mrrefChr5 220265 5 + 294540 ATCTC +s simCow_chr6.simCow.chr6 346008 5 + 602619 GCACT +s simDog_chr6.simDog.chr6 336875 5 + 593897 ATACA +s simMouse_chr6.simMouse.chr6 624781 5 - 636262 ATCCC +s simMouse_chr6.simMouse.chr6 11603 5 + 636262 ATCCC +s simRat_chr6.simRat.chr6 636287 5 - 647215 CTCCC +s simRat_chr6.simRat.chr6 11050 5 + 647215 ACCCC +s simRat_chr6.simRat.chr6 365749 5 + 647215 ATCTC + +a +s simMouse_chr6.simMouse.chr6 373655 1 + 636262 A +s Anc0.Anc0refChr2 6533 1 + 17989 A +s Anc1.Anc1refChr6 34617 1 + 197743 A +s Anc2.Anc2refChr17 28491 1 + 28526 A +s mr.mrrefChr0 119693 1 - 130230 A +s mr.mrrefChr0 10669 1 + 130230 A +s mr.mrrefChr5 220270 1 + 294540 A +s simCow_chr6.simCow.chr6 346017 1 + 602619 A +s simDog_chr6.simDog.chr6 336884 1 + 593897 A +s simMouse_chr6.simMouse.chr6 624786 1 - 636262 A +s simMouse_chr6.simMouse.chr6 11608 1 + 636262 A +s simRat_chr6.simRat.chr6 636292 1 - 647215 A +s simRat_chr6.simRat.chr6 11055 1 + 647215 A +s simRat_chr6.simRat.chr6 365754 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 373656 3 + 636262 AGC +s Anc0.Anc0refChr2 6534 3 + 17989 AGC +s Anc1.Anc1refChr6 34618 3 + 197743 AGC +s Anc2.Anc2refChr17 28492 3 + 28526 AGA +s mr.mrrefChr0 119694 3 - 130230 GGT +s mr.mrrefChr0 10670 3 + 130230 ACC +s mr.mrrefChr5 220271 3 + 294540 AGC +s simCow_chr6.simCow.chr6 346018 3 + 602619 AGA +s simDog_chr6.simDog.chr6 336885 3 + 593897 AGA +s simMouse_chr6.simMouse.chr6 624787 3 - 636262 GGT +s simMouse_chr6.simMouse.chr6 11609 3 + 636262 ACC +s simRat_chr6.simRat.chr6 636293 3 - 647215 GGC +s simRat_chr6.simRat.chr6 11058 3 + 647215 ATC +s simRat_chr6.simRat.chr6 365755 3 + 647215 AGA + +a +s simMouse_chr6.simMouse.chr6 373659 3 + 636262 CCA +s Anc0.Anc0refChr2 6537 3 + 17989 TCA +s Anc1.Anc1refChr6 34621 3 + 197743 TCA +s Anc2.Anc2refChr17 28495 3 + 28526 TCA +s mr.mrrefChr0 119697 3 - 130230 TCA +s mr.mrrefChr0 10673 3 + 130230 TCA +s mr.mrrefChr5 220274 3 + 294540 CCA +s simCow_chr6.simCow.chr6 346021 3 + 602619 TAA +s simDog_chr6.simDog.chr6 336888 3 + 593897 TCA +s simMouse_chr6.simMouse.chr6 624790 3 - 636262 TCA +s simMouse_chr6.simMouse.chr6 11612 3 + 636262 TCA +s simRat_chr6.simRat.chr6 636296 3 - 647215 TCA +s simRat_chr6.simRat.chr6 11067 3 + 647215 TCA +s simRat_chr6.simRat.chr6 365758 3 + 647215 CTA + +a +s simMouse_chr6.simMouse.chr6 373662 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 11616 3 + 636262 TCA +s simRat_chr6.simRat.chr6 11071 3 + 647215 TTA +s simRat_chr6.simRat.chr6 365761 3 + 647215 TCA + +a +s simMouse_chr6.simMouse.chr6 373665 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 11619 2 + 636262 GA +s simRat_chr6.simRat.chr6 11074 2 + 647215 GA +s simRat_chr6.simRat.chr6 365764 2 + 647215 GA + +a +s simMouse_chr6.simMouse.chr6 373667 2 + 636262 AA +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 11621 2 + 636262 AG +s simRat_chr6.simRat.chr6 11076 2 + 647215 GT +s simRat_chr6.simRat.chr6 365766 2 + 647215 AA + +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 +s simMouse_chr6.simMouse.chr6 373675 4 + 636262 AAAG +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 11623 4 + 636262 AAAA +s simRat_chr6.simRat.chr6 11078 4 + 647215 AAGG +s simRat_chr6.simRat.chr6 365774 4 + 647215 AAAG + +a +s simMouse_chr6.simMouse.chr6 373679 4 + 636262 AGGG +s Anc0.Anc0refChr2 6551 4 + 17989 ACAG +s Anc1.Anc1refChr2 113615 4 - 144309 ACAG +s Anc1.Anc1refChr6 34635 4 + 197743 ATAC +s Anc2.Anc2refChr0 51606 4 + 56053 ACAG +s mr.mrrefChr0 119700 4 - 130230 ATAC +s mr.mrrefChr0 10688 4 + 130230 ATAC +s mr.mrrefChr5 220294 4 + 294540 AGGG +s simCow_chr6.simCow.chr6 55081 4 + 602619 ACAG +s simDog_chr6.simDog.chr6 48656 4 + 593897 ACAG +s simHuman_chr6.simHuman.chr6 551636 4 - 601863 ACAG +s simMouse_chr6.simMouse.chr6 624793 4 - 636262 ATAC +s simMouse_chr6.simMouse.chr6 11627 4 + 636262 ATAC +s simRat_chr6.simRat.chr6 636299 4 - 647215 ACAC +s simRat_chr6.simRat.chr6 11082 4 + 647215 ATAC +s simRat_chr6.simRat.chr6 365778 4 + 647215 AGAG + +a +s simMouse_chr6.simMouse.chr6 373683 2 + 636262 GT +s Anc0.Anc0refChr2 6555 2 + 17989 GG +s Anc1.Anc1refChr2 113619 2 - 144309 GG +s Anc1.Anc1refChr6 34639 2 + 197743 GT +s Anc2.Anc2refChr0 51610 2 + 56053 GG +s mr.mrrefChr0 119704 2 - 130230 GC +s mr.mrrefChr0 10692 2 + 130230 TT +s mr.mrrefChr5 220298 2 + 294540 GT +s simCow_chr6.simCow.chr6 55085 2 + 602619 GG +s simDog_chr6.simDog.chr6 48660 2 + 593897 GG +s simHuman_chr6.simHuman.chr6 551640 2 - 601863 AG +s simMouse_chr6.simMouse.chr6 624797 2 - 636262 GC +s simMouse_chr6.simMouse.chr6 11632 2 + 636262 TT +s simRat_chr6.simRat.chr6 636303 2 - 647215 GC +s simRat_chr6.simRat.chr6 11086 2 + 647215 TT +s simRat_chr6.simRat.chr6 365782 2 + 647215 AT + +a +s simMouse_chr6.simMouse.chr6 373685 3 + 636262 CCA +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 11634 3 + 636262 TCA +s simRat_chr6.simRat.chr6 11088 3 + 647215 TCA +s simRat_chr6.simRat.chr6 365784 3 + 647215 CCA + +a +s simMouse_chr6.simMouse.chr6 373688 9 + 636262 GTATTATCA +s Anc0.Anc0refChr2 6560 9 + 17989 GTGTTAAGA +s Anc1.Anc1refChr2 113624 9 - 144309 GTGTTAAGA +s Anc1.Anc1refChr6 34644 9 + 197743 GTATTATCA +s Anc2.Anc2refChr0 51615 9 + 56053 GTGTTAAGA +s mr.mrrefChr0 119706 9 - 130230 GTATTAACA +s mr.mrrefChr0 10697 9 + 130230 GTATTAGCA +s mr.mrrefChr5 220303 9 + 294540 GTATTATCA +s simCow_chr6.simCow.chr6 55090 9 + 602619 GTGTTAAGA +s simDog_chr6.simDog.chr6 48665 9 + 593897 GTGTTAAGA +s simHuman_chr6.simHuman.chr6 551645 9 - 601863 ATGTAAAGA +s simMouse_chr6.simMouse.chr6 624799 9 - 636262 GTATTAACA +s simMouse_chr6.simMouse.chr6 11637 9 + 636262 GTATTAGCA +s simRat_chr6.simRat.chr6 636335 9 - 647215 GTATTAACA +s simRat_chr6.simRat.chr6 11091 9 + 647215 GTATTAGTA +s simRat_chr6.simRat.chr6 365787 9 + 647215 ATATGAACA + +a +s simMouse_chr6.simMouse.chr6 373697 2 + 636262 TG +s Anc0.Anc0refChr2 6569 2 + 17989 TG +s Anc1.Anc1refChr2 113633 2 - 144309 TG +s Anc1.Anc1refChr6 34653 2 + 197743 TG +s Anc2.Anc2refChr0 51624 2 + 56053 TG +s mr.mrrefChr0 119715 2 - 130230 TG +s mr.mrrefChr0 10706 2 + 130230 TG +s mr.mrrefChr5 220312 2 + 294540 TG +s simCow_chr6.simCow.chr6 55099 2 + 602619 TG +s simDog_chr6.simDog.chr6 48674 2 + 593897 TG +s simHuman_chr6.simHuman.chr6 551654 2 - 601863 TG +s simMouse_chr6.simMouse.chr6 624808 2 - 636262 TG +s simMouse_chr6.simMouse.chr6 11646 2 + 636262 TG +s simRat_chr6.simRat.chr6 636346 2 - 647215 TG +s simRat_chr6.simRat.chr6 11100 2 + 647215 TG +s simRat_chr6.simRat.chr6 365796 2 + 647215 TG + +a +s simMouse_chr6.simMouse.chr6 373699 9 + 636262 GAATGTTGA +s Anc0.Anc0refChr2 6571 9 + 17989 AAATGTTAA +s Anc1.Anc1refChr2 113635 9 - 144309 AAATGTTAA +s Anc1.Anc1refChr6 34655 9 + 197743 GAATGTTGA +s Anc2.Anc2refChr0 51626 9 + 56053 AAATGTTAA +s mr.mrrefChr0 119717 9 - 130230 GAAAGTTGT +s mr.mrrefChr0 10708 9 + 130230 AATGCTAAA +s mr.mrrefChr5 220314 9 + 294540 GAATGTTGA +s simCow_chr6.simCow.chr6 55101 8 + 602619 AAATGTTA- +s simDog_chr6.simDog.chr6 48676 9 + 593897 AGATGATAA +s simHuman_chr6.simHuman.chr6 551656 9 - 601863 AAATGTTAA +s simMouse_chr6.simMouse.chr6 624810 9 - 636262 GAAAGTTGT +s simMouse_chr6.simMouse.chr6 11648 9 + 636262 AATGCTAAA +s simRat_chr6.simRat.chr6 636348 9 - 647215 GAATGTTGA +s simRat_chr6.simRat.chr6 11157 9 + 647215 AATTATACA +s simRat_chr6.simRat.chr6 365798 9 + 647215 GAGTGCTGA + +a +s simMouse_chr6.simMouse.chr6 373708 31 + 636262 CCGAGTCTTGAACAGATCTTTATTATCTGGG +s Anc0.Anc0refChr2 6580 31 + 17989 TTCAGTCTTAGAAAGATTTTGATTATCTGGG +s Anc1.Anc1refChr2 113644 31 - 144309 TTCAGTCTTAGAAAGATTTTGATTATCTGGG +s Anc1.Anc1refChr6 34664 31 + 197743 CTCAGTCTTGAACAGATCTTTATTATCTGGG +s Anc2.Anc2refChr0 51635 31 + 56053 TTCAGTCTTAGAAAGATTTTGATTATCTGGG +s mr.mrrefChr0 119726 31 - 130230 CTCAGTCTTGAACAGACCTTTATTATCTGGG +s mr.mrrefChr0 10717 31 + 130230 CTCAGTCTTGGACCAATTCTGATTGTCTAGG +s mr.mrrefChr5 220323 31 + 294540 CCGAGTCTTGAACAGATCTTTATTATCTGGG +s simCow_chr6.simCow.chr6 55109 15 + 602619 -----------AAAGATTTTCATT-----TG +s simDog_chr6.simDog.chr6 48685 31 + 593897 TTCAGTCTTAGATATATTTTGATTATCTGGG +s simHuman_chr6.simHuman.chr6 551665 31 - 601863 CTCAGCCTTGGAAAGCTTTTGATTGTCCAGG +s simMouse_chr6.simMouse.chr6 624819 31 - 636262 CTCAGTCTTGAACAGACCTTTATTATCTGGG +s simMouse_chr6.simMouse.chr6 11657 31 + 636262 CTCAGTCTTGGACCAATTCTGATTGTCTAGG +s simRat_chr6.simRat.chr6 636357 31 - 647215 TTAAGTCTTGAACAGACCTTTATTATCTGGG +s simRat_chr6.simRat.chr6 234007 31 - 647215 CTCAGTCTTGGACAGATTTTGATTGTCTAGG +s simRat_chr6.simRat.chr6 365807 31 + 647215 CTGTATCTTGAACAGATCTTTATTATCTGGG + +a +s simMouse_chr6.simMouse.chr6 373739 11 + 636262 AATGTTCTTTC +s Anc0.Anc0refChr2 6612 11 + 17989 AATGTTCTTTC +s Anc1.Anc1refChr2 113676 11 - 144309 AATGTTCTTTC +s Anc1.Anc1refChr6 34695 11 + 197743 AATGTTCCTTC +s Anc2.Anc2refChr0 51667 11 + 56053 AATGTTCTTTC +s mr.mrrefChr0 119757 11 - 130230 AATGTTCCTTC +s mr.mrrefChr0 10748 11 + 130230 AATTTTCCTTT +s mr.mrrefChr5 220354 11 + 294540 AATGTTCTTTC +s simCow_chr6.simCow.chr6 55125 11 + 602619 AATGTTCTTTT +s simDog_chr6.simDog.chr6 48717 11 + 593897 AGTGTTCCTTC +s simHuman_chr6.simHuman.chr6 551697 11 - 601863 AAAGACGTTTC +s simMouse_chr6.simMouse.chr6 624850 11 - 636262 AATGTTCCTTC +s simMouse_chr6.simMouse.chr6 11688 11 + 636262 AATTTTCCTTT +s simRat_chr6.simRat.chr6 636388 11 - 647215 AATGTTCTTTC +s simRat_chr6.simRat.chr6 234038 11 - 647215 AATATGCCTTT +s simRat_chr6.simRat.chr6 365838 11 + 647215 AATGTTCTCTC + +a +s simMouse_chr6.simMouse.chr6 373750 6 + 636262 TAGTGA +s Anc0.Anc0refChr2 6623 6 + 17989 TTGTAA +s Anc1.Anc1refChr2 113687 6 - 144309 TTGTAA +s Anc1.Anc1refChr6 34706 6 + 197743 TAGTGA +s Anc2.Anc2refChr0 51678 6 + 56053 TTGTAA +s mr.mrrefChr0 119768 6 - 130230 TAGTGA +s mr.mrrefChr0 10759 6 + 130230 TGGTGA +s mr.mrrefChr5 220365 6 + 294540 TAGTGA +s simCow_chr6.simCow.chr6 55136 6 + 602619 TGGTAA +s simDog_chr6.simDog.chr6 48756 6 + 593897 GTCTGA +s simHuman_chr6.simHuman.chr6 551708 6 - 601863 TTGTAA +s simMouse_chr6.simMouse.chr6 624861 6 - 636262 TAGTGA +s simMouse_chr6.simMouse.chr6 11699 6 + 636262 TGGTGA +s simRat_chr6.simRat.chr6 636399 6 - 647215 TAGTGA +s simRat_chr6.simRat.chr6 234049 6 - 647215 TGGTGA +s simRat_chr6.simRat.chr6 365849 6 + 647215 TAGTGA + +a +s simMouse_chr6.simMouse.chr6 373756 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 11705 6 + 636262 CCTGTT +s simRat_chr6.simRat.chr6 234055 6 - 647215 CCTGTT +s simRat_chr6.simRat.chr6 365855 6 + 647215 CCTGTT + +a +s simMouse_chr6.simMouse.chr6 373762 12 + 636262 AGGCAGGGCCCT +s Anc0.Anc0refChr2 6635 12 + 17989 AGGCAGGCCTAT +s Anc1.Anc1refChr2 113699 12 - 144309 AGGCAGGCCTAT +s Anc1.Anc1refChr6 34718 12 + 197743 AGACAGGGCCAT +s Anc2.Anc2refChr0 51690 12 + 56053 AGGCAGGCCTAT +s mr.mrrefChr0 119774 12 - 130230 AGACAGGGTCAT +s mr.mrrefChr0 10771 12 + 130230 GGACAGGGCCAT +s mr.mrrefChr5 220377 12 + 294540 AGGCAGGGCCCT +s simCow_chr6.simCow.chr6 55148 4 + 602619 AGTT-------- +s simDog_chr6.simDog.chr6 48768 12 + 593897 AGGCAGGCCTAT +s simHuman_chr6.simHuman.chr6 551720 12 - 601863 GGGCAGGGCTCT +s simMouse_chr6.simMouse.chr6 624873 12 - 636262 AGACAGGGTCAT +s simMouse_chr6.simMouse.chr6 11711 12 + 636262 GGACAGGGCCAT +s simRat_chr6.simRat.chr6 636405 12 - 647215 AGGCAGAGCCAT +s simRat_chr6.simRat.chr6 234061 12 - 647215 GGACAGGGCCAT +s simRat_chr6.simRat.chr6 365861 12 + 647215 AGGCAGTGCCAT + +a +s simMouse_chr6.simMouse.chr6 373774 16 + 636262 TTGCTCAATACCATTT +s Anc0.Anc0refChr2 6654 16 + 17989 TCATTTAAGTCTAGTT +s Anc1.Anc1refChr2 113718 16 - 144309 TCATTTAAGTCTAGTT +s Anc1.Anc1refChr6 34730 16 + 197743 TTGCTCAATACCATTT +s Anc2.Anc2refChr0 51709 16 + 56053 TCATTTAAGTCTAGTT +s mr.mrrefChr0 119786 16 - 130230 TTGCTCAATACCATTT +s mr.mrrefChr0 10783 16 + 130230 TCGCTCATATTCATTT +s mr.mrrefChr5 220389 16 + 294540 TTGCTCAATACCATTT +s simCow_chr6.simCow.chr6 55152 8 + 602619 --------GTTGAGTT +s simDog_chr6.simDog.chr6 48787 16 + 593897 TCATTTAAGTCTAGTT +s simHuman_chr6.simHuman.chr6 551739 16 - 601863 TTGCTCAAAACCAGTG +s simMouse_chr6.simMouse.chr6 624885 16 - 636262 TTGCTCAATACCATTT +s simMouse_chr6.simMouse.chr6 11723 16 + 636262 TCGCTCATATTCATTT +s simRat_chr6.simRat.chr6 636417 16 - 647215 TTGCTCAATACCATTT +s simRat_chr6.simRat.chr6 234073 16 - 647215 TTGCTCATATTCATTT +s simRat_chr6.simRat.chr6 365873 16 + 647215 TTGCTCAGTTCCATTT + +a +s simMouse_chr6.simMouse.chr6 373790 3 + 636262 TCA +s Anc0.Anc0refChr2 6680 3 + 17989 TCA +s Anc1.Anc1refChr2 113744 3 - 144309 TCA +s Anc1.Anc1refChr6 34746 3 + 197743 TCA +s Anc2.Anc2refChr0 51735 3 + 56053 TCA +s mr.mrrefChr0 119802 3 - 130230 TCA +s mr.mrrefChr0 10799 3 + 130230 TCA +s mr.mrrefChr5 220405 3 + 294540 TCA +s simCow_chr6.simCow.chr6 55170 3 + 602619 TGA +s simDog_chr6.simDog.chr6 48813 3 + 593897 TCA +s simHuman_chr6.simHuman.chr6 551768 3 - 601863 TCA +s simMouse_chr6.simMouse.chr6 624901 3 - 636262 TCA +s simMouse_chr6.simMouse.chr6 11739 3 + 636262 TCA +s simRat_chr6.simRat.chr6 636433 3 - 647215 TCA +s simRat_chr6.simRat.chr6 234089 3 - 647215 TCA +s simRat_chr6.simRat.chr6 365889 3 + 647215 TCA + +a +s simMouse_chr6.simMouse.chr6 373793 16 + 636262 TGGTGAAGATTTATGT +s Anc0.Anc0refChr2 6685 16 + 17989 TAGTGAACACCCGAGT +s Anc1.Anc1refChr2 113749 16 - 144309 TAGTGAACACCCGAGT +s Anc1.Anc1refChr6 34749 16 + 197743 TGGTGAAGACCTTTGT +s Anc2.Anc2refChr0 51740 16 + 56053 TAGTGAACACCCGAGT +s mr.mrrefChr0 119805 16 - 130230 TGGTAAAAACCTTCGT +s mr.mrrefChr0 10802 16 + 130230 TGGTGAAGACGTTTGT +s mr.mrrefChr5 220408 16 + 294540 TGGTGAAGATTTATGT +s simCow_chr6.simCow.chr6 55175 16 + 602619 TGGTGAGCACCCGCGT +s simDog_chr6.simDog.chr6 48818 16 + 593897 TAGTGAAGGCTTGAGG +s simHuman_chr6.simHuman.chr6 551773 16 - 601863 TAGTGAACACCCTTGT +s simMouse_chr6.simMouse.chr6 624904 16 - 636262 TGGTAAAAACCTTCGT +s simMouse_chr6.simMouse.chr6 11742 16 + 636262 TGGTGAAGACGTTTGT +s simRat_chr6.simRat.chr6 636436 16 - 647215 TGGTGAGGGCCTTTGT +s simRat_chr6.simRat.chr6 234092 16 - 647215 TGGTGAAGACTTTTGT +s simRat_chr6.simRat.chr6 365892 16 + 647215 TGTTGAAGACCTTCGC + +a +s simMouse_chr6.simMouse.chr6 373809 3 + 636262 TGG +s Anc0.Anc0refChr2 6701 3 + 17989 TGG +s Anc1.Anc1refChr2 113765 3 - 144309 TGG +s Anc1.Anc1refChr6 34765 3 + 197743 TGG +s Anc2.Anc2refChr0 51756 3 + 56053 TGG +s mr.mrrefChr0 119821 3 - 130230 GAG +s mr.mrrefChr0 10818 3 + 130230 TGG +s mr.mrrefChr5 220424 3 + 294540 TGG +s simCow_chr6.simCow.chr6 55191 3 + 602619 TGG +s simDog_chr6.simDog.chr6 48834 3 + 593897 TGG +s simHuman_chr6.simHuman.chr6 551789 3 - 601863 TGG +s simMouse_chr6.simMouse.chr6 624920 3 - 636262 GAG +s simMouse_chr6.simMouse.chr6 11758 3 + 636262 TGG +s simRat_chr6.simRat.chr6 636470 3 - 647215 AGG +s simRat_chr6.simRat.chr6 234108 3 - 647215 TGG +s simRat_chr6.simRat.chr6 365908 3 + 647215 CAG + +a +s simMouse_chr6.simMouse.chr6 373812 18 + 636262 TGTGTTAGCTAGTAGTGG +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 11761 18 + 636262 TCTATTCACTGGTTAGAA +s simRat_chr6.simRat.chr6 234111 18 - 647215 TTTATTCACTGATTGGAC +s simRat_chr6.simRat.chr6 365911 18 + 647215 TGCGTTAGCTAGTAGGAG + +a +s simMouse_chr6.simMouse.chr6 373830 2 + 636262 CA +s Anc0.Anc0refChr2 6722 2 + 17989 CA +s Anc1.Anc1refChr2 113786 2 - 144309 CA +s Anc1.Anc1refChr6 34786 2 + 197743 CA +s Anc2.Anc2refChr0 51777 2 + 56053 CA +s mr.mrrefChr0 119824 2 - 130230 CA +s mr.mrrefChr0 10839 2 + 130230 AG +s mr.mrrefChr5 220445 2 + 294540 CA +s simCow_chr6.simCow.chr6 55212 2 + 602619 CA +s simDog_chr6.simDog.chr6 48855 2 + 593897 CA +s simHuman_chr6.simHuman.chr6 551810 2 - 601863 CA +s simMouse_chr6.simMouse.chr6 624923 2 - 636262 CA +s simMouse_chr6.simMouse.chr6 11779 2 + 636262 AG +s simRat_chr6.simRat.chr6 636473 2 - 647215 CA +s simRat_chr6.simRat.chr6 234129 2 - 647215 TG +s simRat_chr6.simRat.chr6 365929 2 + 647215 CA + +a +s simMouse_chr6.simMouse.chr6 373832 12 + 636262 CTACCTGAATAT +s Anc0.Anc0refChr2 6724 12 + 17989 CTCCCTGAGCAC +s Anc1.Anc1refChr2 113788 12 - 144309 CTCCCTGAGCAC +s Anc1.Anc1refChr6 34788 12 + 197743 CTACCTGAATAT +s Anc2.Anc2refChr0 51779 12 + 56053 CTCCCTGAGCAC +s mr.mrrefChr0 119826 12 - 130230 CTGCCTGAATAC +s mr.mrrefChr0 10841 12 + 130230 CTACCTGAATAT +s mr.mrrefChr5 220447 12 + 294540 CTACCTGAATAT +s simCow_chr6.simCow.chr6 55214 12 + 602619 CTACCTGAGCAC +s simDog_chr6.simDog.chr6 48857 12 + 593897 CTCACTGAGCAC +s simHuman_chr6.simHuman.chr6 551812 12 - 601863 CTCCATGAGCAC +s simMouse_chr6.simMouse.chr6 624925 12 - 636262 CTGCCTGAATAC +s simMouse_chr6.simMouse.chr6 11783 12 + 636262 CTACCTGAATAT +s simRat_chr6.simRat.chr6 636475 12 - 647215 CTACCTGAATAC +s simRat_chr6.simRat.chr6 234131 12 - 647215 CTACCCGAATAC +s simRat_chr6.simRat.chr6 365931 12 + 647215 ATACCTGAATAT + +a +s simMouse_chr6.simMouse.chr6 373844 32 + 636262 AGTACTCCTGTGGTTGAGCATTCTTTGCAGAG +s Anc0.Anc0refChr2 6740 27 + 17989 AGCACTCCTGTGGC---ACATTCCGTGCGG-- +s Anc1.Anc1refChr2 113804 27 - 144309 AGCACTCCTGTGGC---ACATTCCGTGCGG-- +s Anc1.Anc1refChr6 34800 30 + 197743 AGTACTCCTGTGGTTGAACATTCTTTGTAG-- +s Anc2.Anc2refChr0 51795 27 + 56053 AGCACTCCTGTGGC---ACATTCCGTGCGG-- +s mr.mrrefChr0 119838 30 - 130230 AGTACTCCTGTGGTTGAATGTTCTTTGTAG-- +s mr.mrrefChr0 10853 30 + 130230 AGTACTCCTGTAGTGGCACATACTTTGTAG-- +s mr.mrrefChr5 220459 30 + 294540 AGTACTCCTGTGGTTGAGCATTCTTTGCAG-- +s simCow_chr6.simCow.chr6 55230 27 + 602619 AGCACTCCTGTGGC---ACATTCCGTGCGG-- +s simDog_chr6.simDog.chr6 48873 3 + 593897 AGC----------------------------- +s simHuman_chr6.simHuman.chr6 551828 27 - 601863 AGCCCTCGTGTGGC---ACATTACTTGTAG-- +s simMouse_chr6.simMouse.chr6 624937 30 - 636262 AGTACTCCTGTGGTTGAATGTTCTTTGTAG-- +s simMouse_chr6.simMouse.chr6 11795 30 + 636262 AGTACTCCTGTAGTGGCACATACTTTGTAG-- +s simRat_chr6.simRat.chr6 636487 30 - 647215 AGTACTCCTGTGGTTGAACATTCTTTATAG-- +s simRat_chr6.simRat.chr6 234143 30 - 647215 AGTACTCCTGTAGTGGAACATTCTTTGTAT-- +s simRat_chr6.simRat.chr6 365943 30 + 647215 AGGACTCCTGTGGTTGAACATTCTTTACGG-- + +a +s simMouse_chr6.simMouse.chr6 373876 11 + 636262 CACCTGTTTTG +s Anc0.Anc0refChr2 6767 6 + 17989 AATGTG----- +s Anc1.Anc1refChr2 113831 6 - 144309 AATGTG----- +s Anc1.Anc1refChr6 34830 11 + 197743 TGTCTGTATTG +s Anc2.Anc2refChr0 51822 6 + 56053 AATGTG----- +s mr.mrrefChr0 119868 11 - 130230 TGTCTGTATTG +s mr.mrrefChr0 10883 11 + 130230 TGTCTGTATTG +s mr.mrrefChr5 220489 11 + 294540 CACCTGTTTTG +s simCow_chr6.simCow.chr6 55258 6 + 602619 AATGTG----- +s simHuman_chr6.simHuman.chr6 551855 6 - 601863 AGTGTA----- +s simMouse_chr6.simMouse.chr6 624967 11 - 636262 TGTCTGTATTG +s simMouse_chr6.simMouse.chr6 11825 11 + 636262 TGTCTGTATTG +s simRat_chr6.simRat.chr6 636517 11 - 647215 TGTCTGTATTG +s simRat_chr6.simRat.chr6 234173 11 - 647215 TGTCTGTATTA +s simRat_chr6.simRat.chr6 365973 11 + 647215 CGCCTGTTTTG a s simMouse_chr6.simMouse.chr6 373887 72 + 636262 CTCTATGAGTTGCAATAAAGCCCGCAGAACTGGTAAGAGCCTGCTAACTGGACTAACCCAGATAATAGCCTG @@ -147301,7 +154608,9 @@ s simRat_chr6.simRat.chr6 378598 68 + 647215 CTC-------------------------------------------------------GGTACTCTTCACAGGTCGCCCTACTCACGCGCCCAACGGCAATCGTTGGCCGCACAGACTGGGTG------------------------------------------------------------------------------------------------------------------------------- a -s simMouse_chr6.simMouse.chr6 379449 36 + 636262 CTTGTACGATTAGTTACTCCAGTAATGTTATTGCGA +s simMouse_chr6.simMouse.chr6 379414 71 + 636262 CGTTGCCGAAGTAACTGATTGCACAAGCTATATAGCTTGTACGATTAGTTACTCCAGTAATGTTATTGCGA +s mr.mrrefChr5 232848 35 + 294540 CGTTGCCAAAGTAACTGATTACACAAGCTATTTTG------------------------------------ +s simMouse_chr6.simMouse.chr6 321930 35 + 636262 TGTTACCAGAGTAACTGATCACACAAGTTATTTTG------------------------------------ a s simMouse_chr6.simMouse.chr6 379485 15 + 636262 AAAAAAATAATATTT @@ -147358,30 +154667,203 @@ 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 +s simMouse_chr6.simMouse.chr6 379549 4 + 636262 TTCA +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 321965 4 + 636262 TACA +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 379553 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 321969 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 379554 5 + 636262 AGGCA +s mr.mrrefChr5 232952 5 + 294540 AGGCA +s simMouse_chr6.simMouse.chr6 321970 5 + 636262 AGGCT +s simRat_chr6.simRat.chr6 378748 5 + 647215 ATGCA +s simRat_chr6.simRat.chr6 194018 5 - 647215 AGGAC + +a +s simMouse_chr6.simMouse.chr6 379559 7 + 636262 CCTGCCC +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 321975 7 + 636262 CCTCCCA +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 379566 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 321982 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 379569 49 + 636262 TAATACAACCTGTTTCGTATGCTCCTTCAAACTGTGTGAGGTTCACCTG +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 321985 49 + 636262 TAATACAATTTCTTTTGTGTGCTCCTTCACACTGTATGAGGTTTACTTG +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 379618 7 + 636262 AATTTCT +s mr.mrrefChr5 233019 7 + 294540 AATTTCT +s simMouse_chr6.simMouse.chr6 322037 7 + 636262 GATTTCT +s simRat_chr6.simRat.chr6 378815 7 + 647215 AACTTCT +s simRat_chr6.simRat.chr6 194081 7 - 647215 GGTTTTT + +a +s simMouse_chr6.simMouse.chr6 379625 2 + 636262 TC +s mr.mrrefChr5 233026 2 + 294540 TC +s simMouse_chr6.simMouse.chr6 322044 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 379627 25 + 636262 CTCTTACTTGAATGTTCCTGTCCTT +s Anc1.Anc1refChr6 31481 25 - 197743 CTTTTACTTGCATGTTCCTGTCCTT +s mr.mrrefChr3 108495 25 - 181027 CTTTTACCTGCATTCTCCTGTCCAT +s mr.mrrefChr5 233028 25 + 294540 CTTTTACTTGAATGTTCCTGTCCTT +s simMouse_chr6.simMouse.chr6 116085 25 - 636262 CTTTTACCTGCATTCTCCTGTCCAT +s simMouse_chr6.simMouse.chr6 322046 25 + 636262 CTTTTACGTGAATGTTCTTGTCCTC +s simRat_chr6.simRat.chr6 115626 25 - 647215 TTCTTACTTGAATGCTCTTGTCCAT +s simRat_chr6.simRat.chr6 378824 25 + 647215 CTTTTATTTGAATGTTCCAGTCCTT +s simRat_chr6.simRat.chr6 194097 25 - 647215 CTTTTACTCAAATGTCCCTGTGCTT + +a +s simMouse_chr6.simMouse.chr6 379652 6 + 636262 CATGCC +s Anc1.Anc1refChr6 31506 6 - 197743 CATGCC +s mr.mrrefChr3 108520 6 - 181027 CATGCC +s mr.mrrefChr5 233053 6 + 294540 CATACC +s simMouse_chr6.simMouse.chr6 116110 6 - 636262 CATGCC +s simMouse_chr6.simMouse.chr6 322075 6 + 636262 CATACC +s simRat_chr6.simRat.chr6 115651 6 - 647215 CATGCT +s simRat_chr6.simRat.chr6 378849 6 + 647215 CAACCG +s simRat_chr6.simRat.chr6 194122 6 - 647215 CAAACA + +a +s simMouse_chr6.simMouse.chr6 379658 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 322081 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 379659 35 + 636262 TACAAGGTTTACTTGACTGTTTTTGTTCCCTCACC +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 322082 35 + 636262 TATGAGATTTACTGGACTGTTTTTATTCCCTCACC +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 379694 8 + 636262 ATATTAGG +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 322117 8 + 636262 ATCTTAGG +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 379702 31 + 636262 GAAGGTGGCACTTCTGAGTATGGCCATTTAT +s Anc1.Anc1refChr6 31563 31 - 197743 GGAGGTGGCACTTCTGACTATGACCATTTTT +s mr.mrrefChr3 108577 31 - 181027 GGAGATGGCACTTATGACCATGACCGCTTTC +s mr.mrrefChr5 233110 31 + 294540 GAAGGTGGCACTTCTGAGTATGGCCATTTTT +s simMouse_chr6.simMouse.chr6 116167 31 - 636262 GGAGATGGCACTTATGACCATGACCGCTTTC +s simMouse_chr6.simMouse.chr6 322132 27 + 636262 GACTGTCGCACTTCTGATTATTTCCAT---- +s simRat_chr6.simRat.chr6 115708 31 - 647215 GAAGGTGGCACTTTTGAGTATGGCCGTTCTC +s simRat_chr6.simRat.chr6 378898 31 + 647215 GAGGGTGGCACTTCTGAGTATGGCCATTTTT +s simRat_chr6.simRat.chr6 194252 31 - 647215 GAAGGTGGCACTTTTGAGTATGGCCGTTTTT + +a +s simMouse_chr6.simMouse.chr6 379733 7 + 636262 GCATGCT +s mr.mrrefChr5 233141 7 + 294540 GTATGCT +s simMouse_chr6.simMouse.chr6 322159 5 + 636262 --ATTCT +s simRat_chr6.simRat.chr6 378929 7 + 647215 GTATGCT +s simRat_chr6.simRat.chr6 194283 7 - 647215 GTGTGCT + +a +s simMouse_chr6.simMouse.chr6 379740 23 + 636262 TCTCCACGACATTAGATTTTTTG +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 322164 23 + 636262 TCTCCACAATATTAGATTTCTTG +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 379763 4 + 636262 ACTT +s Anc1.Anc1refChr6 31617 4 - 197743 ATTG +s mr.mrrefChr3 108631 4 - 181027 ATTG +s mr.mrrefChr5 233171 4 + 294540 ATTG +s simMouse_chr6.simMouse.chr6 116228 4 - 636262 ATTG +s simMouse_chr6.simMouse.chr6 322203 4 + 636262 ATTG +s simRat_chr6.simRat.chr6 115805 4 - 647215 ATTG +s simRat_chr6.simRat.chr6 378959 4 + 647215 ATTT +s simRat_chr6.simRat.chr6 194300 3 - 647215 -TCG + +a +s simMouse_chr6.simMouse.chr6 379767 13 + 636262 GGCTCACCAGAGT +s Anc1.Anc1refChr6 31631 13 - 197743 GGCTCTTCAGAGT +s mr.mrrefChr3 108645 13 - 181027 GGCTCTTCAGAGT +s mr.mrrefChr5 233185 13 + 294540 GGCTCTTCAGAGT +s simMouse_chr6.simMouse.chr6 116242 13 - 636262 GGCTCTTCAGAGT +s simMouse_chr6.simMouse.chr6 322217 13 + 636262 GTCTCCTCAGAGT +s simRat_chr6.simRat.chr6 115819 13 - 647215 GACTCTTCAGAGT +s simRat_chr6.simRat.chr6 378973 13 + 647215 GGCTCTTCAGAAT +s simRat_chr6.simRat.chr6 194313 11 - 647215 GGCTTTTCAGA-- + +a +s simMouse_chr6.simMouse.chr6 379780 14 + 636262 ATCACTACTGGACC +s mr.mrrefChr5 233198 14 + 294540 ATCACTGCTGGCTC +s simMouse_chr6.simMouse.chr6 322230 14 + 636262 ATCACCGCCGGCTC +s simRat_chr6.simRat.chr6 378986 14 + 647215 ATCAGTGCTGGCTC +s simRat_chr6.simRat.chr6 194324 2 - 647215 ------------CC + +a +s simMouse_chr6.simMouse.chr6 379794 35 + 636262 TTTACTGCTGGCCTTTTTCGTACACTTATCCAGTA +s Anc1.Anc1refChr6 31644 35 - 197743 TTTAGTGCTGGCCTTCTTCATGTGCTTTTCCACTA +s mr.mrrefChr3 108658 35 - 181027 TTGAGTGCTGGTCCTCTTCATGTGCTTTTCCACTA +s mr.mrrefChr5 233212 35 + 294540 TTTACTGCTGGCCTTTTTCGTATGCTTCTCCACTA +s simMouse_chr6.simMouse.chr6 116255 35 - 636262 TTGAGTGCTGGTCCTCTTCATGTGCTTTTCCACTA +s simMouse_chr6.simMouse.chr6 322244 21 + 636262 TTT--------------CCGTATGCTTCTCCACTG +s simRat_chr6.simRat.chr6 115832 35 - 647215 TTCACTGCTGGTCCTCTTCGTGTGCTTCTCCACTG +s simRat_chr6.simRat.chr6 379000 35 + 647215 TTTACTGCAGGCTTTTTACATACGTTTCTCCGGTT +s simRat_chr6.simRat.chr6 194326 35 - 647215 TTTACCACTGTTCCTTTTCGTGTGCTTTTCCCCTA a s simMouse_chr6.simMouse.chr6 379829 11 + 636262 AGGTTTTTTAA @@ -147429,86 +154911,163 @@ 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 +s simMouse_chr6.simMouse.chr6 379880 26 + 636262 CAGTTCAGATATCAACCGTTTCTCCA +s Anc1.Anc1refChr6 31732 26 - 197743 CAGTGCAGATATCAACGGTTTATCCA +s mr.mrrefChr3 108811 26 - 181027 TAGTGCAGATATCAGCGGCTTCACCA +s mr.mrrefChr5 233302 26 + 294540 CAGTTCAGATATCAACCGTTTATCCA +s simMouse_chr6.simMouse.chr6 116408 26 - 636262 TAGTGCAGATATCAGCGGCTTCACCA +s simMouse_chr6.simMouse.chr6 322267 5 + 636262 ---------------------ACCAC +s simRat_chr6.simRat.chr6 115986 26 - 647215 ATGTGCACATATCGACTGCTTCTCCA +s simRat_chr6.simRat.chr6 379090 26 + 647215 CAGTCCAGAAATCAACCACTTCTCCA +s simRat_chr6.simRat.chr6 194406 5 - 647215 ---------------------ATCCC + +a +s simMouse_chr6.simMouse.chr6 379906 2 + 636262 TT +s mr.mrrefChr5 233328 2 + 294540 TT +s simMouse_chr6.simMouse.chr6 322272 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 379908 8 + 636262 GCATGCAT +s Anc1.Anc1refChr6 31758 8 - 197743 ACGTACAT +s mr.mrrefChr3 108837 8 - 181027 ACGCACAT +s mr.mrrefChr5 233330 8 + 294540 ACATGCAT +s simMouse_chr6.simMouse.chr6 116456 8 - 636262 ACGCACAT +s simMouse_chr6.simMouse.chr6 322274 4 + 636262 AAAC---- +s simRat_chr6.simRat.chr6 116012 8 - 647215 ACGTACAT +s simRat_chr6.simRat.chr6 379118 8 + 647215 ACATGCAT +s simRat_chr6.simRat.chr6 194413 8 - 647215 GCACGTGT + +a +s simMouse_chr6.simMouse.chr6 379916 10 + 636262 AACCCATCCC +s mr.mrrefChr5 233338 10 + 294540 AACCCATCCC +s simMouse_chr6.simMouse.chr6 322278 9 + 636262 -ACCCATCCC +s simRat_chr6.simRat.chr6 379126 10 + 647215 AGCCCATCCC +s simRat_chr6.simRat.chr6 194421 2 - 647215 G--------T + +a +s simMouse_chr6.simMouse.chr6 379926 9 + 636262 CCCCTAcaa +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 322287 9 + 636262 CCCCTAAaa +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 379935 17 + 636262 tcttattgggacaagct +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 322296 17 + 636262 tcttattggaatgagct +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 379952 2 + 636262 ga +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 322313 2 + 636262 ac +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 379954 25 + 636262 atgtatacttttgtaagtgcttctt +s Anc1.Anc1refChr6 31794 25 - 197743 atgtacacttttgtaaatgcttctt +s mr.mrrefChr3 108877 25 - 181027 atgtacacttttgtaaatgcttctt +s mr.mrrefChr5 233376 25 + 294540 atgtacacttttgtaaatgcttctt +s simMouse_chr6.simMouse.chr6 116496 25 - 636262 atgtacacttttgtaaatgcttctt +s simMouse_chr6.simMouse.chr6 322315 24 + 636262 a-aaacacttttgtaaatgcttctt +s simRat_chr6.simRat.chr6 116052 25 - 647215 atgtacacttttgtagatgcttctt +s simRat_chr6.simRat.chr6 379164 25 + 647215 atggatacttttgtaaatgcttctt +s simRat_chr6.simRat.chr6 194467 25 - 647215 atgtacacttttgtaaatgcttctt + +a +s simMouse_chr6.simMouse.chr6 379979 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 322339 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 379980 10 + 636262 gaaatgtaga +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 322340 10 + 636262 ggagtgtaga +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 379990 22 + 636262 cttcttgtgtagtaagaggatg +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 322350 22 + 636262 cttcttctccagcaagagaatg +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 380012 15 + 636262 tctatttatgtctcc +s Anc0.Anc0refChr3 12691 11 + 222631 ----tctaggtTGCA +s Anc1.Anc1refChr6 45596 11 + 197743 ----tctaggtTGCA +s Anc2.Anc2refChr13 15429 11 + 96486 ----TCTAGGTTGTA +s mr.mrrefChr5 233434 15 + 294540 tctatttatgtctct +s simCow_chr6.simCow.chr6 371446 11 + 602619 ----TCTAGGTTGTA +s simDog_chr6.simDog.chr6 361495 11 + 593897 ----TCTAGGTTGTA +s simHuman_chr6.simHuman.chr6 369792 4 + 601863 -----------GGCA +s simMouse_chr6.simMouse.chr6 322372 14 + 636262 cctatccatgactc- +s simRat_chr6.simRat.chr6 379221 15 + 647215 tctatttgtgtctct +s simRat_chr6.simRat.chr6 194522 15 - 647215 tctattcatgtctct + +a +s simMouse_chr6.simMouse.chr6 380027 22 + 636262 agcccatcttttattgttgtcg +s Anc0.Anc0refChr3 12702 11 + 222631 CCCCCAACTTT----------- +s Anc1.Anc1refChr6 45607 11 + 197743 CCCCCAACTTT----------- +s Anc2.Anc2refChr13 15441 11 + 96486 CCCCCAACCTT----------- +s mr.mrrefChr5 233449 22 + 294540 agcccatcttttaatggtgtcg +s simCow_chr6.simCow.chr6 371458 11 + 602619 TCCTCAACCCT----------- +s simDog_chr6.simDog.chr6 361507 11 + 593897 CCCCCAACCTT----------- +s simHuman_chr6.simHuman.chr6 369796 11 + 601863 CCCCTAGCTTT----------- +s simMouse_chr6.simMouse.chr6 322386 17 + 636262 -----gtctcttaatggtgttg +s simRat_chr6.simRat.chr6 379236 22 + 647215 agcccatcttattatgttgtca +s simRat_chr6.simRat.chr6 194537 22 - 647215 agcccatctcttaatagtgttg + +a +s simMouse_chr6.simMouse.chr6 380049 15 + 636262 gtttttcatgttgtg +s mr.mrrefChr5 233473 15 + 294540 ggttttcgttttgtg +s simMouse_chr6.simMouse.chr6 322407 13 + 636262 ggtgactgttttg-- +s simRat_chr6.simRat.chr6 379258 15 + 647215 aattataattttgtg +s simRat_chr6.simRat.chr6 194561 15 - 647215 ggttttcgttttgtg + +a +s simMouse_chr6.simMouse.chr6 380064 22 + 636262 atttctgtaattctgttataga +s mr.mrrefChr5 233488 22 + 294540 atctctgtaattctgttatgga +s simMouse_chr6.simMouse.chr6 322420 17 + 636262 -----tgtatatctgttaagga +s simRat_chr6.simRat.chr6 379273 22 + 647215 atctctgtgattctattatgga +s simRat_chr6.simRat.chr6 194577 22 - 647215 atctctgtaagtatgttatgga + +a +s simMouse_chr6.simMouse.chr6 380086 172 + 636262 cctgtgcaaccaggccactctcagacgaatatgtggcaaaatgttactcttaattggtatattcacagttggctgtggcaacagtcttttgttcctatgacccacacagcatgttatggaccagtggaaccaggcccctcttagacgattaagtggcagaatctttgtccca +s mr.mrrefChr5 233510 144 + 294540 cctgtgca--------------------------ggcaaaatgttactcttaattggtatattcacagttgg--gtggcaacagtcttttgttcctatgacccacacagcatgttatggaccagtgaaaccaggcccctcttagatgaataagtggcagaatttttgtccca +s simMouse_chr6.simMouse.chr6 322445 44 + 636262 t--------------------------------------------------------------------------------------------------------------------------gtgataccaggctcctctcaaatgagtaagtggcaaaATTTAT------ +s simRat_chr6.simRat.chr6 379295 144 + 647215 cccatgaa--------------------------ggcgacattcctgtcttaattggtaggtacacacctgg--gtggtaacgggcttttgatcctttggcccacacaGCAcattatggacctgagaaaccaggcacctcttacatgaataagtggcagaatctttgtccca +s simRat_chr6.simRat.chr6 194599 50 - 647215 c--------------------------------------------------------------------------------------------------------------------------gtgaaaccaggcccctctcagatgaataagtggcaaaatttttgtccca a s simMouse_chr6.simMouse.chr6 380258 2 + 636262 ag @@ -147528,16 +155087,18 @@ 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 +s simMouse_chr6.simMouse.chr6 380361 21 + 636262 ttcacatcttttctgggagtg +s mr.mrrefChr5 233757 21 + 294540 ttcgcatctttttttggagtg +s simMouse_chr6.simMouse.chr6 322489 5 + 636262 ----------------CAATG +s simRat_chr6.simRat.chr6 379540 21 + 647215 ttcgcagctgtttttggtgtg +s simRat_chr6.simRat.chr6 194792 21 - 647215 tttgcaactttttttggcatg + +a +s simMouse_chr6.simMouse.chr6 380382 31 + 636262 ggcatcaagggttcttcagtagctatatctt +s mr.mrrefChr5 233781 31 + 294540 agcatcaagggttcttcagtagctatatctt +s simMouse_chr6.simMouse.chr6 322497 27 + 636262 AACATCAAGGCCCTTTC----CATGTAACTC +s simRat_chr6.simRat.chr6 379564 31 + 647215 agcattataggttcttcagtagctatatctt +s simRat_chr6.simRat.chr6 194816 31 - 647215 agcataaaaggctcttcagttcctatatctt a s simMouse_chr6.simMouse.chr6 380413 3 + 636262 gga @@ -147545,16 +155106,74 @@ 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 +s simMouse_chr6.simMouse.chr6 380416 1 + 636262 t +s mr.mrrefChr5 233815 1 + 294540 t +s simMouse_chr6.simMouse.chr6 322524 1 + 636262 T +s simRat_chr6.simRat.chr6 379595 1 + 647215 t +s simRat_chr6.simRat.chr6 194850 1 - 647215 t + +a +s simMouse_chr6.simMouse.chr6 380417 94 + 636262 tagaaggtcaatttccctagcaccagttattgaagagggactcctgtggccattgatttcttcctgatgtatggaagatagagcaatggggaag +s mr.mrrefChr5 233937 94 + 294540 tagaaggccaattcccctagcaccaggtattgaagagggactcctgtggccattgatttcttcctgatgtatggaagatagagcaattggaaag +s simMouse_chr6.simMouse.chr6 322568 36 + 636262 ----------------------------------------------------------ctttcctgatgtatggaagatggagcaattagaaag +s simRat_chr6.simRat.chr6 379734 94 + 647215 tgaatggccaattcccctggcatcacgtattgaagaggggcttctggggctattgatttcttcctgatgtatggaagatagagcaatgggaaag +s simRat_chr6.simRat.chr6 194972 94 - 647215 tagaaggccaattcctccagtaccatgtattgaaaaaggaatcctgtgcccattgatttcttcctgacgtgtggaagatagagcaattggaaag + +a +s simMouse_chr6.simMouse.chr6 380511 15 + 636262 gagggatagccagga +s mr.mrrefChr5 234033 15 + 294540 gagggatgaacttga +s simMouse_chr6.simMouse.chr6 322606 15 + 636262 gaaggatgaacttga +s simRat_chr6.simRat.chr6 379830 15 + 647215 tagggatgaacttga +s simRat_chr6.simRat.chr6 195068 15 - 647215 gagggatgaacttga + +a +s simMouse_chr6.simMouse.chr6 380526 39 + 636262 ggggtagccatcttactgccaagggctatgggccgaatc +s mr.mrrefChr5 234053 39 + 294540 agcaagtccatcttactgccatgggctatgggccgaatc +s simMouse_chr6.simMouse.chr6 322626 39 + 636262 agcaagaccatcttattgccatggcatatgggccaaatc +s simRat_chr6.simRat.chr6 379850 39 + 647215 aacaagtccatcttaccgccatgagctaagggctgaatc +s simRat_chr6.simRat.chr6 195088 34 - 647215 gacaagtccatcttattgccatggtcta-----tgattc + +a +s simMouse_chr6.simMouse.chr6 380565 34 + 636262 tcgtggcaccagtatagtgctgttttgctaagag +s mr.mrrefChr5 234092 34 + 294540 ttgtggtaccagaatagtgttgttttactgagag +s simMouse_chr6.simMouse.chr6 322665 34 + 636262 ttgtagtatcagaatggtgttgttccagtgagtg +s simRat_chr6.simRat.chr6 379889 34 + 647215 tcgtggtaccagtatagtgtagttttactgagag +s simRat_chr6.simRat.chr6 195123 34 - 647215 ttgtgggaccagaatggtgttgttttaatgagag + +a +s simMouse_chr6.simMouse.chr6 380599 78 + 636262 tcactcattggaaccaaaaaagggagcccatggcaaagtccattccaggtcagaagaatcaagcaggcagcataaccc +s mr.mrrefChr5 234126 53 + 294540 tcactca----------------------atagtagaatttgtgata---tgggaggattatgccgccggcttgattc +s simMouse_chr6.simMouse.chr6 322699 53 + 636262 ttgctta----------------------atagtagaatttgtgatc---tgggaggattatgccaccggcccgatgc +s simRat_chr6.simRat.chr6 379929 53 + 647215 tcactca----------------------atagtagaatttgttata---cgggagggttatgctgccagctcaattc +s simRat_chr6.simRat.chr6 195157 53 - 647215 tcgctcg----------------------atagtggaatttgtggtc---tgggagggttatgccgctggcttgattc + +a +s simMouse_chr6.simMouse.chr6 380677 13 + 636262 tcctggatcacaa +s mr.mrrefChr5 234179 13 + 294540 ttctggcttggaa +s simMouse_chr6.simMouse.chr6 322764 13 + 636262 ttctggcttggaa +s simRat_chr6.simRat.chr6 379982 13 + 647215 ttttggcctggaa +s simRat_chr6.simRat.chr6 195210 13 - 647215 ttctggcttggaa + +a +s simMouse_chr6.simMouse.chr6 380690 6 + 636262 gttcta +s mr.mrrefChr5 234212 6 + 294540 tttctg +s simMouse_chr6.simMouse.chr6 322829 6 + 636262 ttttcg +s simRat_chr6.simRat.chr6 380015 6 + 647215 tttttg +s simRat_chr6.simRat.chr6 195237 6 - 647215 tttctg + +a +s simMouse_chr6.simMouse.chr6 380696 18 + 636262 ctatttgaacttgacaat +s mr.mrrefChr5 234221 18 + 294540 ccaattaaacttaacgat +s simMouse_chr6.simMouse.chr6 322838 18 + 636262 ccaagtaaacctaactct +s simRat_chr6.simRat.chr6 380024 18 + 647215 ccaattaaacctgacgat +s simRat_chr6.simRat.chr6 195246 18 - 647215 ccaagtaaacttaatgat + +a +s simMouse_chr6.simMouse.chr6 380714 40 + 636262 tttttttacactcagtaaacagggccacagggcttttgat +s mr.mrrefChr5 234241 40 + 294540 tttttttacactcagtaaacagggccacagggcttttgat +s simMouse_chr6.simMouse.chr6 322858 40 + 636262 tctctttatactcagggaacagggccatagggcttttaat +s simRat_chr6.simRat.chr6 380044 40 + 647215 tttttttacactcagtaaacagggccacagttcttttaat +s simRat_chr6.simRat.chr6 195266 40 - 647215 tttttttacattcagtgaacagggccatcagacttttgat a s simMouse_chr6.simMouse.chr6 380754 22 + 636262 tcatgctctcagtgccttgttg @@ -147563,31 +155182,94 @@ 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 +s simMouse_chr6.simMouse.chr6 380776 31 + 636262 attcttctacaagaaagtctcagattttaat +s mr.mrrefChr5 234526 31 + 294540 attcttctacaagaaagtctcagattttaat +s simMouse_chr6.simMouse.chr6 323082 14 + 636262 -----------------tttcagattttaat +s simRat_chr6.simRat.chr6 380286 31 + 647215 attctactacaagaaagtctcagattttaat +s simRat_chr6.simRat.chr6 195589 31 - 647215 atttttatacaaaaaagtttcacattttaat + +a +s simMouse_chr6.simMouse.chr6 380807 32 + 636262 ccttaattttgtaactagagacttcagctata +s mr.mrrefChr5 234558 32 + 294540 ccttaattttgtaaccagagacttcagctaaa +s simMouse_chr6.simMouse.chr6 323097 32 + 636262 cattaattatgtaatcagagacttcagttaaa +s simRat_chr6.simRat.chr6 380317 32 + 647215 ccttaattttgtaactggggactccagctaaa +s simRat_chr6.simRat.chr6 195621 32 - 647215 cattaattttgtagccggaaacttcagctaaa + +a +s simMouse_chr6.simMouse.chr6 380839 45 + 636262 tcgcttatcagcttatgtaagtttccagctgccgccatcagatta +s mr.mrrefChr5 234590 45 + 294540 ttgcttatcagcttaagtaagtttccagctgccgccattggatta +s simMouse_chr6.simMouse.chr6 323129 45 + 636262 ttgtttatcagcttaagcaagtctacagctcctgccattggatta +s simRat_chr6.simRat.chr6 380349 45 + 647215 ttgcttatcagcttaagtaaggttccagcagccaccattgaatga +s simRat_chr6.simRat.chr6 195679 45 - 647215 ttgcttatcagcttaagcaagtttccagctactgccattgggtta + +a +s simMouse_chr6.simMouse.chr6 380884 1 + 636262 c +s mr.mrrefChr5 234635 1 + 294540 c +s simMouse_chr6.simMouse.chr6 323174 1 + 636262 c +s simRat_chr6.simRat.chr6 380394 1 + 647215 c +s simRat_chr6.simRat.chr6 195725 1 - 647215 c + +a +s simMouse_chr6.simMouse.chr6 380885 26 + 636262 gaggtatactatcatatcatctgcaa +s mr.mrrefChr5 234637 26 + 294540 gaggtatactatcatatcatccgcaa +s simMouse_chr6.simMouse.chr6 323176 26 + 636262 gaggtaaacagacatatcatccctga +s simRat_chr6.simRat.chr6 380396 26 + 647215 gaggtgtactatcgtaccatcagcaa +s simRat_chr6.simRat.chr6 195727 25 - 647215 tgggtatact-tcatatcgtccacaa + +a +s simMouse_chr6.simMouse.chr6 380911 139 + 636262 atattgaaggttttatttcttcttcatccaattgtatacaccgtttatctttatcctgtctggttgtctgtgccaatagttccaggactttgttaaacagcagcgatgatatggaacagccctgctggcttttcgtgtc +s mr.mrrefChr5 234663 139 + 294540 atattgaaagctttatttcttcttcatccaattggataccctgtttatctttatcctgtcgggttgtctgcgccaatagttccaggattttgttaaacagcagtgatgatatggaacagccctgctgccttttcgtgcc +s simMouse_chr6.simMouse.chr6 323290 134 + 636262 atattgaaagctttacttcttcttcatccaattg-----cctgcttatcttgatcctgttgggttgtctgcaccaatagctccaggattttgttgaagagcagtggtgatatggaacagccctgcctcctttttgtgcc +s simRat_chr6.simRat.chr6 380422 139 + 647215 atattgaaggctctatttcttcttcatccaatttgatacattgtttatctttaacctgtctggttgtctgcgccaatagttccaggactttgttaaacagcagtaatgatatagaacaaccctgctggcttttcacacc +s simRat_chr6.simRat.chr6 195752 139 - 647215 atattgaaagtttcatctccccttcttccaataggataccctatttatctttatcctgtcgggctgtccacaccaatagttccaggattctgttgaacagcagcggtgatatggaaccgccctgccaccttgtcatgcc + +a +s simMouse_chr6.simMouse.chr6 381050 15 + 636262 ctttaaagggaagac +s mr.mrrefChr5 234802 15 + 294540 ctttaaagggaagac +s simMouse_chr6.simMouse.chr6 323424 15 + 636262 ctttaaaagaaagac +s simRat_chr6.simRat.chr6 380561 15 + 647215 ctttaaagggaaggc +s simRat_chr6.simRat.chr6 195903 15 - 647215 ttttaaagggaagac + +a +s simMouse_chr6.simMouse.chr6 381065 57 + 636262 tcaagcctgcatccatttattattagattgcaaatcagtttgtagtaaattactcta +s mr.mrrefChr5 234818 57 + 294540 tcaagcctgcatccatttactattagattgcaaatcggtttatcgtaaattgcccta +s simMouse_chr6.simMouse.chr6 323440 57 + 636262 tcaatcctgcacccatttactattagattgcaagccggtttatcgtaaattgccctc +s simRat_chr6.simRat.chr6 380577 57 + 647215 tcaagcctgcatacatttactctgagatcgcagatcagttaattgtatattgctcta +s simRat_chr6.simRat.chr6 195919 57 - 647215 tcaagcctgcatccatttactattagattgcacgtgggtttatcgtaaattgcccta + +a +s simMouse_chr6.simMouse.chr6 381122 60 + 636262 cccttgatgcaccatgcattgaggatcgttggacatgcaatcctgcttagtctgtttgat +s mr.mrrefChr5 234893 59 + 294540 ccctcgatgcacaactcattgaggatcattag-catgcaatcctgctcagtctgttcgat +s simMouse_chr6.simMouse.chr6 323515 59 + 636262 ccctcgacacacaactcattgaggatcattag-catgtgatcctgctctgcctgtacggc +s simRat_chr6.simRat.chr6 380634 59 + 647215 ccctcaatgcacaactcattgaggatcattag-catgcagtcctgtttagtctgtttgat +s simRat_chr6.simRat.chr6 195994 59 - 647215 cccttgatgcataactcattaagaatccttag-catgtaatcctgctccacctgttcgat + +a +s simMouse_chr6.simMouse.chr6 381182 2 + 636262 tg +s mr.mrrefChr5 234952 2 + 294540 tg +s simMouse_chr6.simMouse.chr6 323574 2 + 636262 cg +s simRat_chr6.simRat.chr6 196053 2 - 647215 gg + +a +s simMouse_chr6.simMouse.chr6 381184 63 + 636262 gcctgacctctctttccaatgttaagacactgtgattctcctgattggccaggttatctgttt +s mr.mrrefChr5 234954 63 + 294540 gcccgtcctctctttccaatgttaagatcatgtgattctcctgattggcccggttaaccgttt +s simMouse_chr6.simMouse.chr6 323576 48 + 636262 gcccgtcatctctt---------------atgtgattcttctgattggcccggttaataggtt +s simRat_chr6.simRat.chr6 380693 63 + 647215 gtcaaacctctctttccaacgttaagatcctgtgattctcctgattgccccagttagccattt +s simRat_chr6.simRat.chr6 196055 63 - 647215 gcccattatctctttccaatgtcagaatcatgtgcttctcccgattagcccagttaaccagtt + +a +s simMouse_chr6.simMouse.chr6 381247 4 + 636262 cata +s mr.mrrefChr5 235023 4 + 294540 catt +s simMouse_chr6.simMouse.chr6 323630 4 + 636262 tgct +s simRat_chr6.simRat.chr6 380756 4 + 647215 catt +s simRat_chr6.simRat.chr6 196124 4 - 647215 catt + +a +s simMouse_chr6.simMouse.chr6 381251 23 + 636262 tcctgggccatgctggcattccc +s mr.mrrefChr5 235041 23 + 294540 tcttgggccatcctggcattcct +s simMouse_chr6.simMouse.chr6 323648 3 + 636262 tct-------------------- +s simRat_chr6.simRat.chr6 380760 23 + 647215 tcttgtgccatcctggcagtact +s simRat_chr6.simRat.chr6 196142 23 - 647215 tcttgagccaccctggcattcct a s simMouse_chr6.simMouse.chr6 381274 6 + 636262 agggtg @@ -147680,6 +155362,12 @@ s simRat_chr6.simRat.chr6 381927 75 + 647215 ctttgtgttgatctattcacagtcgatagtggcgagttgacatcacccttgactcactgtatgtgagtgtgggcc a +s simMouse_chr6.simMouse.chr6 382010 4 + 636262 tttt +s mr.mrrefChr5 236044 4 + 294540 gttt +s simMouse_chr6.simMouse.chr6 323651 4 + 636262 Gtta +s simRat_chr6.simRat.chr6 382002 4 + 647215 gttt + +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 @@ -151441,6 +159129,36 @@ s simRat_chr6.simRat.chr6 393486 13 + 647215 CATATCTCAAACT a +s simMouse_chr6.simMouse.chr6 393401 2 + 636262 AG +s Anc0.Anc0refChr3 25707 2 + 222631 TA +s Anc1.Anc1refChr6 55270 2 + 197743 TA +s Anc2.Anc2refChr13 29172 2 + 96486 TA +s mr.mrrefChr5 247093 2 + 294540 AG +s mr.mrrefChr5 176442 2 - 294540 CT +s simCow_chr6.simCow.chr6 385154 2 + 602619 TA +s simDog_chr6.simDog.chr6 375690 2 + 593897 TA +s simHuman_chr6.simHuman.chr6 379720 2 + 601863 TA +s simHuman_chr6.simHuman.chr6 444632 2 + 601863 CA +s simMouse_chr6.simMouse.chr6 369779 2 - 636262 CT +s simRat_chr6.simRat.chr6 391929 2 - 647215 CT +s simRat_chr6.simRat.chr6 393499 2 + 647215 CG + +a +s simMouse_chr6.simMouse.chr6 393403 4 + 636262 TGAT +s Anc0.Anc0refChr3 25709 4 + 222631 TGTG +s Anc1.Anc1refChr6 55272 4 + 197743 TGTG +s Anc2.Anc2refChr13 29174 4 + 96486 TGTG +s mr.mrrefChr5 247095 4 + 294540 TGAT +s mr.mrrefChr5 176444 4 - 294540 GGAC +s simCow_chr6.simCow.chr6 385156 4 + 602619 GATG +s simDog_chr6.simDog.chr6 375692 4 + 593897 TGTG +s simHuman_chr6.simHuman.chr6 379722 4 + 601863 TGTG +s simHuman_chr6.simHuman.chr6 444634 4 + 601863 TTTA +s simMouse_chr6.simMouse.chr6 369781 4 - 636262 GGAC +s simRat_chr6.simRat.chr6 255174 4 + 647215 GCAG +s simRat_chr6.simRat.chr6 393501 4 + 647215 TGAC + +a s simMouse_chr6.simMouse.chr6 393407 4 + 636262 GAAG s Anc0.Anc0refChr3 25713 4 + 222631 TAAG s Anc1.Anc1refChr6 55276 4 + 197743 TAAG @@ -151453,6 +159171,34 @@ s simRat_chr6.simRat.chr6 393505 4 + 647215 TAAG a +s simMouse_chr6.simMouse.chr6 393411 2 + 636262 AA +s Anc0.Anc0refChr3 25717 2 + 222631 GA +s Anc1.Anc1refChr6 55280 2 + 197743 GA +s Anc2.Anc2refChr13 29182 2 + 96486 GA +s mr.mrrefChr5 247103 2 + 294540 AA +s mr.mrrefChr5 176448 2 - 294540 AA +s simCow_chr6.simCow.chr6 385164 2 + 602619 GA +s simDog_chr6.simDog.chr6 375700 2 + 593897 AA +s simHuman_chr6.simHuman.chr6 379730 2 + 601863 GA +s simMouse_chr6.simMouse.chr6 369785 2 - 636262 AA +s simRat_chr6.simRat.chr6 255178 2 + 647215 TA +s simRat_chr6.simRat.chr6 393509 2 + 647215 AA + +a +s simMouse_chr6.simMouse.chr6 393413 10 + 636262 TGGGTATGCT +s Anc0.Anc0refChr3 25719 10 + 222631 TAGTTGTATT +s Anc1.Anc1refChr6 55282 10 + 197743 TAGTTGTATT +s Anc2.Anc2refChr13 29185 10 + 96486 TAGTTGTATT +s mr.mrrefChr5 247105 10 + 294540 TGGGTATGCT +s mr.mrrefChr5 176450 10 - 294540 TAGACTCACT +s simCow_chr6.simCow.chr6 385210 10 + 602619 TAGTCACATT +s simDog_chr6.simDog.chr6 375703 10 + 593897 TAGTTGTATT +s simHuman_chr6.simHuman.chr6 379732 10 + 601863 TGGTTGTGTT +s simMouse_chr6.simMouse.chr6 369787 10 - 636262 TAGACTCACT +s simRat_chr6.simRat.chr6 255180 10 + 647215 TAGACTCACT +s simRat_chr6.simRat.chr6 393511 10 + 647215 TGGGGATGCT + +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 @@ -151461,11 +159207,41 @@ s simRat_chr6.simRat.chr6 393542 25 + 647215 CTTATCCATGGAGCACATTCAACTA a +s simMouse_chr6.simMouse.chr6 393448 8 + 636262 AGCTCATG +s Anc0.Anc0refChr3 25748 8 + 222631 AGCTCATC +s Anc1.Anc1refChr6 55335 8 + 197743 AGCTCATC +s Anc2.Anc2refChr13 29214 8 + 96486 AGCTCATC +s mr.mrrefChr5 247160 8 + 294540 AGCTCATG +s mr.mrrefChr5 176491 8 - 294540 TGGTCATC +s simCow_chr6.simCow.chr6 385239 8 + 602619 AACTCATC +s simDog_chr6.simDog.chr6 375732 8 + 593897 AGCTCATC +s simHuman_chr6.simHuman.chr6 379785 8 + 601863 AGCTCATT +s simHuman_chr6.simHuman.chr6 444678 8 + 601863 AGATCATT +s simMouse_chr6.simMouse.chr6 369829 8 - 636262 TGGTCATC +s simRat_chr6.simRat.chr6 255221 8 + 647215 TGGTCATC +s simRat_chr6.simRat.chr6 393567 8 + 647215 ATCTCATG + +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 393472 8 + 636262 CAGCTCCC +s Anc0.Anc0refChr3 25756 8 + 222631 CACCCCCT +s Anc1.Anc1refChr6 55343 8 + 197743 CACCCCCT +s Anc2.Anc2refChr13 29222 8 + 96486 CAACCTCT +s mr.mrrefChr5 247184 8 + 294540 CAGCTCCT +s mr.mrrefChr5 176499 8 - 294540 AAGTTCCA +s simCow_chr6.simCow.chr6 385247 8 + 602619 CAACCTGT +s simDog_chr6.simDog.chr6 375740 8 + 593897 CAACCTAT +s simHuman_chr6.simHuman.chr6 379793 8 + 601863 CACTCACA +s simHuman_chr6.simHuman.chr6 444686 8 + 601863 CACGCCCT +s simMouse_chr6.simMouse.chr6 369837 8 - 636262 AAGTTCCA +s simRat_chr6.simRat.chr6 255229 8 + 647215 AAGTTCCA +s simRat_chr6.simRat.chr6 393591 8 + 647215 CAGGTAGT + +a s simMouse_chr6.simMouse.chr6 393480 3 + 636262 TTC s Anc0.Anc0refChr3 25764 3 + 222631 CCC s Anc1.Anc1refChr6 55351 3 + 197743 CCC @@ -151478,11 +159254,71 @@ s simRat_chr6.simRat.chr6 393599 3 + 647215 TTC a +s simMouse_chr6.simMouse.chr6 393483 5 + 636262 TTTAC +s Anc0.Anc0refChr3 25767 5 + 222631 TTTCC +s Anc1.Anc1refChr6 55354 5 + 197743 TTTCC +s Anc2.Anc2refChr13 29233 5 + 96486 TTTCC +s mr.mrrefChr5 247195 5 + 294540 TTTAC +s mr.mrrefChr5 176507 5 - 294540 TTTAT +s simCow_chr6.simCow.chr6 385258 5 + 602619 TTTCC +s simDog_chr6.simDog.chr6 375751 5 + 593897 TTGAC +s simHuman_chr6.simHuman.chr6 379804 5 + 601863 CTTCC +s simHuman_chr6.simHuman.chr6 444697 5 + 601863 TTTCC +s simMouse_chr6.simMouse.chr6 369845 5 - 636262 TTTAT +s simRat_chr6.simRat.chr6 255237 5 + 647215 TTTGA +s simRat_chr6.simRat.chr6 393602 5 + 647215 TTGAC + +a +s simMouse_chr6.simMouse.chr6 393488 1 + 636262 C +s Anc0.Anc0refChr3 25772 1 + 222631 A +s Anc1.Anc1refChr6 55359 1 + 197743 A +s Anc2.Anc2refChr13 29246 1 + 96486 A +s mr.mrrefChr5 247200 1 + 294540 C +s mr.mrrefChr5 176512 1 - 294540 C +s simCow_chr6.simCow.chr6 385271 1 + 602619 G +s simDog_chr6.simDog.chr6 375764 1 + 593897 A +s simHuman_chr6.simHuman.chr6 379809 1 + 601863 A +s simHuman_chr6.simHuman.chr6 444702 1 + 601863 A +s simMouse_chr6.simMouse.chr6 369850 1 - 636262 C +s simRat_chr6.simRat.chr6 255242 1 + 647215 C +s simRat_chr6.simRat.chr6 393607 1 + 647215 C + +a +s simMouse_chr6.simMouse.chr6 393489 15 + 636262 TATGGGGAATTCTAG +s Anc0.Anc0refChr3 25773 15 + 222631 TATGGGGAACCCAAG +s Anc1.Anc1refChr6 55360 15 + 197743 TATGGGGAACCCAAG +s Anc2.Anc2refChr13 29247 15 + 96486 TATGGGGAACCCAAG +s mr.mrrefChr5 247201 15 + 294540 TATGGGGAATTCTAG +s mr.mrrefChr5 176513 15 - 294540 TAGAGGGCAGCCGGG +s simCow_chr6.simCow.chr6 385287 15 + 602619 TATAGGGAATCCTAG +s simDog_chr6.simDog.chr6 375765 14 + 593897 TATGGGGA-CCCAAG +s simHuman_chr6.simHuman.chr6 379810 15 + 601863 TATGGGAAATCCAAC +s simHuman_chr6.simHuman.chr6 444703 15 + 601863 TATGGGAAACCCAAG +s simMouse_chr6.simMouse.chr6 369851 15 - 636262 TAGAGGGCAGCCGGG +s simRat_chr6.simRat.chr6 255243 15 + 647215 TAGAGGGCAACCAGG +s simRat_chr6.simRat.chr6 393608 15 + 647215 TATGGGGAATTCTAG + +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 393508 1 + 636262 A +s Anc0.Anc0refChr3 25788 1 + 222631 A +s Anc1.Anc1refChr6 55375 1 + 197743 A +s Anc2.Anc2refChr13 29262 1 + 96486 A +s mr.mrrefChr5 247220 1 + 294540 A +s mr.mrrefChr5 176528 1 - 294540 A +s simCow_chr6.simCow.chr6 385302 1 + 602619 A +s simDog_chr6.simDog.chr6 375779 1 + 593897 A +s simHuman_chr6.simHuman.chr6 379825 1 + 601863 A +s simHuman_chr6.simHuman.chr6 444718 1 + 601863 A +s simMouse_chr6.simMouse.chr6 369866 1 - 636262 A +s simRat_chr6.simRat.chr6 255258 1 + 647215 A +s simRat_chr6.simRat.chr6 393627 1 + 647215 A + +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 @@ -151507,6 +159343,36 @@ s simRat_chr6.simRat.chr6 393682 3 + 647215 TGT a +s simMouse_chr6.simMouse.chr6 393566 10 + 636262 GCTTACTTCA +s Anc0.Anc0refChr3 25831 10 + 222631 GTTAACTCCA +s Anc1.Anc1refChr6 55418 10 + 197743 GTTAACTCCA +s Anc2.Anc2refChr13 29305 10 + 96486 GTTAACTCCA +s mr.mrrefChr5 247278 10 + 294540 GCTTACTTCA +s mr.mrrefChr5 176529 10 - 294540 AATGAAACAA +s simCow_chr6.simCow.chr6 385345 10 + 602619 GTTAACTCTG +s simDog_chr6.simDog.chr6 375836 10 + 593897 GTAAACTCAA +s simHuman_chr6.simHuman.chr6 379868 10 + 601863 GTCAACTCCA +s simHuman_chr6.simHuman.chr6 444761 10 + 601863 GTTGACTCCG +s simMouse_chr6.simMouse.chr6 369867 10 - 636262 AATGAAACAA +s simRat_chr6.simRat.chr6 255259 10 + 647215 AATGAAACAA +s simRat_chr6.simRat.chr6 393685 10 + 647215 GCTTACTTCA + +a +s simMouse_chr6.simMouse.chr6 393576 4 + 636262 TACC +s Anc0.Anc0refChr3 25859 4 + 222631 CTCT +s Anc1.Anc1refChr6 55446 4 + 197743 CTCT +s Anc2.Anc2refChr13 29333 4 + 96486 CTCT +s mr.mrrefChr5 247306 4 + 294540 CACC +s mr.mrrefChr5 176557 4 - 294540 CTCC +s simCow_chr6.simCow.chr6 385373 4 + 602619 CTCT +s simDog_chr6.simDog.chr6 375864 4 + 593897 CTCT +s simHuman_chr6.simHuman.chr6 379896 4 + 601863 CTCT +s simHuman_chr6.simHuman.chr6 444818 4 + 601863 CTCT +s simMouse_chr6.simMouse.chr6 370624 4 - 636262 CTCC +s simRat_chr6.simRat.chr6 392055 4 - 647215 CTCC +s simRat_chr6.simRat.chr6 393713 4 + 647215 CACT + +a s simMouse_chr6.simMouse.chr6 393580 5 + 636262 TAACA s Anc0.Anc0refChr3 25865 5 + 222631 CCACA s Anc1.Anc1refChr6 55452 5 + 197743 CCACA @@ -151519,6 +159385,49 @@ s simRat_chr6.simRat.chr6 393719 5 + 647215 TGACA a +s simMouse_chr6.simMouse.chr6 393585 4 + 636262 CTTA +s Anc0.Anc0refChr3 25870 4 + 222631 ATTA +s Anc1.Anc1refChr6 55457 4 + 197743 ATTA +s Anc2.Anc2refChr13 29344 4 + 96486 ATTA +s mr.mrrefChr5 247317 4 + 294540 CTTA +s mr.mrrefChr5 176563 4 - 294540 AGTA +s simCow_chr6.simCow.chr6 385384 4 + 602619 CTTA +s simDog_chr6.simDog.chr6 375878 3 + 593897 AGT- +s simHuman_chr6.simHuman.chr6 379907 1 + 601863 A--- +s simHuman_chr6.simHuman.chr6 444829 1 + 601863 A--- +s simMouse_chr6.simMouse.chr6 370630 4 - 636262 AGTA +s simRat_chr6.simRat.chr6 392061 4 - 647215 ATTA +s simRat_chr6.simRat.chr6 393724 4 + 647215 CTTA + +a +s simMouse_chr6.simMouse.chr6 393589 15 + 636262 AGAATGCCTCTGGCA +s Anc0.Anc0refChr3 25876 15 + 222631 AGACTACCTCTGGCC +s Anc1.Anc1refChr6 55463 15 + 197743 AGACTACCTCTGGCC +s Anc2.Anc2refChr13 29350 15 + 96486 AGCCTACCTCTGCTC +s mr.mrrefChr5 247321 15 + 294540 AGAATGCCTCTGGCA +s mr.mrrefChr5 176569 15 - 294540 AGAGTAGCACAGGCC +s simCow_chr6.simCow.chr6 385390 15 + 602619 AGCCTACCTCTGCTC +s simHuman_chr6.simHuman.chr6 379908 1 + 601863 --------------C +s simHuman_chr6.simHuman.chr6 444830 1 + 601863 --------------T +s simMouse_chr6.simMouse.chr6 370636 15 - 636262 AGAGTAGCACAGGCC +s simRat_chr6.simRat.chr6 392067 15 - 647215 AGTGTAGCACAGGCC +s simRat_chr6.simRat.chr6 393728 15 + 647215 AGAACGCCTCTGGCA + +a +s simMouse_chr6.simMouse.chr6 393604 2 + 636262 AA +s Anc0.Anc0refChr3 25891 2 + 222631 AT +s Anc1.Anc1refChr6 55478 2 + 197743 AT +s Anc2.Anc2refChr13 29365 2 + 96486 AC +s mr.mrrefChr5 247336 2 + 294540 AA +s mr.mrrefChr5 176585 2 - 294540 AT +s simCow_chr6.simCow.chr6 385405 2 + 602619 AC +s simHuman_chr6.simHuman.chr6 379909 2 + 601863 AT +s simHuman_chr6.simHuman.chr6 444831 1 + 601863 G- +s simMouse_chr6.simMouse.chr6 370652 2 - 636262 AT +s simRat_chr6.simRat.chr6 392083 2 - 647215 AT +s simRat_chr6.simRat.chr6 393743 2 + 647215 AT + +a s simMouse_chr6.simMouse.chr6 393606 5 + 636262 ATTTA s Anc0.Anc0refChr3 25893 5 + 222631 TCTTA s Anc1.Anc1refChr6 55480 5 + 197743 TCTTA @@ -151528,6 +159437,21 @@ s simRat_chr6.simRat.chr6 393745 5 + 647215 GCTTA a +s simMouse_chr6.simMouse.chr6 393611 7 + 636262 GCATCTA +s Anc0.Anc0refChr3 25898 7 + 222631 GCAGCCA +s Anc1.Anc1refChr6 55485 7 + 197743 GCAGCCA +s Anc2.Anc2refChr13 29372 7 + 96486 GCAGCCA +s mr.mrrefChr5 247343 7 + 294540 GCATCCA +s mr.mrrefChr5 176587 7 - 294540 GAATCCA +s simCow_chr6.simCow.chr6 385412 7 + 602619 GCAGCCA +s simDog_chr6.simDog.chr6 375881 5 + 593897 --AGCTA +s simHuman_chr6.simHuman.chr6 379911 7 + 601863 GCAACCA +s simHuman_chr6.simHuman.chr6 444832 5 + 601863 --AGCCA +s simMouse_chr6.simMouse.chr6 370654 7 - 636262 GAATCCA +s simRat_chr6.simRat.chr6 392085 7 - 647215 GAATCCA +s simRat_chr6.simRat.chr6 393750 7 + 647215 GCATCCA + +a s simMouse_chr6.simMouse.chr6 393618 4 + 636262 GCAC s Anc0.Anc0refChr3 25905 4 + 222631 GCAC s Anc1.Anc1refChr6 55492 4 + 197743 GCAC @@ -151552,6 +159476,95 @@ s simRat_chr6.simRat.chr6 393761 3 + 647215 AAT a +s simMouse_chr6.simMouse.chr6 393625 12 + 636262 TCATCTTAAGGC +s Anc0.Anc0refChr3 25914 12 + 222631 TCATGTTGAGCC +s Anc1.Anc1refChr6 55501 12 + 197743 TCATGTTGAGCC +s Anc2.Anc2refChr13 29388 12 + 96486 TCATGTTGAGGC +s mr.mrrefChr5 247357 12 + 294540 TCATCTTAAGGC +s mr.mrrefChr5 176594 12 - 294540 CCGTGTTCAGCC +s simCow_chr6.simCow.chr6 385428 11 + 602619 TCAT-TTGAGGC +s simDog_chr6.simDog.chr6 375895 12 + 593897 TCATGTTGAGGC +s simHuman_chr6.simHuman.chr6 379927 12 + 601863 TCATGTTGAGCC +s simHuman_chr6.simHuman.chr6 444846 12 + 601863 TCATGTTGAGCC +s simMouse_chr6.simMouse.chr6 370661 12 - 636262 CCGTGTTCAGCC +s simRat_chr6.simRat.chr6 392092 12 - 647215 TTATGTTCAGCT +s simRat_chr6.simRat.chr6 393764 9 + 647215 TC---TTAAGGC + +a +s simMouse_chr6.simMouse.chr6 393637 2 + 636262 CC +s Anc0.Anc0refChr3 25926 2 + 222631 CC +s Anc1.Anc1refChr6 55513 2 + 197743 CC +s Anc2.Anc2refChr13 29400 2 + 96486 TC +s mr.mrrefChr5 247369 2 + 294540 CC +s mr.mrrefChr5 176787 2 - 294540 ta +s simCow_chr6.simCow.chr6 385439 2 + 602619 TT +s simDog_chr6.simDog.chr6 375907 2 + 593897 TC +s simHuman_chr6.simHuman.chr6 379939 2 + 601863 CC +s simHuman_chr6.simHuman.chr6 444858 2 + 601863 CC +s simMouse_chr6.simMouse.chr6 370854 2 - 636262 ta +s simRat_chr6.simRat.chr6 392287 2 - 647215 ta +s simRat_chr6.simRat.chr6 393773 2 + 647215 CC + +a +s simMouse_chr6.simMouse.chr6 393639 15 + 636262 AATCATAGGAAGAGA +s Anc0.Anc0refChr3 25929 15 + 222631 AATCATGGGGAAGAG +s Anc1.Anc1refChr6 55516 15 + 197743 AATCATGGGGAAGAG +s Anc2.Anc2refChr13 29403 15 + 96486 AATCATGGAGGAGAG +s mr.mrrefChr5 247371 15 + 294540 AATCATAGGGAGAGA +s mr.mrrefChr5 176789 15 - 294540 aaaaatggagatgtg +s simCow_chr6.simCow.chr6 385442 14 + 602619 -ATCATGGAGGAGAG +s simDog_chr6.simDog.chr6 375910 15 + 593897 AATCATGGAGGAGAG +s simHuman_chr6.simHuman.chr6 379979 15 + 601863 AATCATGGGGAAGAG +s simHuman_chr6.simHuman.chr6 444861 15 + 601863 AATCATGGGGGAGAG +s simMouse_chr6.simMouse.chr6 370856 15 - 636262 aaaaatggagatgtg +s simRat_chr6.simRat.chr6 392289 15 - 647215 aaagatggaaatgtg +s simRat_chr6.simRat.chr6 393775 15 + 647215 AATCATAGGGAGAGA + +a +s simMouse_chr6.simMouse.chr6 393654 4 + 636262 AAGA +s Anc0.Anc0refChr3 25944 4 + 222631 AAAG +s Anc1.Anc1refChr6 55531 4 + 197743 AAAG +s Anc2.Anc2refChr13 29419 4 + 96486 AAAG +s mr.mrrefChr5 247386 4 + 294540 AAGA +s mr.mrrefChr5 176804 4 - 294540 atgc +s simCow_chr6.simCow.chr6 385457 4 + 602619 AAAA +s simDog_chr6.simDog.chr6 375926 4 + 593897 AAAG +s simHuman_chr6.simHuman.chr6 379994 4 + 601863 AAAG +s simHuman_chr6.simHuman.chr6 444876 4 + 601863 AAAA +s simMouse_chr6.simMouse.chr6 370871 4 - 636262 atgc +s simRat_chr6.simRat.chr6 392304 4 - 647215 atgc +s simRat_chr6.simRat.chr6 393790 4 + 647215 AAGA + +a +s simMouse_chr6.simMouse.chr6 393658 7 + 636262 AACTAGC +s Anc0.Anc0refChr3 25948 7 + 222631 CACCAGC +s Anc1.Anc1refChr6 55535 7 + 197743 CACCAGC +s Anc2.Anc2refChr13 29423 7 + 96486 CACCAGC +s mr.mrrefChr5 247390 7 + 294540 AACTAGC +s mr.mrrefChr5 176808 7 - 294540 tgatggt +s simCow_chr6.simCow.chr6 385461 7 + 602619 CACGAGC +s simDog_chr6.simDog.chr6 375930 7 + 593897 CGCCAGC +s simHuman_chr6.simHuman.chr6 444880 7 + 601863 CACCAGT +s simMouse_chr6.simMouse.chr6 370875 7 - 636262 tgatggt +s simRat_chr6.simRat.chr6 392308 7 - 647215 tgatggt +s simRat_chr6.simRat.chr6 393794 7 + 647215 ATCTAGC + +a +s simMouse_chr6.simMouse.chr6 393665 2 + 636262 AT +s Anc0.Anc0refChr3 25956 2 + 222631 AT +s Anc1.Anc1refChr6 55543 2 + 197743 AT +s Anc2.Anc2refChr13 29431 2 + 96486 AT +s mr.mrrefChr5 247397 2 + 294540 AT +s mr.mrrefChr5 176816 2 - 294540 cc +s simCow_chr6.simCow.chr6 385469 2 + 602619 AT +s simDog_chr6.simDog.chr6 375938 2 + 593897 GT +s simHuman_chr6.simHuman.chr6 379999 2 + 601863 CT +s simHuman_chr6.simHuman.chr6 444888 2 + 601863 AT +s simMouse_chr6.simMouse.chr6 370883 2 - 636262 cc +s simRat_chr6.simRat.chr6 392316 2 - 647215 tc +s simRat_chr6.simRat.chr6 393801 2 + 647215 AT + +a s simMouse_chr6.simMouse.chr6 393667 5 + 636262 GGTCT s Anc0.Anc0refChr3 25958 5 + 222631 GGGCT s Anc1.Anc1refChr6 55545 5 + 197743 GGGCT @@ -151562,6 +159575,21 @@ s simRat_chr6.simRat.chr6 393803 5 + 647215 GGTCT a +s simMouse_chr6.simMouse.chr6 393672 3 + 636262 ATG +s Anc0.Anc0refChr3 25963 3 + 222631 ATC +s Anc1.Anc1refChr6 55550 3 + 197743 ATC +s Anc2.Anc2refChr13 29438 3 + 96486 ATC +s mr.mrrefChr5 247404 3 + 294540 ATC +s mr.mrrefChr5 176818 3 - 294540 agc +s simCow_chr6.simCow.chr6 385476 3 + 602619 ATG +s simDog_chr6.simDog.chr6 375945 3 + 593897 ATA +s simHuman_chr6.simHuman.chr6 380001 3 + 601863 ATC +s simHuman_chr6.simHuman.chr6 444890 3 + 601863 ATC +s simMouse_chr6.simMouse.chr6 370885 3 - 636262 agc +s simRat_chr6.simRat.chr6 392318 3 - 647215 agt +s simRat_chr6.simRat.chr6 393808 3 + 647215 GTC + +a s simMouse_chr6.simMouse.chr6 393675 2 + 636262 TT s Anc0.Anc0refChr3 25966 2 + 222631 TT s Anc1.Anc1refChr6 55553 2 + 197743 TT @@ -151574,6 +159602,21 @@ s simRat_chr6.simRat.chr6 393811 2 + 647215 TT a +s simMouse_chr6.simMouse.chr6 393677 17 + 636262 AACGTTGTGATCTATTC +s Anc0.Anc0refChr3 25968 17 + 222631 AGCATTGTAGTCTAGAC +s Anc1.Anc1refChr6 55555 17 + 197743 AGCATTGTAGTCTAGAC +s Anc2.Anc2refChr13 29443 17 + 96486 AGCCTTGTAGTCTAGAC +s mr.mrrefChr5 247409 17 + 294540 AACATTGTGATCTATTC +s mr.mrrefChr5 176821 17 - 294540 agtactgcagcccagac +s simCow_chr6.simCow.chr6 385481 17 + 602619 GGTCTTGTGGTCTTAAC +s simDog_chr6.simDog.chr6 375950 17 + 593897 AGCCTTGTAGTCCGGAC +s simHuman_chr6.simHuman.chr6 380006 17 + 601863 AGCATTTTAGTCTAGAC +s simHuman_chr6.simHuman.chr6 444895 17 + 601863 AGCCTTTTAGTCTAGAC +s simMouse_chr6.simMouse.chr6 370888 17 - 636262 agtactgcagcccagac +s simRat_chr6.simRat.chr6 392321 17 - 647215 aatactgcagcccagac +s simRat_chr6.simRat.chr6 393813 17 + 647215 AAGATTGTGATTTATGC + +a s simMouse_chr6.simMouse.chr6 393694 2 + 636262 AT s Anc0.Anc0refChr3 25985 2 + 222631 AG s Anc1.Anc1refChr6 55572 2 + 197743 AG @@ -151586,7 +159629,19 @@ s simRat_chr6.simRat.chr6 393830 2 + 647215 AG a -s simMouse_chr6.simMouse.chr6 393700 36 + 636262 TGGGGTGAGCGCCCTTCCCCAATGATGTTACTCAGT +s simMouse_chr6.simMouse.chr6 393696 53 + 636262 CACTTGGGGTGAGCGCCCTTCCCCAATGATGTTACTCAGTATCTCTTAGGGGA +s Anc0.Anc0refChr3 25987 17 + 222631 CTCC------------------------------------ATCCTTTAGAAGA +s Anc1.Anc1refChr6 55574 17 + 197743 CTCC------------------------------------ATCCTTTAGAAGA +s Anc2.Anc2refChr13 29462 17 + 96486 CTCC------------------------------------ATCCTTTAGAGGA +s mr.mrrefChr5 247428 17 + 294540 CACT------------------------------------ATCTCTTAGGGGA +s mr.mrrefChr5 176838 17 - 294540 ttct------------------------------------agctcccaaaatg +s simCow_chr6.simCow.chr6 385500 17 + 602619 CTTT------------------------------------ATCCTTTAGAGGA +s simDog_chr6.simDog.chr6 375969 15 + 593897 CT--------------------------------------ATTCTTTCGAGGA +s simHuman_chr6.simHuman.chr6 380025 17 + 601863 CTCC------------------------------------ATCCTTTAGAAAA +s simHuman_chr6.simHuman.chr6 444914 17 + 601863 CTCC------------------------------------ATCCTTTAGAAGA +s simMouse_chr6.simMouse.chr6 370905 17 - 636262 ttct------------------------------------agctcccaaaatg +s simRat_chr6.simRat.chr6 392338 17 - 647215 ttct------------------------------------ggctcgcaaaatg +s simRat_chr6.simRat.chr6 393832 17 + 647215 CACT------------------------------------GTCTCTTAGGGGA a s simMouse_chr6.simMouse.chr6 393749 5 + 636262 AGTAC @@ -151600,6 +159655,63 @@ s simRat_chr6.simRat.chr6 393849 5 + 647215 AATGC a +s simMouse_chr6.simMouse.chr6 393754 1 + 636262 A +s Anc0.Anc0refChr3 26009 1 + 222631 A +s Anc1.Anc1refChr6 55596 1 + 197743 A +s Anc2.Anc2refChr13 29484 1 + 96486 A +s mr.mrrefChr5 247450 1 + 294540 A +s mr.mrrefChr5 176855 1 - 294540 a +s simCow_chr6.simCow.chr6 385522 1 + 602619 A +s simDog_chr6.simDog.chr6 375989 1 + 593897 A +s simHuman_chr6.simHuman.chr6 380052 1 + 601863 A +s simHuman_chr6.simHuman.chr6 444931 1 + 601863 A +s simMouse_chr6.simMouse.chr6 370922 1 - 636262 a +s simRat_chr6.simRat.chr6 392355 1 - 647215 a +s simRat_chr6.simRat.chr6 393854 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 393755 5 + 636262 ACTGG +s Anc0.Anc0refChr3 26010 2 + 222631 AC--- +s Anc1.Anc1refChr6 55597 5 + 197743 ACttg +s Anc2.Anc2refChr13 29485 2 + 96486 AC--- +s mr.mrrefChr5 247451 5 + 294540 ACTGG +s mr.mrrefChr5 176858 5 - 294540 ccttg +s simDog_chr6.simDog.chr6 375990 2 + 593897 AC--- +s simHuman_chr6.simHuman.chr6 380053 2 + 601863 AC--- +s simHuman_chr6.simHuman.chr6 444932 2 + 601863 AC--- +s simMouse_chr6.simMouse.chr6 370925 5 - 636262 ccttg +s simRat_chr6.simRat.chr6 392358 5 - 647215 ccttg +s simRat_chr6.simRat.chr6 393855 5 + 647215 ACTGG + +a +s simMouse_chr6.simMouse.chr6 393760 17 + 636262 ACAGAGACAATATGCCT +s Anc0.Anc0refChr3 26012 17 + 222631 ACAGAATCAATAAGTAT +s Anc1.Anc1refChr6 55602 17 + 197743 ACAGAATCAATAAGTAT +s Anc2.Anc2refChr13 29487 17 + 96486 ACAGAATGAATAAGTAT +s mr.mrrefChr5 247456 17 + 294540 ACAGAGACAATATGCAT +s mr.mrrefChr5 176863 17 - 294540 agggatgcaacattcat +s simDog_chr6.simDog.chr6 375995 17 + 593897 ACAGAATGAATAAGTAT +s simHuman_chr6.simHuman.chr6 380055 17 + 601863 ACAGAATGAAAAAGTAT +s simHuman_chr6.simHuman.chr6 444934 17 + 601863 ACAGAGTCAACAAGTAT +s simMouse_chr6.simMouse.chr6 370930 17 - 636262 agggatgcaacattcat +s simRat_chr6.simRat.chr6 392363 17 - 647215 agagattcaacattctt +s simRat_chr6.simRat.chr6 393860 17 + 647215 ATATAGACAATATGCAT + +a +s simMouse_chr6.simMouse.chr6 393777 14 + 636262 ATTATTATTTTCTT +s Anc0.Anc0refChr3 26029 14 + 222631 ACTGTTATGTCCCT +s Anc1.Anc1refChr6 55619 14 + 197743 ACTGTTATGTCCCT +s Anc2.Anc2refChr13 29504 14 + 96486 ACTGTTATGTCCCT +s mr.mrrefChr5 247473 14 + 294540 ATTGTTATTTTCTT +s mr.mrrefChr5 176881 14 - 294540 attattattttaat +s simDog_chr6.simDog.chr6 376012 14 + 593897 ACTGTTATGTCCTT +s simHuman_chr6.simHuman.chr6 380072 14 + 601863 ACTGTCATGTCCCT +s simHuman_chr6.simHuman.chr6 444951 14 + 601863 ACTGTAATGTCCCC +s simMouse_chr6.simMouse.chr6 370948 14 - 636262 attattattttaat +s simRat_chr6.simRat.chr6 392381 14 - 647215 gttattattttaat +s simRat_chr6.simRat.chr6 393877 14 + 647215 ATCGTTATTTTCTT + +a s simMouse_chr6.simMouse.chr6 393791 1 + 636262 A s Anc1.Anc1refChr6 55633 1 + 197743 A s mr.mrrefChr5 247487 1 + 294540 A @@ -151608,6 +159720,36 @@ s simRat_chr6.simRat.chr6 393891 1 + 647215 A a +s simMouse_chr6.simMouse.chr6 393792 12 + 636262 TGACTATTTTTT +s Anc0.Anc0refChr3 26043 12 + 222631 TGATTACTTTTA +s Anc1.Anc1refChr6 55634 12 + 197743 TGATTACTTTTA +s Anc2.Anc2refChr13 29518 12 + 96486 TGATTAGTTTTT +s mr.mrrefChr5 247488 12 + 294540 TGACTATTTTTA +s mr.mrrefChr5 176895 12 - 294540 agactgctttta +s simCow_chr6.simCow.chr6 385523 7 + 602619 -----AATTTTT +s simDog_chr6.simDog.chr6 376026 12 + 593897 TGATTAGTTTTT +s simHuman_chr6.simHuman.chr6 380087 12 + 601863 TGATTATACTGA +s simHuman_chr6.simHuman.chr6 444966 12 + 601863 GGATTACTCTGA +s simMouse_chr6.simMouse.chr6 370962 12 - 636262 agactgctttta +s simRat_chr6.simRat.chr6 392395 12 - 647215 agactgcttata +s simRat_chr6.simRat.chr6 393892 12 + 647215 TGACTATTTTTA + +a +s simMouse_chr6.simMouse.chr6 393804 2 + 636262 AA +s Anc0.Anc0refChr3 26055 2 + 222631 CA +s Anc1.Anc1refChr6 55646 2 + 197743 CA +s Anc2.Anc2refChr13 29530 2 + 96486 CA +s mr.mrrefChr5 247500 2 + 294540 CA +s mr.mrrefChr5 176907 2 - 294540 ca +s simCow_chr6.simCow.chr6 385530 2 + 602619 GA +s simDog_chr6.simDog.chr6 376038 2 + 593897 CC +s simHuman_chr6.simHuman.chr6 380099 2 + 601863 CA +s simHuman_chr6.simHuman.chr6 444978 2 + 601863 CA +s simMouse_chr6.simMouse.chr6 370975 2 - 636262 ca +s simRat_chr6.simRat.chr6 392407 2 - 647215 ca +s simRat_chr6.simRat.chr6 393904 2 + 647215 CA + +a s simMouse_chr6.simMouse.chr6 393806 7 + 636262 TATTAGG s Anc0.Anc0refChr3 26057 7 + 222631 TATCAGG s Anc1.Anc1refChr6 55648 7 + 197743 TATCAGG @@ -151620,6 +159762,36 @@ s simRat_chr6.simRat.chr6 393906 7 + 647215 TATCAGG a +s simMouse_chr6.simMouse.chr6 393813 7 + 636262 CTCAACA +s Anc0.Anc0refChr3 26064 7 + 222631 ATCCACA +s Anc1.Anc1refChr6 55655 7 + 197743 ATCCACA +s Anc2.Anc2refChr13 29539 7 + 96486 ATCCACA +s mr.mrrefChr5 247509 7 + 294540 CTCAACA +s mr.mrrefChr5 176909 7 - 294540 atcctta +s simCow_chr6.simCow.chr6 385539 7 + 602619 GCCCACA +s simDog_chr6.simDog.chr6 376047 7 + 593897 ATCCACA +s simHuman_chr6.simHuman.chr6 380108 7 + 601863 ATCTACT +s simHuman_chr6.simHuman.chr6 444986 5 + 601863 --CTACA +s simMouse_chr6.simMouse.chr6 370977 7 - 636262 atcctta +s simRat_chr6.simRat.chr6 392409 7 - 647215 atCCTTG +s simRat_chr6.simRat.chr6 393913 7 + 647215 CTCAATG + +a +s simMouse_chr6.simMouse.chr6 393820 28 + 636262 GGAAATAATGCCTGGGAGATGGTAGGTG +s Anc0.Anc0refChr3 26071 28 + 222631 GGAAGGGAGCCCTGGGATATAACTAGTG +s Anc1.Anc1refChr6 55662 28 + 197743 GGAAGGGAGCCCTGGGATATAACTAGTG +s Anc2.Anc2refChr13 29546 28 + 96486 GGAAGGGATCCCTGGGATATAGCTAGTG +s mr.mrrefChr5 247516 28 + 294540 GGAAAGAATGCCTGGGAGATGGCTGGTG +s mr.mrrefChr5 176916 28 - 294540 ggaagctggctgctagagataacccaag +s simCow_chr6.simCow.chr6 385546 28 + 602619 GTAAGGGATCCCTGAGATATCGCTAGTG +s simDog_chr6.simDog.chr6 376054 28 + 593897 GAAAGAGATTCCTGGGATATGGCTAGTG +s simHuman_chr6.simHuman.chr6 380115 28 + 601863 GGACGGGAGCCTTGGGATATAACTAGTG +s simHuman_chr6.simHuman.chr6 444991 28 + 601863 GGACGGGAGCCCTGGGACATAACTAATG +s simMouse_chr6.simMouse.chr6 370995 28 - 636262 ggaagctggctgctagagataacccaag +s simRat_chr6.simRat.chr6 392416 28 - 647215 Ggaagccagctgctagagataacccaag +s simRat_chr6.simRat.chr6 393920 28 + 647215 GGAAAGAATTCCTGGGAGATGGCTGGTG + +a s simMouse_chr6.simMouse.chr6 393848 2 + 636262 CC s Anc0.Anc0refChr3 26099 2 + 222631 CC s Anc1.Anc1refChr6 55690 2 + 197743 CC @@ -151728,7 +159900,19 @@ s simRat_chr6.simRat.chr6 394050 5 + 647215 CTGTT a -s simMouse_chr6.simMouse.chr6 393964 4 + 636262 ATTT +s simMouse_chr6.simMouse.chr6 393955 18 + 636262 TAGGTATTCATTTCCTAC +s Anc0.Anc0refChr3 26253 14 + 222631 AATTTATTC----TCTGC +s Anc1.Anc1refChr6 55844 14 + 197743 AATTTATTC----TCTGC +s Anc2.Anc2refChr13 29728 14 + 96486 AATTTACTC----TCAGC +s mr.mrrefChr5 247651 14 + 294540 TATGTATTC----CCTGC +s mr.mrrefChr5 176944 14 - 294540 aatgttgtc----tctgt +s simCow_chr6.simCow.chr6 385850 14 + 602619 AACTTGCTC----TCAGC +s simDog_chr6.simDog.chr6 376197 14 + 593897 AATTTACTC----ACAGC +s simHuman_chr6.simHuman.chr6 380306 14 + 601863 CATTTATTC----TCTGC +s simHuman_chr6.simHuman.chr6 445148 14 + 601863 CATTTATTC----TCTGC +s simMouse_chr6.simMouse.chr6 371023 14 - 636262 aatgttgtc----tctgt +s simRat_chr6.simRat.chr6 392444 14 - 647215 aaggccatc----tctgg +s simRat_chr6.simRat.chr6 394055 14 + 647215 AATGTGTTC----CCTGC a s simMouse_chr6.simMouse.chr6 393973 4 + 636262 TCGG @@ -151743,6 +159927,21 @@ s simRat_chr6.simRat.chr6 394069 4 + 647215 TCTG a +s simMouse_chr6.simMouse.chr6 393977 22 + 636262 GAGTTAACTTATTAGTTGTGAT +s Anc0.Anc0refChr3 26271 22 + 222631 AAATTAACTTAATAGATGTGAT +s Anc1.Anc1refChr6 55862 22 + 197743 AAATTAACTTAATAGATGTGAT +s Anc2.Anc2refChr13 29746 22 + 96486 AAATCAACTTAATGGATGTGAT +s mr.mrrefChr5 247669 22 + 294540 GAGTTAACTTATTAGATGTGAT +s mr.mrrefChr5 176958 22 - 294540 aaggacactgaatacacctgct +s simCow_chr6.simCow.chr6 385868 22 + 602619 AAGTCTACTTAACGGATGTGAC +s simDog_chr6.simDog.chr6 376215 21 + 593897 AAATCAACTCAATGGACA-AAT +s simHuman_chr6.simHuman.chr6 380324 22 + 601863 AAATTAACTTAATAAATTTGAT +s simHuman_chr6.simHuman.chr6 445166 22 + 601863 AAATTAACTTAATAGATGTGAT +s simMouse_chr6.simMouse.chr6 371037 22 - 636262 aaggacactgaatacacctgct +s simRat_chr6.simRat.chr6 392458 22 - 647215 aaagacactaaatacacctgct +s simRat_chr6.simRat.chr6 394073 22 + 647215 GAGCTAACTTATTAGATGTGAT + +a s simMouse_chr6.simMouse.chr6 393999 2 + 636262 TG s Anc0.Anc0refChr3 26293 2 + 222631 TG s Anc1.Anc1refChr6 55884 2 + 197743 TG @@ -151755,11 +159954,101 @@ s simRat_chr6.simRat.chr6 394095 2 + 647215 TG a +s simMouse_chr6.simMouse.chr6 394001 1 + 636262 G +s Anc0.Anc0refChr3 26295 1 + 222631 G +s Anc1.Anc1refChr6 55886 1 + 197743 G +s Anc2.Anc2refChr13 29770 1 + 96486 G +s mr.mrrefChr5 247693 1 + 294540 G +s mr.mrrefChr5 176980 1 - 294540 a +s simCow_chr6.simCow.chr6 385892 1 + 602619 G +s simDog_chr6.simDog.chr6 376238 1 + 593897 G +s simHuman_chr6.simHuman.chr6 380348 1 + 601863 G +s simHuman_chr6.simHuman.chr6 445190 1 + 601863 G +s simMouse_chr6.simMouse.chr6 371059 1 - 636262 a +s simRat_chr6.simRat.chr6 392480 1 - 647215 a +s simRat_chr6.simRat.chr6 394097 1 + 647215 G + +a +s simMouse_chr6.simMouse.chr6 394002 8 + 636262 GAACACAA +s Anc0.Anc0refChr3 26296 8 + 222631 CAAGCCGA +s Anc1.Anc1refChr6 55887 8 + 197743 CAAGCCGA +s Anc2.Anc2refChr13 29771 8 + 96486 CAAGCTGA +s mr.mrrefChr5 247694 8 + 294540 GAACACAA +s mr.mrrefChr5 176981 8 - 294540 catgccag +s simCow_chr6.simCow.chr6 385893 8 + 602619 CAAGCCGA +s simDog_chr6.simDog.chr6 376239 8 + 593897 CAAGCTTA +s simHuman_chr6.simHuman.chr6 380349 8 + 601863 CAAGCCGA +s simHuman_chr6.simHuman.chr6 445196 8 + 601863 CAAACTGA +s simMouse_chr6.simMouse.chr6 371060 8 - 636262 catgccag +s simRat_chr6.simRat.chr6 392481 8 - 647215 catgccag +s simRat_chr6.simRat.chr6 394098 8 + 647215 GCACACAA + +a +s simMouse_chr6.simMouse.chr6 394010 1 + 636262 T +s Anc0.Anc0refChr3 26304 1 + 222631 T +s Anc1.Anc1refChr6 55895 1 + 197743 T +s Anc2.Anc2refChr13 29779 1 + 96486 T +s mr.mrrefChr5 247702 1 + 294540 T +s mr.mrrefChr5 176989 1 - 294540 g +s simCow_chr6.simCow.chr6 385904 1 + 602619 T +s simDog_chr6.simDog.chr6 376247 1 + 593897 A +s simHuman_chr6.simHuman.chr6 380357 1 + 601863 T +s simHuman_chr6.simHuman.chr6 445204 1 + 601863 T +s simMouse_chr6.simMouse.chr6 371068 1 - 636262 g +s simRat_chr6.simRat.chr6 392489 1 - 647215 g +s simRat_chr6.simRat.chr6 394106 1 + 647215 T + +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 394025 7 + 636262 ATACTGT +s Anc0.Anc0refChr3 26305 7 + 222631 ATATAGT +s Anc1.Anc1refChr6 55896 7 + 197743 ATATAGT +s Anc2.Anc2refChr13 29780 7 + 96486 ATATAGA +s mr.mrrefChr5 247714 7 + 294540 ATACTGT +s mr.mrrefChr5 176990 7 - 294540 atccagt +s simCow_chr6.simCow.chr6 385905 7 + 602619 ATATAGG +s simDog_chr6.simDog.chr6 376248 7 + 593897 ATATAGA +s simHuman_chr6.simHuman.chr6 380358 7 + 601863 ATATAGT +s simHuman_chr6.simHuman.chr6 445205 7 + 601863 ATATAGT +s simMouse_chr6.simMouse.chr6 371069 7 - 636262 atccagt +s simRat_chr6.simRat.chr6 392490 7 - 647215 cacCAGT +s simRat_chr6.simRat.chr6 394116 7 + 647215 ATACGGT + +a +s simMouse_chr6.simMouse.chr6 394032 5 + 636262 CTAGT +s Anc0.Anc0refChr3 26312 5 + 222631 CTAGC +s Anc1.Anc1refChr6 55903 5 + 197743 CTAGC +s Anc2.Anc2refChr13 29787 5 + 96486 CCAGC +s mr.mrrefChr5 247721 5 + 294540 CTAGT +s mr.mrrefChr5 176997 5 - 294540 caacc +s simCow_chr6.simCow.chr6 385912 5 + 602619 CCAAC +s simDog_chr6.simDog.chr6 376261 5 + 593897 CCAGC +s simHuman_chr6.simHuman.chr6 380365 5 + 601863 CTAGT +s simHuman_chr6.simHuman.chr6 445212 5 + 601863 CTAGC +s simMouse_chr6.simMouse.chr6 371076 5 - 636262 caacc +s simRat_chr6.simRat.chr6 392497 5 - 647215 CAACC +s simRat_chr6.simRat.chr6 394123 5 + 647215 CTAGC + +a +s simMouse_chr6.simMouse.chr6 394037 3 + 636262 ATG +s Anc0.Anc0refChr3 26333 3 + 222631 GTC +s Anc1.Anc1refChr6 55924 3 + 197743 GTC +s Anc2.Anc2refChr13 29811 3 + 96486 GTA +s mr.mrrefChr5 247726 3 + 294540 ATG +s mr.mrrefChr5 177019 3 - 294540 GTC +s simCow_chr6.simCow.chr6 385936 3 + 602619 GTG +s simDog_chr6.simDog.chr6 376285 3 + 593897 GTA +s simHuman_chr6.simHuman.chr6 380370 3 + 601863 TTC +s simHuman_chr6.simHuman.chr6 445217 3 + 601863 GTC +s simMouse_chr6.simMouse.chr6 371099 3 - 636262 GTC +s simRat_chr6.simRat.chr6 392519 3 - 647215 GTC +s simRat_chr6.simRat.chr6 394128 3 + 647215 ATG + +a s simMouse_chr6.simMouse.chr6 394040 5 + 636262 GATGC s Anc0.Anc0refChr3 26336 5 + 222631 CATTC s Anc1.Anc1refChr6 55927 5 + 197743 CATTC @@ -151771,6 +160060,21 @@ s simRat_chr6.simRat.chr6 394131 5 + 647215 GATAC a +s simMouse_chr6.simMouse.chr6 394045 53 + 636262 CTCTCGATGATTAAACCCAGTATTTAGAATTAACAGCTGGTTGTGCCAAAGCC +s Anc0.Anc0refChr3 26341 53 + 222631 CCCTGTATAATTAAACCCAGTGTTAGAAAGTAACAGCTTATTGTGGTAAAACC +s Anc1.Anc1refChr6 55932 53 + 197743 CCCTGTATAATTAAACCCAGTGTTAGAAAGTAACAGCTTATTGTGGTAAAACC +s Anc2.Anc2refChr13 29819 53 + 96486 CCCTGTATAATTAAACCCAGTGTTAGAAAGCAAAACCTTATTGTAGTAAAACC +s mr.mrrefChr5 247734 53 + 294540 CTCTGGATGATTAAACCCAGTATTTAGAATTAACAGCTGGTTGTGCCAAAGCC +s mr.mrrefChr5 177022 53 - 294540 CAATGAATGTTTAAACCCAGACTTTGAAAGTGACAGCTTACTGTGGTAGAACC +s simCow_chr6.simCow.chr6 385944 53 + 602619 CCCTGTATAATTAAACCCAGTGTTAGAAAGAAACACCTTAATGTGGTAAAACC +s simDog_chr6.simDog.chr6 376293 53 + 593897 CCCTGTATAATTAAGCCCAATGTTAGAAAGCAAAACCTTATTGTAGTAAAACC +s simHuman_chr6.simHuman.chr6 380373 25 + 601863 CCAAGTATAATGAAACCCAGTGTTA---------------------------- +s simHuman_chr6.simHuman.chr6 445225 25 + 601863 CCCAATATAATTAAACGCAGTGTTA---------------------------- +s simMouse_chr6.simMouse.chr6 371102 53 - 636262 TAATGAATGTTTAAACCCAGACTTTGAAAGTGACAGATTACTGTGCTAGAACC +s simRat_chr6.simRat.chr6 392522 53 - 647215 CAATGAATGTTTAAACCCAGCCTTTGAAAGTGACAGCTTTCTGTGGTAGAACC +s simRat_chr6.simRat.chr6 394136 53 + 647215 ATCTGGATGATTAAACGCAGTATTGAGGATTAACAACTGATTGTGATAAAACC + +a s simMouse_chr6.simMouse.chr6 394098 1 + 636262 T s Anc0.Anc0refChr3 26394 1 + 222631 C s Anc1.Anc1refChr6 55985 1 + 197743 C @@ -151782,21 +160086,137 @@ 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 +s simMouse_chr6.simMouse.chr6 394099 8 + 636262 GAGTGCTA +s Anc0.Anc0refChr3 26419 8 + 222631 GAGTGCTA +s Anc1.Anc1refChr6 56010 8 + 197743 GAGTGCTA +s Anc2.Anc2refChr13 29897 8 + 96486 GAGTGCTA +s mr.mrrefChr5 247788 8 + 294540 GAGTGCTA +s mr.mrrefChr5 177099 8 - 294540 GAGTGCTA +s simCow_chr6.simCow.chr6 386021 8 + 602619 GAGTGCTA +s simDog_chr6.simDog.chr6 376489 8 + 593897 GAGTATTA +s simHuman_chr6.simHuman.chr6 380423 8 + 601863 GAGTGCTA +s simHuman_chr6.simHuman.chr6 445275 8 + 601863 GAGTGCTA +s simMouse_chr6.simMouse.chr6 371179 8 - 636262 GAGTGCTA +s simRat_chr6.simRat.chr6 392599 8 - 647215 GAATGCTA +s simRat_chr6.simRat.chr6 394214 8 + 647215 GAGTGCTA + +a +s simMouse_chr6.simMouse.chr6 394107 33 + 636262 AACAATGTTGGTGTCAATAAACCTGGGACAGCA +s Anc0.Anc0refChr3 26433 33 + 222631 GATAATGATGTTGTCAATAAACTTGGGAGGGCA +s Anc1.Anc1refChr6 56024 33 + 197743 GATAATGATGTTGTCAATAAACTTGGGAGGGCA +s Anc2.Anc2refChr13 29911 33 + 96486 GATAATAATGTTATCAATAAACTTGGGAGGGTG +s mr.mrrefChr5 247796 33 + 294540 AACAATGTTGTTGTCAATAAACCTGGGACAGCA +s mr.mrrefChr5 177107 33 - 294540 GGTAAGGCTTTCGTCGATAAACCTGGGAGGGTA +s simCow_chr6.simCow.chr6 386035 33 + 602619 AATAACACTGTCATTGATGAACTTGGGAGGGTG +s simDog_chr6.simDog.chr6 376503 33 + 593897 GATAATATCATTATCAATAAACTTGGGAGGGTG +s simHuman_chr6.simHuman.chr6 380437 33 + 601863 GATAATGATGTCGTCAATAAACTTCGAAGGGCA +s simHuman_chr6.simHuman.chr6 445289 27 + 601863 GATAATGATGTTGTCAATAGACTCC------CA +s simMouse_chr6.simMouse.chr6 371187 33 - 636262 GGTAAGGTCTTCGTCGATAAACCTGGGAGGGCA +s simRat_chr6.simRat.chr6 392607 33 - 647215 TGTAAGGCTTTTGTCAATAAACCTCAGTGGATA +s simRat_chr6.simRat.chr6 394222 33 + 647215 CACAATGTTATTGTTAATAAACCTGGGATAACA + +a +s simMouse_chr6.simMouse.chr6 394140 8 + 636262 TACTCAGA +s Anc0.Anc0refChr3 26466 8 + 222631 TACTTGCA +s Anc1.Anc1refChr6 56057 8 + 197743 TACTTGCA +s Anc2.Anc2refChr13 29944 8 + 96486 TATTTGCA +s mr.mrrefChr5 247829 8 + 294540 TACTCAGA +s mr.mrrefChr5 177140 8 - 294540 TACTTGAG +s simCow_chr6.simCow.chr6 386076 8 + 602619 CCTTTGAA +s simDog_chr6.simDog.chr6 376536 8 + 593897 TGTTTGGA +s simHuman_chr6.simHuman.chr6 380470 8 + 601863 TACTTGCA +s simHuman_chr6.simHuman.chr6 445316 8 + 601863 TACTTACA +s simMouse_chr6.simMouse.chr6 371220 8 - 636262 TACTTGGG +s simRat_chr6.simRat.chr6 392640 8 - 647215 TGCTTGAG +s simRat_chr6.simRat.chr6 394255 8 + 647215 CACTCAGA + +a +s simMouse_chr6.simMouse.chr6 394148 8 + 636262 ATGGTTGT +s Anc0.Anc0refChr3 26474 8 + 222631 ATGTGTCT +s Anc1.Anc1refChr6 56065 8 + 197743 ATGTGTCT +s Anc2.Anc2refChr13 29952 8 + 96486 ATGTGTCT +s mr.mrrefChr5 247837 8 + 294540 ATGGTTGT +s mr.mrrefChr5 177148 8 - 294540 ATGGGTCT +s simCow_chr6.simCow.chr6 386084 8 + 602619 ATGTGTCT +s simDog_chr6.simDog.chr6 376544 8 + 593897 AAGTGTAT +s simHuman_chr6.simHuman.chr6 445324 8 + 601863 ATATGCCT +s simMouse_chr6.simMouse.chr6 371228 8 - 636262 ATGGGTCT +s simRat_chr6.simRat.chr6 392648 8 - 647215 GTGGGTCT +s simRat_chr6.simRat.chr6 394263 8 + 647215 ATGGTTGT + +a +s simMouse_chr6.simMouse.chr6 394156 16 + 636262 CTGTAAACTTAAAGAG +s Anc0.Anc0refChr3 26482 16 + 222631 CTCCAAACTTAAGGAG +s Anc1.Anc1refChr6 56073 16 + 197743 CTCCAAACTTAAGGAG +s Anc2.Anc2refChr13 29960 16 + 96486 CTCAAAAGTTAAAGAG +s mr.mrrefChr5 247845 16 + 294540 CTGTAAACTTAAAGAG +s mr.mrrefChr5 177156 16 - 294540 GTCCAAACATGAGGAG +s simCow_chr6.simCow.chr6 386092 16 + 602619 GTCAAAAGTAAAGGAG +s simDog_chr6.simDog.chr6 376552 16 + 593897 CTCAAATGTTAAAGAG +s simHuman_chr6.simHuman.chr6 380478 16 + 601863 CTCCAAACTCAAGGAG +s simHuman_chr6.simHuman.chr6 445332 16 + 601863 TTCCAAACTTGAGGAG +s simMouse_chr6.simMouse.chr6 371236 9 - 636262 GTCCA-------GGAG +s simRat_chr6.simRat.chr6 392656 16 - 647215 ATCCAAACATGAGAAG +s simRat_chr6.simRat.chr6 394271 16 + 647215 CTGTAAACTCTAAGAG + +a +s simMouse_chr6.simMouse.chr6 394172 10 + 636262 TTCTTGGGGT +s Anc0.Anc0refChr3 26498 10 + 222631 TTCTTGGAAT +s Anc1.Anc1refChr6 56089 10 + 197743 TTCTTGGAAT +s Anc2.Anc2refChr13 29980 10 + 96486 TGCTTGGAAT +s mr.mrrefChr5 247861 10 + 294540 TTCTTGGAAT +s mr.mrrefChr5 177172 10 - 294540 CTTTTGGAAT +s simCow_chr6.simCow.chr6 386112 10 + 602619 TGCATGAGCT +s simDog_chr6.simDog.chr6 376572 10 + 593897 TGCGTGGAAT +s simHuman_chr6.simHuman.chr6 380494 10 + 601863 TTCTTGGAAT +s simHuman_chr6.simHuman.chr6 445348 10 + 601863 TTCTTGGAAT +s simMouse_chr6.simMouse.chr6 371245 10 - 636262 CTTTTGGAAT +s simRat_chr6.simRat.chr6 392672 10 - 647215 CTTTTGGAAT +s simRat_chr6.simRat.chr6 394287 10 + 647215 TTCTTGGAAT + +a +s simMouse_chr6.simMouse.chr6 394182 45 + 636262 TTTCTCTGAAAGTAAGTCAATTGAGCTCAAATGAGCAGTATCATT +s Anc0.Anc0refChr3 26509 35 + 222631 TTTCTCACAAAGTAA----------CTCAACTGAGCAATATTATT +s Anc1.Anc1refChr6 56100 35 + 197743 TTTCTCACAAAGTAA----------CTCAACTGAGCAATATTATT +s Anc2.Anc2refChr13 29991 35 + 96486 TTTCTCACAAAGTAA----------CACAACTGAGCAATATTATA +s mr.mrrefChr5 247871 35 + 294540 TTTCTCTGAAAGTAA----------CTCAAATGAGCAATATCATT +s mr.mrrefChr5 177182 35 - 294540 TTTGTTAGAAAGTAA----------TTCTATTGAGCAATATCATC +s simCow_chr6.simCow.chr6 386123 31 + 602619 TTTCTCCGAAAGTAA----------CAAAACTCAGCAAGAT---- +s simDog_chr6.simDog.chr6 376583 35 + 593897 TTGCTCTCAAAGTAA----------CACAACTTAGCAATACGCTA +s simHuman_chr6.simHuman.chr6 380505 35 + 601863 TTTCTCACAAAGTAA----------CTCAACTGAGCAATATTATT +s simHuman_chr6.simHuman.chr6 445359 35 + 601863 TTTCTCACAAAGTAA----------CTCAACTGATCAATATTATC +s simMouse_chr6.simMouse.chr6 371255 35 - 636262 TTTGTTAGAAAGTAA----------TTCTATTGAGCAATATCATC +s simRat_chr6.simRat.chr6 392682 35 - 647215 TTTGTTTGAAAGTAA----------TTCTATTGAGCAATATCATC +s simRat_chr6.simRat.chr6 394297 35 + 647215 TTCCTCTGAAAGTCA----------CTCAATTGAGCAATATCATT + +a +s simMouse_chr6.simMouse.chr6 394227 1 + 636262 C +s Anc0.Anc0refChr3 26544 1 + 222631 G +s Anc1.Anc1refChr6 56135 1 + 197743 G +s Anc2.Anc2refChr13 30026 1 + 96486 G +s mr.mrrefChr5 247906 1 + 294540 C +s mr.mrrefChr5 177218 1 - 294540 A +s simDog_chr6.simDog.chr6 376618 1 + 593897 A +s simHuman_chr6.simHuman.chr6 380540 1 + 601863 G +s simHuman_chr6.simHuman.chr6 445394 1 + 601863 G +s simMouse_chr6.simMouse.chr6 371291 1 - 636262 A +s simRat_chr6.simRat.chr6 392718 1 - 647215 G +s simRat_chr6.simRat.chr6 394332 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 394228 23 + 636262 AGCAGAAGGAGCCCTCTTGTATT +s Anc0.Anc0refChr3 26545 23 + 222631 GATAGAAGGTGGCCTCTTATATT +s Anc1.Anc1refChr6 56136 23 + 197743 GATAGAAGGTGGCCTCTTATATT +s Anc2.Anc2refChr13 30027 23 + 96486 GATAGAAGGTGGTCTCTTATATT +s mr.mrrefChr5 247907 23 + 294540 GGCAGAAGGAGCCCTCTTGTATT +s mr.mrrefChr5 177219 23 - 294540 AACAGACAGAGCCCTATTGTATT +s simCow_chr6.simCow.chr6 386154 23 + 602619 GATAGAGGGAGGCCTCTTATATT +s simDog_chr6.simDog.chr6 376628 23 + 593897 GATAGAAAGTGGTCTCTTCTATC +s simHuman_chr6.simHuman.chr6 380541 23 + 601863 GATAGAAGATGGTCCCTTATATT +s simHuman_chr6.simHuman.chr6 445395 23 + 601863 GATAGAAGATGGCCACTTATATT +s simMouse_chr6.simMouse.chr6 371292 23 - 636262 AACAGACAGAGCCCTATTGTATT +s simRat_chr6.simRat.chr6 392719 23 - 647215 AACAGACAGAGCCCTATTGTACT +s simRat_chr6.simRat.chr6 394333 23 + 647215 GGCAGAAGGAGCCCTCTTGTATT a s simMouse_chr6.simMouse.chr6 394251 1 + 636262 C @@ -151804,23 +160224,107 @@ 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 +s simMouse_chr6.simMouse.chr6 394252 1 + 636262 A +s Anc0.Anc0refChr3 26568 1 + 222631 G +s Anc1.Anc1refChr6 56159 1 + 197743 G +s Anc2.Anc2refChr13 30050 1 + 96486 G +s mr.mrrefChr5 247931 1 + 294540 A +s mr.mrrefChr5 177242 1 - 294540 G +s simCow_chr6.simCow.chr6 386177 1 + 602619 G +s simDog_chr6.simDog.chr6 376651 1 + 593897 G +s simHuman_chr6.simHuman.chr6 380564 1 + 601863 G +s simHuman_chr6.simHuman.chr6 445418 1 + 601863 G +s simMouse_chr6.simMouse.chr6 371315 1 - 636262 G +s simRat_chr6.simRat.chr6 392742 1 - 647215 G +s simRat_chr6.simRat.chr6 394357 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 394253 14 + 636262 TATTGAAGCTTCCT +s Anc0.Anc0refChr3 26569 14 + 222631 TGGCAAAGATTCCT +s Anc1.Anc1refChr6 56160 14 + 197743 TGGCAAAGATTCCT +s Anc2.Anc2refChr13 30051 14 + 96486 TGACAAAGATTCCT +s mr.mrrefChr5 247932 14 + 294540 TGGTAAAGCTTCCT +s mr.mrrefChr5 177243 14 - 294540 TGGCAAGGCTTCCT +s simCow_chr6.simCow.chr6 386178 13 + 602619 TGGCAAATAGT-CT +s simDog_chr6.simDog.chr6 376652 14 + 593897 TAACAGAGATTCCT +s simHuman_chr6.simHuman.chr6 380565 14 + 601863 TGATAAAGATTCCT +s simHuman_chr6.simHuman.chr6 445419 14 + 601863 TGGCAAAGATTCCT +s simMouse_chr6.simMouse.chr6 371316 14 - 636262 TGGCAAGGCTTCCT +s simRat_chr6.simRat.chr6 394358 14 + 647215 TGGCAATGTTTCCT + +a +s simMouse_chr6.simMouse.chr6 394267 10 + 636262 TGAGAGCTCA +s Anc0.Anc0refChr3 26583 5 + 222631 TGAAA----- +s Anc1.Anc1refChr6 56174 5 + 197743 TGAAA----- +s Anc2.Anc2refChr13 30065 5 + 96486 TGAAA----- +s mr.mrrefChr5 247946 10 + 294540 TGAGAGCTCA +s mr.mrrefChr5 177258 5 - 294540 TAAGA----- +s simCow_chr6.simCow.chr6 386191 5 + 602619 TGAAA----- +s simDog_chr6.simDog.chr6 376666 5 + 593897 TGAAA----- +s simHuman_chr6.simHuman.chr6 380579 5 + 601863 TGAAA----- +s simHuman_chr6.simHuman.chr6 445433 5 + 601863 TGAAA----- +s simMouse_chr6.simMouse.chr6 371332 5 - 636262 TAAGA----- +s simRat_chr6.simRat.chr6 394372 10 + 647215 TGTGAGTCCA + +a +s simMouse_chr6.simMouse.chr6 394277 4 + 636262 CCCA +s Anc0.Anc0refChr3 26616 4 + 222631 CTCA +s Anc1.Anc1refChr6 56207 4 + 197743 CTCA +s Anc2.Anc2refChr13 30098 4 + 96486 CTCA +s mr.mrrefChr5 248048 4 + 294540 CCCA +s mr.mrrefChr5 177924 4 - 294540 cata +s simCow_chr6.simCow.chr6 386232 4 + 602619 ACCA +s simDog_chr6.simDog.chr6 376695 4 + 593897 CTCA +s simHuman_chr6.simHuman.chr6 380604 4 + 601863 CCCG +s simHuman_chr6.simHuman.chr6 445466 4 + 601863 CTCA +s simMouse_chr6.simMouse.chr6 372206 4 - 636262 cata +s simRat_chr6.simRat.chr6 393381 4 - 647215 cacg +s simRat_chr6.simRat.chr6 394541 4 + 647215 TCCA + +a +s simMouse_chr6.simMouse.chr6 394281 1 + 636262 C +s Anc0.Anc0refChr3 26620 1 + 222631 C +s Anc1.Anc1refChr6 56211 1 + 197743 C +s Anc2.Anc2refChr13 30102 1 + 96486 C +s mr.mrrefChr5 248052 1 + 294540 C +s mr.mrrefChr5 177934 1 - 294540 g +s simCow_chr6.simCow.chr6 386236 1 + 602619 C +s simDog_chr6.simDog.chr6 376699 1 + 593897 T +s simHuman_chr6.simHuman.chr6 380608 1 + 601863 C +s simHuman_chr6.simHuman.chr6 445470 1 + 601863 A +s simMouse_chr6.simMouse.chr6 372216 1 - 636262 g +s simRat_chr6.simRat.chr6 393391 1 - 647215 g +s simRat_chr6.simRat.chr6 394545 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 394282 36 + 636262 AGGATTACGTACAATTGAGGTTGCTGCAATCATAAA +s Anc0.Anc0refChr3 26621 33 + 222631 GGTGTGATGTGCAATAAAAC---ATGCAGTCATAAG +s Anc1.Anc1refChr6 56212 33 + 197743 GGTGTGATGTGCAATAAAAC---ATGCAGTCATAAG +s Anc2.Anc2refChr13 30103 33 + 96486 GGTGTGATGTGCAATAAAAC---ATGCAGTCATAAG +s mr.mrrefChr5 248053 33 + 294540 AGGATTATGTACAATTGAGG---CTGCAATCATAAA +s mr.mrrefChr5 177935 32 - 294540 ggtatgctatacgctttgta---ctgc-gccttggg +s simCow_chr6.simCow.chr6 386237 33 + 602619 AGGGTGATGTGCAATAGAAT---GTGCAATCATAAG +s simDog_chr6.simDog.chr6 376700 32 + 593897 GGTATGATTTGCAA-GACAC---ATGCAGTCGTGAG +s simHuman_chr6.simHuman.chr6 380609 33 + 601863 AGTGTGATGTGCAGTAAAAC---ATGCAGTCACCAG +s simHuman_chr6.simHuman.chr6 445471 33 + 601863 GGTGTGATGTGCAGTAAAAC---ATGCAGTCACAAG +s simMouse_chr6.simMouse.chr6 372217 32 - 636262 ggtatgctatacgctttgta---ctgc-gccttggg +s simRat_chr6.simRat.chr6 393392 32 - 647215 gatattctatacactttgta---ccgc-actttggg +s simRat_chr6.simRat.chr6 394553 19 + 647215 AGGATTATGTACA-----------------CATAAA + +a +s simMouse_chr6.simMouse.chr6 394318 7 + 636262 ATTAGTT +s Anc0.Anc0refChr3 26654 7 + 222631 ATCAATT +s Anc1.Anc1refChr6 56245 7 + 197743 ATCAATT +s Anc2.Anc2refChr13 30136 7 + 96486 ATCACTT +s mr.mrrefChr5 248086 7 + 294540 ATTAGTT +s mr.mrrefChr5 177967 7 - 294540 aacaggc +s simCow_chr6.simCow.chr6 386303 7 + 602619 ATCAGTT +s simDog_chr6.simDog.chr6 376732 7 + 593897 GTCACCT +s simHuman_chr6.simHuman.chr6 380642 7 + 601863 ATCAATT +s simHuman_chr6.simHuman.chr6 445504 7 + 601863 ATCAAAT +s simMouse_chr6.simMouse.chr6 372249 7 - 636262 aaCAGGC +s simRat_chr6.simRat.chr6 393424 7 - 647215 aactggt +s simRat_chr6.simRat.chr6 394572 7 + 647215 ATTATTT a s simMouse_chr6.simMouse.chr6 394325 1 + 636262 T @@ -151834,6 +160338,36 @@ s simRat_chr6.simRat.chr6 394579 1 + 647215 C a +s simMouse_chr6.simMouse.chr6 394326 1 + 636262 C +s Anc0.Anc0refChr3 26662 1 + 222631 T +s Anc1.Anc1refChr6 56253 1 + 197743 T +s Anc2.Anc2refChr13 30144 1 + 96486 T +s mr.mrrefChr5 248094 1 + 294540 T +s mr.mrrefChr5 177974 1 - 294540 t +s simCow_chr6.simCow.chr6 386311 1 + 602619 T +s simDog_chr6.simDog.chr6 376740 1 + 593897 A +s simHuman_chr6.simHuman.chr6 380650 1 + 601863 T +s simHuman_chr6.simHuman.chr6 445511 1 + 601863 T +s simMouse_chr6.simMouse.chr6 372256 1 - 636262 T +s simRat_chr6.simRat.chr6 393431 1 - 647215 t +s simRat_chr6.simRat.chr6 394580 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 394327 5 + 636262 CCTGT +s Anc0.Anc0refChr3 26663 5 + 222631 CTTGC +s Anc1.Anc1refChr6 56254 5 + 197743 CTTGC +s Anc2.Anc2refChr13 30145 5 + 96486 CATGC +s mr.mrrefChr5 248095 5 + 294540 CCTGT +s mr.mrrefChr5 177978 5 - 294540 cctgC +s simCow_chr6.simCow.chr6 386312 5 + 602619 CATGT +s simDog_chr6.simDog.chr6 376741 5 + 593897 TATGC +s simHuman_chr6.simHuman.chr6 380651 5 + 601863 CTTGC +s simHuman_chr6.simHuman.chr6 445512 4 + 601863 CTTG- +s simMouse_chr6.simMouse.chr6 372260 5 - 636262 CCTGC +s simRat_chr6.simRat.chr6 393435 5 - 647215 cctgc +s simRat_chr6.simRat.chr6 394581 5 + 647215 CCTGT + +a s simMouse_chr6.simMouse.chr6 394332 13 + 636262 TTTGAACTTCCCA s Anc0.Anc0refChr3 26668 13 + 222631 TTTCATATTTTCA s Anc1.Anc1refChr6 56259 13 + 197743 TTTCATATTTTCA @@ -153460,15 +161994,148 @@ 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--------------- +s simMouse_chr6.simMouse.chr6 398505 50 + 636262 TGGTGGCTAGTAGTGATATATATGATTTTGGTGGGTAGGAGAGTATGCAA +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 398257 50 + 636262 TGGTGGCTAGTAGTGATATAGACAATTTTGGTAGGGAGCAGAGTATCCAA +s simRat_chr6.simRat.chr6 398589 50 + 647215 TAATGGCTAGTACTGATCTATACAATTTTGGTAGGCAGCAGAGCATTCAA + +a +s simMouse_chr6.simMouse.chr6 398555 24 + 636262 GACCCTTGGAAGTAGATTACATTG +s Anc0.Anc0refChr3 30323 24 + 222631 AACCATTGGAAGGATATTGCATTT +s Anc1.Anc1refChr6 60034 24 + 197743 AACCATTGGAAGGATATTGCATTT +s Anc2.Anc2refChr13 33914 24 + 96486 AGCCATTGGAAGGATATTGCATTT +s mr.mrrefChr5 251811 24 + 294540 GACCCTTGGAAGTAGATTACATTG +s simCow_chr6.simCow.chr6 390332 24 + 602619 AGCCATTGGAAAGATGTTGCATTT +s simDog_chr6.simDog.chr6 380329 23 + 593897 AGCCCTT-GAAGGGTATTACATTT +s simHuman_chr6.simHuman.chr6 384408 24 + 601863 AACCATTGGAAGGATATTGCATTT +s simMouse_chr6.simMouse.chr6 398307 24 + 636262 GACCCTTGGAAGTAGATTACATTG +s simRat_chr6.simRat.chr6 398639 24 + 647215 GACCCTCGAAAGTAGATTACATTG + +a +s simMouse_chr6.simMouse.chr6 398579 13 + 636262 CAATGACTACCAT +s Anc0.Anc0refChr3 30348 7 + 222631 CA------ACCAT +s Anc1.Anc1refChr6 60059 7 + 197743 CA------ACCAT +s Anc2.Anc2refChr13 33939 7 + 96486 CA------ACCTT +s mr.mrrefChr5 251836 13 + 294540 CAATGACTACCAT +s simCow_chr6.simCow.chr6 390357 7 + 602619 CA------AGTTC +s simDog_chr6.simDog.chr6 380353 7 + 593897 CA------ACCTT +s simHuman_chr6.simHuman.chr6 384433 7 + 601863 CA------ACCAT +s simMouse_chr6.simMouse.chr6 398332 13 + 636262 CAATGACTACCAT +s simRat_chr6.simRat.chr6 398664 13 + 647215 CAACCACTACCAT + +a +s simMouse_chr6.simMouse.chr6 398592 23 + 636262 ATGAGAATTGCAGGCTGTGTATT +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 398345 23 + 636262 ATGAGAAATGCAGGGAGTGTATT +s simRat_chr6.simRat.chr6 398677 20 + 647215 --GAGAAACGCAGGCAGTG-ACG + +a +s simMouse_chr6.simMouse.chr6 398615 2 + 636262 TC +s Anc0.Anc0refChr3 30376 2 + 222631 CC +s Anc1.Anc1refChr6 60087 2 + 197743 CC +s Anc2.Anc2refChr13 33967 2 + 96486 CC +s mr.mrrefChr5 251872 2 + 294540 TC +s simCow_chr6.simCow.chr6 390385 2 + 602619 CC +s simDog_chr6.simDog.chr6 380414 2 + 593897 CC +s simHuman_chr6.simHuman.chr6 384466 2 + 601863 CC +s simMouse_chr6.simMouse.chr6 398368 2 + 636262 TC +s simRat_chr6.simRat.chr6 398697 2 + 647215 CA + +a +s simMouse_chr6.simMouse.chr6 398617 34 + 636262 AATATTCATGAGACAATAGTGCAAGTCATAATTT +s Anc0.Anc0refChr3 30383 34 + 222631 AATATTCTTGAGACACCAGGGCTAGTACTGATGT +s Anc1.Anc1refChr6 60094 34 + 197743 AATATTCTTGAGACACCAGGGCTAGTACTGATGT +s Anc2.Anc2refChr13 33974 34 + 96486 AAAATTCTTGGGACACCAGGGCTAGTACTGATGT +s mr.mrrefChr5 251879 34 + 294540 AATATTCATGAGACAATAGTGCAAGTAATAATTT +s simCow_chr6.simCow.chr6 390397 34 + 602619 AACATTCTTGGGACACCTGGGCTAGTACTGATAT +s simDog_chr6.simDog.chr6 380421 33 + 593897 AAAATTATTGGGACACCACGATTAGTACT-ATGC +s simHuman_chr6.simHuman.chr6 384473 34 + 601863 AATATTCTTGAGACACCAGGGCTAGTACTGATGT +s simMouse_chr6.simMouse.chr6 398375 34 + 636262 AATATTCATGGAACAATAGTGCAAGTAATAATTT +s simRat_chr6.simRat.chr6 398699 34 + 647215 AATGTCCATGAGACAATAGTACAAGTAGTAATTC + +a +s simMouse_chr6.simMouse.chr6 398651 37 + 636262 GTAGCCAGCAGGACATTCAGGGAACATAGGAAGCCTT +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 398409 37 + 636262 GTAGCCACCAGGGTATTCAAGGAACATAGGAAGTCTT +s simRat_chr6.simRat.chr6 398733 37 + 647215 GTAGCCAGCAGGGCATTCAAGAAACACAGGAAGCCTG + +a +s simMouse_chr6.simMouse.chr6 398688 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 398446 7 + 636262 CATTTTT +s simRat_chr6.simRat.chr6 398771 7 + 647215 CATTTTC + +a +s simMouse_chr6.simMouse.chr6 398695 26 + 636262 GTATATGTAAACAGCTGATTAAAGAT +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 398453 26 + 636262 GTATATGTAAACAGCTGATTAAAGGT +s simRat_chr6.simRat.chr6 398779 25 + 647215 GTATAT-TAAACAGCTGATTAAAGGT + +a +s simMouse_chr6.simMouse.chr6 398721 10 + 636262 GGACCACACT +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 398479 10 + 636262 GGACCACACC +s simRat_chr6.simRat.chr6 398804 10 + 647215 GGATCACACT + +a +s simMouse_chr6.simMouse.chr6 398731 7 + 636262 AGACAGA +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 398489 7 + 636262 AGACAGG +s simRat_chr6.simRat.chr6 398814 7 + 647215 AAACAGG + +a +s simMouse_chr6.simMouse.chr6 398738 40 + 636262 ATGCCATATTGACTTTTCAATATCTTCCAGGGGCATGTTT +s Anc0.Anc0refChr3 30527 12 + 222631 ATGTCAT----------------------------TGTTA +s Anc1.Anc1refChr6 60238 12 + 197743 ATGTCAT----------------------------TGTTA +s Anc2.Anc2refChr13 34118 12 + 96486 ATATCAT----------------------------CATTA +s mr.mrrefChr5 252000 36 + 294540 ATGCCATAATGACTTTTCAATATCT----GGGGCATGTTT +s simCow_chr6.simCow.chr6 390533 12 + 602619 ATACCAT----------------------------CATTC +s simDog_chr6.simDog.chr6 380593 12 + 593897 ATATCAT----------------------------CATTA +s simHuman_chr6.simHuman.chr6 384617 12 + 601863 ATGTCAT----------------------------TGTTG +s simMouse_chr6.simMouse.chr6 398496 9 + 636262 ATGCCATAA------------------------------- +s simRat_chr6.simRat.chr6 398821 25 + 647215 ATGACATAATGAATATGCAGTACCC--------------- a s simMouse_chr6.simMouse.chr6 398778 15 + 636262 ACTCATTGGTATTAG @@ -159421,7 +168088,110 @@ s simRat_chr6.simRat.chr6 419295 57 + 647215 CCGTGATTGACTGATCTGCCATGAGCACAGGCCAAGATGAATTCCACTCAATGAAGA a -s simMouse_chr6.simMouse.chr6 413088 5 + 636262 TGCCA +s simMouse_chr6.simMouse.chr6 413084 10 + 636262 GGCATGCCAC +s Anc0.Anc0refChr3 41864 5 + 222631 GGTG-----C +s Anc1.Anc1refChr6 72188 5 + 197743 GGTG-----C +s Anc2.Anc2refChr13 45880 5 + 96486 GGTG-----C +s mr.mrrefChr5 265778 5 + 294540 GGCA-----C +s mr.mrrefChr5 263506 5 + 294540 GGTG-----C +s simCow_chr6.simCow.chr6 401732 5 + 602619 GGTG-----C +s simDog_chr6.simDog.chr6 392491 5 + 593897 GCTG-----C +s simHuman_chr6.simHuman.chr6 396933 5 + 601863 GGTG-----C +s simMouse_chr6.simMouse.chr6 410770 5 + 636262 AGTG-----C +s simRat_chr6.simRat.chr6 417171 5 + 647215 GGTG-----C +s simRat_chr6.simRat.chr6 419352 5 + 647215 GATA-----C + +a +s simMouse_chr6.simMouse.chr6 413094 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 265783 2 + 294540 AA +s mr.mrrefChr5 263511 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 410775 2 + 636262 AA +s simRat_chr6.simRat.chr6 417176 2 + 647215 AA +s simRat_chr6.simRat.chr6 419357 2 + 647215 AA + +a +s simMouse_chr6.simMouse.chr6 413096 9 + 636262 TTTAACCCA +s Anc0.Anc0refChr3 41870 9 + 222631 TACGACCTT +s Anc1.Anc1refChr6 72195 9 + 197743 TACGACCTT +s Anc2.Anc2refChr13 45886 9 + 96486 TGCGACCTT +s mr.mrrefChr5 265785 9 + 294540 TTTAACCCA +s mr.mrrefChr5 263513 9 + 294540 TATGACCAG +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 410777 9 + 636262 TATTACCAG +s simRat_chr6.simRat.chr6 417178 9 + 647215 TATGACCAG +s simRat_chr6.simRat.chr6 419359 9 + 647215 TTTAACCCA + +a +s simMouse_chr6.simMouse.chr6 413105 29 + 636262 TACCTAACATGTGTGTGGTGCTTGGGGCT +s Anc0.Anc0refChr3 41879 29 + 222631 TAGCTAGTATATGTGTGGTGCTTGGGGGT +s Anc1.Anc1refChr6 72204 29 + 197743 TAGCTAGTATATGTGTGGTGCTTGGGGGT +s Anc2.Anc2refChr13 45895 29 + 96486 TAGCTAGTAGATGTGTAGTGCATGGGGGT +s mr.mrrefChr5 265794 29 + 294540 TACCTAATATATGTGTGGTGCTTGGGGCT +s mr.mrrefChr5 263522 29 + 294540 TACCAAATATATGTCTGGTGCTTGGGGGT +s simCow_chr6.simCow.chr6 401748 29 + 602619 TAGCCAGTACATGTGTAGTGCATGAGGGT +s simDog_chr6.simDog.chr6 392506 29 + 593897 TAGCTGGTAGATGTATAGTGCCTGGGGGT +s simHuman_chr6.simHuman.chr6 396969 29 + 601863 CAGCTAGTATATATTTGGTGTGTGAGGCT +s simMouse_chr6.simMouse.chr6 410786 29 + 636262 TACCACATATATGTCTGGTGCTTGGGGGT +s simRat_chr6.simRat.chr6 417187 29 + 647215 TACCAAATATGTGTGTAGTGCTTGGGGGT +s simRat_chr6.simRat.chr6 419370 29 + 647215 TACCTAATATATGTGTGGTGCGCGGGGCT + +a +s simMouse_chr6.simMouse.chr6 413134 5 + 636262 CATGA +s Anc0.Anc0refChr3 41908 5 + 222631 CAAAA +s Anc1.Anc1refChr6 72233 5 + 197743 CAAAA +s Anc2.Anc2refChr13 45924 5 + 96486 CAAAA +s mr.mrrefChr5 265823 5 + 294540 CATAA +s mr.mrrefChr5 263551 5 + 294540 GAAAA +s simCow_chr6.simCow.chr6 401777 5 + 602619 CAACA +s simDog_chr6.simDog.chr6 392535 5 + 593897 CAAAA +s simHuman_chr6.simHuman.chr6 396998 5 + 601863 CAAAA +s simMouse_chr6.simMouse.chr6 410815 5 + 636262 GAAAA +s simRat_chr6.simRat.chr6 419399 5 + 647215 CATAA + +a +s simMouse_chr6.simMouse.chr6 413139 2 + 636262 TT +s Anc1.Anc1refChr6 72244 2 + 197743 TT +s mr.mrrefChr5 265828 2 + 294540 TT +s mr.mrrefChr5 263562 2 + 294540 TT +s simHuman_chr6.simHuman.chr6 397017 2 + 601863 AT +s simMouse_chr6.simMouse.chr6 410826 2 + 636262 TT +s simRat_chr6.simRat.chr6 419404 2 + 647215 CT + +a +s simMouse_chr6.simMouse.chr6 413141 2 + 636262 AA +s Anc0.Anc0refChr3 41915 2 + 222631 AA +s Anc1.Anc1refChr6 72255 2 + 197743 AA +s Anc2.Anc2refChr13 45931 2 + 96486 AA +s mr.mrrefChr5 265830 2 + 294540 AA +s mr.mrrefChr5 263573 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 410837 2 + 636262 GA +s simRat_chr6.simRat.chr6 417219 2 + 647215 AA +s simRat_chr6.simRat.chr6 419406 2 + 647215 TA + +a +s simMouse_chr6.simMouse.chr6 413143 13 + 636262 GGAATGTGACATG +s Anc0.Anc0refChr3 41917 13 + 222631 GGACTATAACATG +s Anc1.Anc1refChr6 72257 13 + 197743 GGACTATAACATG +s Anc2.Anc2refChr13 45933 13 + 96486 GGACTATAACATG +s mr.mrrefChr5 265832 13 + 294540 GGAATGTGACATG +s mr.mrrefChr5 263575 13 + 294540 GGACTATGACATA +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 410839 13 + 636262 GGACTATGACATA +s simRat_chr6.simRat.chr6 417221 13 + 647215 AGACCATGACATA +s simRat_chr6.simRat.chr6 419408 13 + 647215 GGTATATGACATG a s simMouse_chr6.simMouse.chr6 413156 1 + 636262 C @@ -159435,22 +168205,162 @@ s simRat_chr6.simRat.chr6 419421 1 + 647215 C a +s simMouse_chr6.simMouse.chr6 413157 33 + 636262 AGACCCCGACATCACTGATTCATTGACCAATAA +s Anc0.Anc0refChr3 41931 33 + 222631 GGACCTTGACAACACTGATTAGTTGACCAATAA +s Anc1.Anc1refChr6 72271 33 + 197743 GGACCTTGACAACACTGATTAGTTGACCAATAA +s Anc2.Anc2refChr13 45947 33 + 96486 GGACCTTGACACCACTGATTAGTTGACCAATAA +s mr.mrrefChr5 265846 33 + 294540 AGACCCCGACATCACTGATTCATTGACCAATAA +s mr.mrrefChr5 263588 33 + 294540 GGACCTTGATAACAATGATTAGTTGACCAATAA +s simCow_chr6.simCow.chr6 401800 32 + 602619 GGACCTTGACACCTGTGCCT-GTTAACCAATAA +s simDog_chr6.simDog.chr6 392558 33 + 593897 GAACTTTGACACCACTGATTAGTTGACCAATAA +s simHuman_chr6.simHuman.chr6 397048 33 + 601863 GGCCCTTGATAACACTGATTAGTTGACCAATAG +s simMouse_chr6.simMouse.chr6 410852 33 + 636262 GGACCTTGATAACAATGATTAGTTGACCAATAA +s simRat_chr6.simRat.chr6 417234 33 + 647215 TGACCTTGATAACAATGGTTAGTTGACCAATAA +s simRat_chr6.simRat.chr6 419422 33 + 647215 AGACCCCAACAGCCCTAATCCATGGACCAATAA + +a +s simMouse_chr6.simMouse.chr6 413190 1 + 636262 G +s Anc0.Anc0refChr3 41987 1 + 222631 G +s Anc1.Anc1refChr6 72327 1 + 197743 G +s Anc2.Anc2refChr13 46003 1 + 96486 G +s mr.mrrefChr5 265884 1 + 294540 G +s mr.mrrefChr5 263626 1 + 294540 G +s simCow_chr6.simCow.chr6 401864 1 + 602619 G +s simDog_chr6.simDog.chr6 392613 1 + 593897 G +s simHuman_chr6.simHuman.chr6 397104 1 + 601863 G +s simMouse_chr6.simMouse.chr6 410890 1 + 636262 G +s simRat_chr6.simRat.chr6 417272 1 + 647215 G +s simRat_chr6.simRat.chr6 419460 1 + 647215 G + +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 +s simMouse_chr6.simMouse.chr6 413192 21 + 636262 AGGGTGGAAATGTGGAGTTAG +s Anc0.Anc0refChr3 41988 21 + 222631 GAAGTGAAAGTGTGGAGTTAA +s Anc1.Anc1refChr6 72328 21 + 197743 GAAGTGAAAGTGTGGAGTTAA +s Anc2.Anc2refChr13 46004 21 + 96486 GAAGTGAAAGTGTGGAGTTAA +s mr.mrrefChr5 265886 21 + 294540 AAGGTGAAAGTGTGGAGTTAA +s mr.mrrefChr5 263627 21 + 294540 GAGGTCAAAGTGTGGTGTTAA +s simCow_chr6.simCow.chr6 401865 21 + 602619 GGAGTGAACGTGCGGAGTCAA +s simDog_chr6.simDog.chr6 392614 21 + 593897 TAAGTGAAAGGGTGGAGTTAA +s simHuman_chr6.simHuman.chr6 397105 21 + 601863 GCAGTAAAAGTATGGTGTTAA +s simMouse_chr6.simMouse.chr6 410891 20 + 636262 -AGGTCAAAGTGTGGAGTTGA +s simRat_chr6.simRat.chr6 417273 21 + 647215 GAGGTCAAAGTGTGGTCTTAA +s simRat_chr6.simRat.chr6 419462 21 + 647215 AAGGTGAATGTGTGGAGTTAA + +a +s simMouse_chr6.simMouse.chr6 413213 53 + 636262 TGGACACTTGTTTTAAGGACTTGTTACAAAGTAACCTCTTGAAACTAGATAGG +s Anc0.Anc0refChr3 42012 53 + 222631 TGGCCACATGTCTTAAGGACCTCAGAAAAAACAACCTCTTGAGAACAGAAACA +s Anc1.Anc1refChr6 72352 53 + 197743 TGGCCACATGTCTTAAGGACCTCAGAAAAAACAACCTCTTGAGAACAGAAACA +s Anc2.Anc2refChr13 46028 53 + 96486 TGGCCACATGTCTTAAGGACCTCAGAAAAAACAACCTCTTGAGAACAGAAACA +s mr.mrrefChr5 265910 53 + 294540 TGGACACTTGTTTTAAGGACTTGTTACAAAGTAACCTCTTGAAACTAGATAGG +s mr.mrrefChr5 263652 53 + 294540 TGGCCTTTTGTCTTAAGGACATGGGAAAAAGCAACCTCTTAAGAACAGAAACA +s simCow_chr6.simCow.chr6 401889 53 + 602619 TAGCCACATGTCTTCAGGACCTCAAAAGACACAACTCCTTGAGAACAAAAGCA +s simDog_chr6.simDog.chr6 392638 53 + 593897 TGGCCACATATCTTAAGGACCTCAGAAAAAACAACCTCTTGACAACAGAAACA +s simHuman_chr6.simHuman.chr6 397129 51 + 601863 TGGCCACAGGTCTTAAGGCCCTCAGAAAAAACAACATCCTGCGAACAGATA-- +s simMouse_chr6.simMouse.chr6 410915 53 + 636262 TGGCCTTTTGTGCCAAGGACATGGGAAAAAGCAACCTCTTAAGAACAGAAACA +s simRat_chr6.simRat.chr6 417298 53 + 647215 TCGCCTTTTGTCTTAAAGACTTGGGAAAAAGCAACCTCTTAAGAACAGAAACA +s simRat_chr6.simRat.chr6 419486 53 + 647215 TGGACACTTGTTTTAAGGACTTGTTACAAAGTAACGTCTTGAGACTATATAGG + +a +s simMouse_chr6.simMouse.chr6 413266 18 + 636262 GAATACACTCCCACATAA +s Anc0.Anc0refChr3 42070 18 + 222631 GAAAAAACTCCCAAGTAA +s Anc1.Anc1refChr6 72410 18 + 197743 GAAAAAACTCCCAAGTAA +s Anc2.Anc2refChr13 46086 18 + 96486 GAAAAAACTCCCTAGTAA +s mr.mrrefChr5 265963 18 + 294540 GAATACACTCCCACATAA +s mr.mrrefChr5 263711 18 + 294540 GAATAAACTTCTGAATAA +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 410974 18 + 636262 GAATAAACTTCTGCATGA +s simRat_chr6.simRat.chr6 417357 18 + 647215 GAATAAACTTCTGAATAA +s simRat_chr6.simRat.chr6 419539 18 + 647215 GAACACACTCCCACATAA + +a +s simMouse_chr6.simMouse.chr6 413284 8 + 636262 AGAGATCC +s Anc0.Anc0refChr3 42088 8 + 222631 AAAGACAT +s Anc1.Anc1refChr6 72428 8 + 197743 AAAGACAT +s Anc2.Anc2refChr13 46104 8 + 96486 AAAGCCAT +s mr.mrrefChr5 265981 8 + 294540 AGAGATAC +s mr.mrrefChr5 263729 8 + 294540 AAAGTCAT +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 410992 8 + 636262 AAAGTCAT +s simRat_chr6.simRat.chr6 417375 8 + 647215 AAAGTCAT +s simRat_chr6.simRat.chr6 419614 8 + 647215 AGACAGAC + +a +s simMouse_chr6.simMouse.chr6 413292 1 + 636262 G +s Anc0.Anc0refChr3 42128 1 + 222631 A +s Anc1.Anc1refChr6 72468 1 + 197743 A +s Anc2.Anc2refChr13 46144 1 + 96486 A +s mr.mrrefChr5 265989 1 + 294540 A +s mr.mrrefChr5 263768 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 411031 1 + 636262 A +s simRat_chr6.simRat.chr6 417414 1 + 647215 A +s simRat_chr6.simRat.chr6 419622 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 413293 29 + 636262 GTTGCACCTGAAACTACTCCCCATCTATC +s Anc0.Anc0refChr3 42129 29 + 222631 GGAGCACTGGATGCTCCTTCCCATATGTC +s Anc1.Anc1refChr6 72469 29 + 197743 GGAGCACTGGATGCTCCTTCCCATATGTC +s Anc2.Anc2refChr13 46145 29 + 96486 GGAGCACTGTATGCCCCTTCCCATATGTC +s mr.mrrefChr5 265990 29 + 294540 GGTGCACTTGATGCTACTCCCCATCTATC +s mr.mrrefChr5 263769 29 + 294540 GGAGTACTGGATGCTATCCCCCATATGTA +s simCow_chr6.simCow.chr6 402009 29 + 602619 GGAGCACTGGATGTCACTTCCCACATATC +s simDog_chr6.simDog.chr6 392755 29 + 593897 GGAACACTGTGTGCCCCTTCCCATATGTC +s simHuman_chr6.simHuman.chr6 397240 29 + 601863 GGAGCAATTCATGCACATTCCCATATGTC +s simMouse_chr6.simMouse.chr6 411032 29 + 636262 GGAGTGCTGGGTGCTATCCCGCATATGTA +s simRat_chr6.simRat.chr6 417415 29 + 647215 GCAGTACTGGATGCTACCCCCCATATGTA +s simRat_chr6.simRat.chr6 419623 23 + 647215 GGGGAACTCAATGCTACTCCC------TC + +a +s simMouse_chr6.simMouse.chr6 413322 3 + 636262 ACC +s Anc0.Anc0refChr3 42158 3 + 222631 AGC +s Anc1.Anc1refChr6 72498 3 + 197743 AGC +s Anc2.Anc2refChr13 46174 3 + 96486 AAC +s mr.mrrefChr5 266019 3 + 294540 ACC +s mr.mrrefChr5 263798 3 + 294540 AGC +s simCow_chr6.simCow.chr6 402038 3 + 602619 ACC +s simDog_chr6.simDog.chr6 392784 3 + 593897 GAC +s simHuman_chr6.simHuman.chr6 397269 3 + 601863 AGT +s simMouse_chr6.simMouse.chr6 411061 3 + 636262 AGC +s simRat_chr6.simRat.chr6 419646 3 + 647215 ACC + +a +s simMouse_chr6.simMouse.chr6 413325 21 + 636262 TCCCGATTTTTACTTTGCTCA +s Anc0.Anc0refChr3 42161 21 + 222631 TCCCTCTCTAGACTTTGCTGA +s Anc1.Anc1refChr6 72501 21 + 197743 TCCCTCTCTAGACTTTGCTGA +s Anc2.Anc2refChr13 46177 21 + 96486 CACCTCTCTAGACTTTGCTAA +s mr.mrrefChr5 266022 21 + 294540 TCCCTCTTTTTACTTTGCTCA +s mr.mrrefChr5 263801 21 + 294540 TCCCTCTTAAGACTTTGCTGA +s simCow_chr6.simCow.chr6 402041 21 + 602619 CACCTCTCTAGACTTTGCTAA +s simDog_chr6.simDog.chr6 392787 21 + 593897 CACCTCTTTAGACTTTGCTAA +s simHuman_chr6.simHuman.chr6 397272 21 + 601863 TGCCTCTCTAGACTTGGCTGA +s simMouse_chr6.simMouse.chr6 411064 21 + 636262 TCCCTCTTATGACTTTGCTGA +s simRat_chr6.simRat.chr6 417444 21 + 647215 TCCCTCTTAAGACTTAGCTGA +s simRat_chr6.simRat.chr6 419649 21 + 647215 TCTTTCTTTTCATTTTGCTCA + +a +s simMouse_chr6.simMouse.chr6 413346 12 + 636262 GTAAAGGACCAC +s Anc0.Anc0refChr3 42182 12 + 222631 GTGAAGGACCAC +s Anc1.Anc1refChr6 72522 12 + 197743 GTGAAGGACCAC +s Anc2.Anc2refChr13 46199 12 + 96486 GTGCAGGACTAC +s mr.mrrefChr5 266043 12 + 294540 GTGAAGGGCCAC +s mr.mrrefChr5 263822 12 + 294540 GTAAAGGACCAC +s simCow_chr6.simCow.chr6 402063 12 + 602619 GTGGAGGACAAC +s simDog_chr6.simDog.chr6 392809 12 + 593897 GTGCAGGGTTAC +s simHuman_chr6.simHuman.chr6 397293 12 + 601863 GTGAAGGACCAC +s simMouse_chr6.simMouse.chr6 411085 12 + 636262 GAAAAAAACCAC +s simRat_chr6.simRat.chr6 417465 12 + 647215 GTAAAGGACCAC +s simRat_chr6.simRat.chr6 419670 9 + 647215 GTGAAGGGC--- a s simMouse_chr6.simMouse.chr6 413358 4 + 636262 ATCA @@ -159464,17 +168374,115 @@ 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 +s simMouse_chr6.simMouse.chr6 413362 6 + 636262 CACATT +s Anc0.Anc0refChr3 42196 6 + 222631 CACATT +s Anc1.Anc1refChr6 72538 6 + 197743 CACATT +s Anc2.Anc2refChr13 46213 6 + 96486 CACACT +s mr.mrrefChr5 266059 6 + 294540 CACATT +s mr.mrrefChr5 263834 6 + 294540 CACATT +s simCow_chr6.simCow.chr6 402077 6 + 602619 CACACT +s simDog_chr6.simDog.chr6 392823 6 + 593897 CATGCT +s simHuman_chr6.simHuman.chr6 397309 6 + 601863 CATTTT +s simMouse_chr6.simMouse.chr6 411097 5 + 636262 -ACATT +s simRat_chr6.simRat.chr6 417477 6 + 647215 CACATT +s simRat_chr6.simRat.chr6 419683 6 + 647215 CACATT + +a +s simMouse_chr6.simMouse.chr6 413368 48 + 636262 GCTAGTCTTACTCGACCTATAGCACAGCCTATGCCACAATGAGGGCCT +s Anc0.Anc0refChr3 42202 48 + 222631 GTTAGCCTCACTCAACCTTTAGTAAGGTCTGTGCCATACCAAGGTCCT +s Anc1.Anc1refChr6 72544 48 + 197743 GTTAGCCTCACTCAACCTTTAGTAAGGTCTGTGCCATACCAAGGTCCT +s Anc2.Anc2refChr13 46219 48 + 96486 GTTAGCCTCACTCAACCTTTAGTGAGGTCTGTGCCATACCAAGGTCTT +s mr.mrrefChr5 266065 48 + 294540 GTTAGTCTTACTCAACCTATAGCACAGTCTGTGCTACAATGAGGGCCT +s mr.mrrefChr5 263840 48 + 294540 GTTAGCCTCACTCTGCCTTTAGTAAAGACTGTGCCATAATAAGGCCCT +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 411102 48 + 636262 GTTAGCCTCACTCTGCCTTTAGTAAAGACTGTGCCATAATAAGGCCCT +s simRat_chr6.simRat.chr6 417483 48 + 647215 GTTAGCCTCGCTCTGCCTTTAGTAAAGACTGTGCCATAATAAGGCCCT +s simRat_chr6.simRat.chr6 419689 48 + 647215 GTTAGGGTTACTCAACCTATAGCACAGTCTGTGCTACAATGAGGACCT + +a +s simMouse_chr6.simMouse.chr6 413416 2 + 636262 GA +s Anc0.Anc0refChr3 42250 2 + 222631 TA +s Anc1.Anc1refChr6 72592 2 + 197743 TA +s Anc2.Anc2refChr13 46267 2 + 96486 TA +s mr.mrrefChr5 266113 2 + 294540 GA +s mr.mrrefChr5 263888 2 + 294540 TA +s simCow_chr6.simCow.chr6 402131 2 + 602619 TA +s simHuman_chr6.simHuman.chr6 397364 2 + 601863 TA +s simMouse_chr6.simMouse.chr6 411150 2 + 636262 AA +s simRat_chr6.simRat.chr6 417531 2 + 647215 TA +s simRat_chr6.simRat.chr6 419740 2 + 647215 GA + +a +s simMouse_chr6.simMouse.chr6 413418 14 + 636262 TGGGATGCTTTCTT +s Anc0.Anc0refChr3 42255 14 + 222631 TGGGATGCTTTCTC +s Anc1.Anc1refChr6 72597 14 + 197743 TGGGATGCTTTCTC +s Anc2.Anc2refChr13 46272 14 + 96486 TGACAGCCTCTCTC +s mr.mrrefChr5 266115 14 + 294540 TGGGATGCTTTCTT +s mr.mrrefChr5 263893 14 + 294540 TGGGATGGTTTCTT +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 411155 14 + 636262 TGGGATGGTTTCTT +s simRat_chr6.simRat.chr6 417536 14 + 647215 TAGGATGGTTTTTT +s simRat_chr6.simRat.chr6 419742 14 + 647215 TGGGATGCTTTCTT + +a +s simMouse_chr6.simMouse.chr6 413432 20 + 636262 AAGACCTGGACAAGGAGTAC +s Anc0.Anc0refChr3 42269 20 + 222631 GAGATCTGAGTAAGAAGTGT +s Anc1.Anc1refChr6 72611 20 + 197743 GAGATCTGAGTAAGAAGTGT +s Anc2.Anc2refChr13 46286 20 + 96486 GAGTTCCCAGTAAGAAGTGT +s mr.mrrefChr5 266129 20 + 294540 GAGACCTGAGTAAGGAGTGC +s mr.mrrefChr5 263907 20 + 294540 GGGACCTGAGTGAGGAGTGC +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 411169 20 + 636262 GAGACCTGAGTGAGGAGTGC +s simRat_chr6.simRat.chr6 417550 20 + 647215 GGGACCTGAGTGAGGAGTGC +s simRat_chr6.simRat.chr6 419756 20 + 647215 GAGACCTGAGTGAGGAGTGC + +a +s simMouse_chr6.simMouse.chr6 413452 12 + 636262 AACAATCTACAG +s Anc0.Anc0refChr3 42289 12 + 222631 AAAAATCCATAG +s Anc1.Anc1refChr6 72631 12 + 197743 AAAAATCCATAG +s Anc2.Anc2refChr13 46306 12 + 96486 AAAAATCCATAG +s mr.mrrefChr5 266149 12 + 294540 AACAATCTACAG +s mr.mrrefChr5 263927 12 + 294540 AATGATCCATAG +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 411189 12 + 636262 AATGATCCATAG +s simRat_chr6.simRat.chr6 417570 12 + 647215 AGTGATCCATAG +s simRat_chr6.simRat.chr6 419776 12 + 647215 AGCAATCTACAG + +a +s simMouse_chr6.simMouse.chr6 413464 5 + 636262 ATGAA +s Anc0.Anc0refChr3 42303 5 + 222631 ATGAA +s Anc1.Anc1refChr6 72645 5 + 197743 ATGAA +s Anc2.Anc2refChr13 46320 5 + 96486 ATGAA +s mr.mrrefChr5 266161 5 + 294540 ATGAA +s mr.mrrefChr5 263939 5 + 294540 ATGGA +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 411201 5 + 636262 ATGGA +s simRat_chr6.simRat.chr6 417582 5 + 647215 ATGGA +s simRat_chr6.simRat.chr6 419788 5 + 647215 ATGAA + +a +s simMouse_chr6.simMouse.chr6 413469 29 + 636262 CCGCAGTGACCTAATGATAAATAATCCAT +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 266166 29 + 294540 CCGCAGTGACCTAATGATAAATAATCCAT +s mr.mrrefChr5 263944 29 + 294540 ACACAATGATCTAAGGGTAAGAGATCCTT +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 411206 29 + 636262 ACACAATGATCTAAGGGTAATAGATCCTT +s simRat_chr6.simRat.chr6 417587 29 + 647215 GCATAAAGATCTAATGGTAAGAGATCCTT +s simRat_chr6.simRat.chr6 419793 29 + 647215 CCACGATGACCTAATGGCAAATGATCCAT a s simMouse_chr6.simMouse.chr6 413498 14 + 636262 AGACAGAACACCAG @@ -159482,57 +168490,389 @@ s simRat_chr6.simRat.chr6 419822 14 + 647215 AGACAGAGCACCAG a +s simMouse_chr6.simMouse.chr6 413512 4 + 636262 GATG +s Anc0.Anc0refChr3 42313 4 + 222631 GATG +s Anc1.Anc1refChr6 72680 4 + 197743 GATG +s Anc2.Anc2refChr13 46330 4 + 96486 GATG +s mr.mrrefChr5 266209 4 + 294540 GATG +s mr.mrrefChr5 263973 4 + 294540 GTTG +s simCow_chr6.simCow.chr6 402208 4 + 602619 GGCG +s simDog_chr6.simDog.chr6 392921 4 + 593897 GATG +s simMouse_chr6.simMouse.chr6 411235 4 + 636262 GTTG +s simRat_chr6.simRat.chr6 417616 4 + 647215 GATG +s simRat_chr6.simRat.chr6 419836 4 + 647215 GATG + +a +s simMouse_chr6.simMouse.chr6 413516 39 + 636262 TAACAGTATCAGCTAACATTTAGGTTCACATTCTATGGG +s Anc0.Anc0refChr3 42317 39 + 222631 TAATGGTATTAGCTAACAGGTAGGTTCACATTCTATGGG +s Anc1.Anc1refChr6 72684 39 + 197743 TAATGGTATTAGCTAACAGGTAGGTTCACATTCTATGGG +s Anc2.Anc2refChr13 46334 39 + 96486 TCATGGCATTAGCTATCTGGTTGGTTCACAGTCCACACG +s mr.mrrefChr5 266213 39 + 294540 TAACAGTATTAGCTAACAGTTAGGTTCACATTCTATGGG +s mr.mrrefChr5 263977 39 + 294540 TAATGGTATCACCTAATAGGCAGTTTTACCTTCTATGAG +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 411239 39 + 636262 TAATGGTATCACCTAATAGGCAGTTTTACCTTCTATGAG +s simRat_chr6.simRat.chr6 417620 39 + 647215 TATTGGTATCAGCTAATAGGCAGTGTCACCTTCTATGGG +s simRat_chr6.simRat.chr6 419840 39 + 647215 TAACAGTATTAGCTAATAGTCAAGTTCACATTCTATGGG + +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 +s simMouse_chr6.simMouse.chr6 413560 5 + 636262 TATAT +s Anc0.Anc0refChr3 42356 5 + 222631 TATGC +s Anc1.Anc1refChr6 72723 5 + 197743 TATGC +s Anc2.Anc2refChr13 46373 5 + 96486 TATGC +s mr.mrrefChr5 266257 5 + 294540 TACAT +s mr.mrrefChr5 264016 5 + 294540 CATAT +s simCow_chr6.simCow.chr6 402345 5 + 602619 CATGT +s simDog_chr6.simDog.chr6 392964 5 + 593897 TACGC +s simHuman_chr6.simHuman.chr6 397439 5 + 601863 TATGC +s simMouse_chr6.simMouse.chr6 411278 5 + 636262 CATAT +s simRat_chr6.simRat.chr6 417659 5 + 647215 TCTCT +s simRat_chr6.simRat.chr6 419884 4 + 647215 T-CAT + +a +s simMouse_chr6.simMouse.chr6 413565 1 + 636262 G +s Anc0.Anc0refChr3 42361 1 + 222631 G +s Anc1.Anc1refChr6 72728 1 + 197743 G +s Anc2.Anc2refChr13 46378 1 + 96486 G +s mr.mrrefChr5 266262 1 + 294540 G +s mr.mrrefChr5 264021 1 + 294540 A +s simCow_chr6.simCow.chr6 402350 1 + 602619 G +s simDog_chr6.simDog.chr6 392969 1 + 593897 G +s simHuman_chr6.simHuman.chr6 397444 1 + 601863 G +s simMouse_chr6.simMouse.chr6 411288 1 + 636262 A +s simRat_chr6.simRat.chr6 419888 1 + 647215 G + +a +s simMouse_chr6.simMouse.chr6 413566 3 + 636262 ATA +s Anc0.Anc0refChr3 42364 3 + 222631 ACA +s Anc1.Anc1refChr6 72731 3 + 197743 ACA +s Anc2.Anc2refChr13 46381 3 + 96486 ACA +s mr.mrrefChr5 266263 3 + 294540 ATA +s mr.mrrefChr5 264022 3 + 294540 CCA +s simCow_chr6.simCow.chr6 402353 3 + 602619 AGA +s simDog_chr6.simDog.chr6 392972 3 + 593897 ACA +s simHuman_chr6.simHuman.chr6 397447 3 + 601863 ACA +s simMouse_chr6.simMouse.chr6 411289 3 + 636262 CCA +s simRat_chr6.simRat.chr6 419889 3 + 647215 ACA + +a +s simMouse_chr6.simMouse.chr6 413569 23 + 636262 AATTAAGGGGGCATCATGTATCA +s Anc0.Anc0refChr3 42367 23 + 222631 AAAAGGCACAGAACTGTGTGTTA +s Anc1.Anc1refChr6 72734 23 + 197743 AAAAGGCACAGAACTGTGTGTTA +s Anc2.Anc2refChr13 46384 23 + 96486 TTAAGGCACAGAACTGTGTGTTA +s mr.mrrefChr5 266266 23 + 294540 AATTAAGGGGGCATCATGTGTCA +s mr.mrrefChr5 264025 23 + 294540 AAAAAGCATAGAACTGTGTATTA +s simCow_chr6.simCow.chr6 402356 11 + 602619 TTAAGCCAC------------TG +s simDog_chr6.simDog.chr6 392975 23 + 593897 TTAAGGCACAGAACTGTGTGTTA +s simHuman_chr6.simHuman.chr6 397450 23 + 601863 CAAAGGCACAGAACTGTGTATTA +s simMouse_chr6.simMouse.chr6 411292 23 + 636262 AAAAAGCATAGAACTGTGTATAA +s simRat_chr6.simRat.chr6 417664 23 + 647215 AAGAAGCATAGAACTGTGTATTA +s simRat_chr6.simRat.chr6 419892 23 + 647215 AACTAAGGAGGCATCATGTGTCA + +a +s simMouse_chr6.simMouse.chr6 413592 1 + 636262 A +s Anc0.Anc0refChr3 42390 1 + 222631 A +s Anc1.Anc1refChr6 72757 1 + 197743 A +s Anc2.Anc2refChr13 46407 1 + 96486 A +s mr.mrrefChr5 266289 1 + 294540 A +s mr.mrrefChr5 264048 1 + 294540 A +s simCow_chr6.simCow.chr6 402367 1 + 602619 A +s simDog_chr6.simDog.chr6 392998 1 + 593897 A +s simHuman_chr6.simHuman.chr6 397473 1 + 601863 A +s simMouse_chr6.simMouse.chr6 411315 1 + 636262 A +s simRat_chr6.simRat.chr6 419915 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 413593 1 + 636262 C +s Anc0.Anc0refChr3 42391 1 + 222631 C +s Anc1.Anc1refChr6 72758 1 + 197743 C +s Anc2.Anc2refChr13 46408 1 + 96486 C +s mr.mrrefChr5 266290 1 + 294540 C +s mr.mrrefChr5 264049 1 + 294540 C +s simCow_chr6.simCow.chr6 402368 1 + 602619 C +s simDog_chr6.simDog.chr6 392999 1 + 593897 C +s simHuman_chr6.simHuman.chr6 397474 1 + 601863 C +s simMouse_chr6.simMouse.chr6 411316 1 + 636262 C +s simRat_chr6.simRat.chr6 417687 1 + 647215 C +s simRat_chr6.simRat.chr6 419916 1 + 647215 C + +a +s simMouse_chr6.simMouse.chr6 413594 40 + 636262 TGTAAGGTGAATACTCAAAATCTGCTGCTCTACACAAATG +s Anc0.Anc0refChr3 42392 40 + 222631 TGTAAGGTGACCACTCAGAAACTATTGCTCCAAATGTATG +s Anc1.Anc1refChr6 72759 40 + 197743 TGTAAGGTGACCACTCAGAAACTATTGCTCCAAATGTATG +s Anc2.Anc2refChr13 46409 40 + 96486 TGTAAGGTGACCACTTGGAAACTATTGCTCCAAATGTATG +s mr.mrrefChr5 266291 40 + 294540 TGTAAGGTGAACACTCAGAATCTATTGCTCTACACAAATG +s mr.mrrefChr5 264050 40 + 294540 TGTAAGTTGACCATTCAGAATCTATTGCTCTAAACATATG +s simCow_chr6.simCow.chr6 402369 40 + 602619 TGTAAGGAGACCACATTAAAATGATCGCTCCAACCATATG +s simDog_chr6.simDog.chr6 393000 40 + 593897 AATAAGGTGACCACTTGGGAACTATTGCACCAAATGTATG +s simHuman_chr6.simHuman.chr6 397475 40 + 601863 TGTAGGGTGACCACTCAGAAACTTTTGCTCCAGATGTACG +s simMouse_chr6.simMouse.chr6 411317 40 + 636262 TGTAAGTTGACCGTTCAGAATCTATCGCTCTAAACATATG +s simRat_chr6.simRat.chr6 417688 40 + 647215 TGTAAGTTTCCCATTCAGAATCTATTGCCCTAAACATATG +s simRat_chr6.simRat.chr6 419920 40 + 647215 TGTAAGGTGAACACTCAGAATCTATTGCTCTACACAAATG + +a +s simMouse_chr6.simMouse.chr6 413634 11 + 636262 GTGGAGACCAT +s Anc0.Anc0refChr3 42432 11 + 222631 GTATATTGCCC +s Anc1.Anc1refChr6 72799 11 + 197743 GTATATTGCCC +s Anc2.Anc2refChr13 46449 11 + 96486 GTATGTTGCCC +s mr.mrrefChr5 266331 11 + 294540 GTATAGATCCC +s mr.mrrefChr5 264090 11 + 294540 GCAAATTGCCC +s simCow_chr6.simCow.chr6 402409 11 + 602619 GTATGTTGCCC +s simDog_chr6.simDog.chr6 393040 11 + 593897 GTATGTATCCC +s simHuman_chr6.simHuman.chr6 397515 11 + 601863 GTATATTGCCC +s simMouse_chr6.simMouse.chr6 411357 11 + 636262 GCAAATTGCCC +s simRat_chr6.simRat.chr6 419960 11 + 647215 GGATAGATCCC + +a +s simMouse_chr6.simMouse.chr6 413645 23 + 636262 ATCATTGACAAACTTAAGAGGCC +s Anc0.Anc0refChr3 42443 23 + 222631 ATCCTGGTCAAATCAAGAAGACT +s Anc1.Anc1refChr6 72810 23 + 197743 ATCCTGGTCAAATCAAGAAGACT +s Anc2.Anc2refChr13 46460 23 + 96486 CTCCTGGTCAAATCAAGAAGACT +s mr.mrrefChr5 266342 23 + 294540 ATCATGGACAAATTTAGGAGGCC +s mr.mrrefChr5 264101 12 + 294540 ATTGTGGACAAA----------- +s simCow_chr6.simCow.chr6 402420 23 + 602619 CTCTAGGTCAGATCAAGAAGGCT +s simDog_chr6.simDog.chr6 393051 23 + 593897 CTTCTGGTCAAATCAAGAAGACT +s simHuman_chr6.simHuman.chr6 397526 12 + 601863 ATCCTGGTGAAA----------- +s simMouse_chr6.simMouse.chr6 411369 12 + 636262 ATTGTGGACAAA----------- +s simRat_chr6.simRat.chr6 419971 23 + 647215 ATCATGGACAAATTTAGGAGGCC + +a +s simMouse_chr6.simMouse.chr6 413668 6 + 636262 AAATGT +s Anc0.Anc0refChr3 42466 6 + 222631 GTATGC +s Anc1.Anc1refChr6 72833 6 + 197743 GTATGC +s Anc2.Anc2refChr13 46483 6 + 96486 GTATTC +s mr.mrrefChr5 266365 6 + 294540 ATATGC +s mr.mrrefChr5 264113 6 + 294540 GCATGC +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 411392 6 + 636262 GCATGC +s simRat_chr6.simRat.chr6 419994 6 + 647215 ATATGC + +a +s simMouse_chr6.simMouse.chr6 413674 12 + 636262 GAGCTTACTACT +s Anc0.Anc0refChr3 42472 12 + 222631 AAGCTCACTTCT +s Anc1.Anc1refChr6 72839 12 + 197743 AAGCTCACTTCT +s Anc2.Anc2refChr13 46489 12 + 96486 AAGCTCACTCCT +s mr.mrrefChr5 266371 12 + 294540 GAGCTTACTACT +s mr.mrrefChr5 264119 12 + 294540 AAGCTCACTTCT +s simCow_chr6.simCow.chr6 402450 12 + 602619 AAGCGCACTCCC +s simDog_chr6.simDog.chr6 393080 12 + 593897 AAACTCACTCCT +s simHuman_chr6.simHuman.chr6 397544 12 + 601863 ATGCTCACCTCT +s simMouse_chr6.simMouse.chr6 411398 12 + 636262 AAGCTCACTTCT +s simRat_chr6.simRat.chr6 420000 12 + 647215 CAGCTTGCTACC + +a +s simMouse_chr6.simMouse.chr6 413686 12 + 636262 GATACCCTTATA +s Anc0.Anc0refChr3 42484 12 + 222631 AATACCCACAGA +s Anc1.Anc1refChr6 72851 12 + 197743 AATACCCACAGA +s Anc2.Anc2refChr13 46501 12 + 96486 AATACCCACAGA +s mr.mrrefChr5 266383 12 + 294540 AATACCCTTATA +s mr.mrrefChr5 264131 7 + 294540 AATAT-----GA +s simCow_chr6.simCow.chr6 402462 12 + 602619 AATACCCACAGA +s simDog_chr6.simDog.chr6 393092 12 + 593897 AATACCCACAGA +s simHuman_chr6.simHuman.chr6 397556 7 + 601863 AATAT-----GA +s simMouse_chr6.simMouse.chr6 411421 7 + 636262 AATAT-----GA +s simRat_chr6.simRat.chr6 420012 12 + 647215 AATACCCTTACA + +a +s simMouse_chr6.simMouse.chr6 413698 1 + 636262 A +s Anc0.Anc0refChr3 42496 1 + 222631 A +s Anc1.Anc1refChr6 72863 1 + 197743 A +s Anc2.Anc2refChr13 46513 1 + 96486 A +s mr.mrrefChr5 266395 1 + 294540 A +s mr.mrrefChr5 264138 1 + 294540 A +s simCow_chr6.simCow.chr6 402474 1 + 602619 A +s simDog_chr6.simDog.chr6 393104 1 + 593897 A +s simHuman_chr6.simHuman.chr6 397563 1 + 601863 A +s simMouse_chr6.simMouse.chr6 411428 1 + 636262 A +s simRat_chr6.simRat.chr6 417728 1 + 647215 A +s simRat_chr6.simRat.chr6 420024 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 413699 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 266396 1 + 294540 T +s mr.mrrefChr5 264140 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 411430 1 + 636262 T +s simRat_chr6.simRat.chr6 417730 1 + 647215 T +s simRat_chr6.simRat.chr6 420025 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 413700 5 + 636262 TAGAA +s Anc0.Anc0refChr3 42499 5 + 222631 TAGAA +s Anc1.Anc1refChr6 72866 5 + 197743 TAGAA +s Anc2.Anc2refChr13 46516 5 + 96486 TAGAA +s mr.mrrefChr5 266397 5 + 294540 TAGAA +s mr.mrrefChr5 264237 5 + 294540 TCGAA +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 411535 5 + 636262 TCAAA +s simRat_chr6.simRat.chr6 417827 5 + 647215 TTGAA +s simRat_chr6.simRat.chr6 420026 5 + 647215 TAAAA + +a +s simMouse_chr6.simMouse.chr6 413705 4 + 636262 TTAT +s Anc0.Anc0refChr3 42504 4 + 222631 TTAT +s Anc1.Anc1refChr6 72871 4 + 197743 TTAT +s Anc2.Anc2refChr13 46521 4 + 96486 TTAT +s mr.mrrefChr5 266402 4 + 294540 TTAT +s mr.mrrefChr5 264242 4 + 294540 TTAC +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 411540 4 + 636262 TTAC +s simRat_chr6.simRat.chr6 417832 4 + 647215 TTAC +s simRat_chr6.simRat.chr6 420031 4 + 647215 TTGT + +a +s simMouse_chr6.simMouse.chr6 413709 24 + 636262 AACAGAACAGGTGCTATGACACCT +s Anc0.Anc0refChr3 42508 19 + 222631 AATAGA-----TGAGATGCCACCT +s Anc1.Anc1refChr6 72875 19 + 197743 AATAGA-----TGAGATGCCACCT +s Anc2.Anc2refChr13 46526 19 + 96486 AATAGA-----TGAGATGCCAGCT +s mr.mrrefChr5 266406 19 + 294540 AACAGA-----TGAGATCACACCT +s mr.mrrefChr5 264246 19 + 294540 AATAAA-----TGAGATGCCACCT +s simCow_chr6.simCow.chr6 402488 19 + 602619 AATGGA-----AGAGATGCCAGCT +s simDog_chr6.simDog.chr6 393117 12 + 593897 AATACA-----TGAGAT------- +s simHuman_chr6.simHuman.chr6 397575 19 + 601863 AATAGA-----TGAGATGCCATCT +s simMouse_chr6.simMouse.chr6 411544 19 + 636262 AACAAA-----TGAGATGCCACCG +s simRat_chr6.simRat.chr6 417836 19 + 647215 AATAAA-----CGAGATGCTACCT +s simRat_chr6.simRat.chr6 420035 19 + 647215 AACAGA-----TGAGATCACACCT + +a +s simMouse_chr6.simMouse.chr6 413733 17 + 636262 TAAAATGAGCTTATGAA +s Anc0.Anc0refChr3 42537 8 + 222631 T---------TAAGAAA +s Anc1.Anc1refChr6 72904 8 + 197743 T---------TAAGAAA +s Anc2.Anc2refChr13 46555 8 + 96486 T---------TAAGAAA +s mr.mrrefChr5 266425 8 + 294540 T---------TTATGAA +s mr.mrrefChr5 264275 8 + 294540 T---------TTAGGAA +s simCow_chr6.simCow.chr6 402517 8 + 602619 T---------TAAGAAG +s simDog_chr6.simDog.chr6 393131 8 + 593897 T---------TAAGAAA +s simHuman_chr6.simHuman.chr6 397604 8 + 601863 T---------TAAGAAA +s simMouse_chr6.simMouse.chr6 411572 5 + 636262 ------------AGGAA +s simRat_chr6.simRat.chr6 417865 8 + 647215 T---------TTAGGAA +s simRat_chr6.simRat.chr6 420054 8 + 647215 T---------TTATGAA + +a +s simMouse_chr6.simMouse.chr6 413750 4 + 636262 AGGA +s Anc0.Anc0refChr3 42545 4 + 222631 AGGA +s Anc1.Anc1refChr6 72912 4 + 197743 AGGA +s Anc2.Anc2refChr13 46563 4 + 96486 AGTA +s mr.mrrefChr5 266433 4 + 294540 AGGA +s mr.mrrefChr5 264283 4 + 294540 TGGA +s simCow_chr6.simCow.chr6 402532 4 + 602619 AGTA +s simHuman_chr6.simHuman.chr6 397612 4 + 601863 AGGA +s simMouse_chr6.simMouse.chr6 411577 4 + 636262 TGGA +s simRat_chr6.simRat.chr6 417873 4 + 647215 TTGA +s simRat_chr6.simRat.chr6 420062 4 + 647215 AGGG + +a +s simMouse_chr6.simMouse.chr6 413754 6 + 636262 ACTCAG +s Anc0.Anc0refChr3 42552 6 + 222631 ACTAAG +s Anc1.Anc1refChr6 72919 6 + 197743 ACTAAG +s Anc2.Anc2refChr13 46570 6 + 96486 ACTAAG +s mr.mrrefChr5 266437 6 + 294540 ACTCAG +s mr.mrrefChr5 264287 6 + 294540 ACTTGG +s simCow_chr6.simCow.chr6 402539 6 + 602619 ACTAAG +s simHuman_chr6.simHuman.chr6 397619 6 + 601863 ACTGGG +s simMouse_chr6.simMouse.chr6 411581 6 + 636262 ACTTGG +s simRat_chr6.simRat.chr6 417877 6 + 647215 AGTTGG +s simRat_chr6.simRat.chr6 420066 6 + 647215 TCTAAG + +a +s simMouse_chr6.simMouse.chr6 413760 31 + 636262 TAGTCTACTGAGTGAAACAGCTAAACAGGGT +s Anc0.Anc0refChr3 42562 30 + 222631 TAGTCTAT-GCATCACACAGCTAAATAAAGT +s Anc1.Anc1refChr6 72929 31 + 197743 TAGTCTATTGCATCACACAGCTAAATAAAGT +s Anc2.Anc2refChr13 46580 30 + 96486 TAGTAGAT-GCTTCACACGGCTAAATATAGT +s mr.mrrefChr5 266443 31 + 294540 TAGTCTACTGAGTGAAACAGCTAAACAGGGT +s mr.mrrefChr5 264293 31 + 294540 TAGTCTGTTGCACCACACAGCTAAACAAAGT +s simCow_chr6.simCow.chr6 402562 30 + 602619 TAGTAGAT-GCTTCACACGGCTAAATATAGT +s simDog_chr6.simDog.chr6 393139 1 + 593897 ------------------------------T +s simHuman_chr6.simHuman.chr6 397629 31 + 601863 TCGTGCCTTGCACCACACAGCCGATTAAAGT +s simMouse_chr6.simMouse.chr6 411587 26 + 636262 TA-----TTACGCCACACAGCTAAACAAACT +s simRat_chr6.simRat.chr6 417883 31 + 647215 TAGTCTGTTGCACCACACAGTGAAACAAAGT +s simRat_chr6.simRat.chr6 420072 31 + 647215 TAGTCTATTGAGTGAAATAGCTAAACAAGTT + +a +s simMouse_chr6.simMouse.chr6 413791 12 + 636262 AGCTCATCCTGC +s Anc0.Anc0refChr3 42593 12 + 222631 AAGTCATCCTAC +s Anc1.Anc1refChr6 72961 12 + 197743 AAGTCATCCTAC +s Anc2.Anc2refChr13 46611 12 + 96486 AAGTCATCCTCC +s mr.mrrefChr5 266475 12 + 294540 AACTCATCCTGC +s mr.mrrefChr5 264325 12 + 294540 AAGTCATTCCAC +s simCow_chr6.simCow.chr6 402593 12 + 602619 AAGTCATCCTCC +s simDog_chr6.simDog.chr6 393141 12 + 593897 AAGTCATCCTCC +s simHuman_chr6.simHuman.chr6 397661 12 + 601863 AAGTCATCCCAC +s simMouse_chr6.simMouse.chr6 411614 12 + 636262 AAGTCATTCCAC +s simRat_chr6.simRat.chr6 417915 12 + 647215 AAGATATTCCAC +s simRat_chr6.simRat.chr6 420104 12 + 647215 AACTCATTCTGC + +a +s simMouse_chr6.simMouse.chr6 413803 1 + 636262 A +s Anc0.Anc0refChr3 42605 1 + 222631 A +s Anc1.Anc1refChr6 72973 1 + 197743 A +s Anc2.Anc2refChr13 46623 1 + 96486 A +s mr.mrrefChr5 266487 1 + 294540 A +s mr.mrrefChr5 264337 1 + 294540 A +s simCow_chr6.simCow.chr6 402605 1 + 602619 A +s simDog_chr6.simDog.chr6 393153 1 + 593897 A +s simHuman_chr6.simHuman.chr6 397673 1 + 601863 A +s simMouse_chr6.simMouse.chr6 411626 1 + 636262 A +s simRat_chr6.simRat.chr6 420116 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 413804 1 + 636262 C +s Anc0.Anc0refChr3 42606 1 + 222631 C +s Anc1.Anc1refChr6 72974 1 + 197743 C +s Anc2.Anc2refChr13 46624 1 + 96486 C +s mr.mrrefChr5 266488 1 + 294540 C +s mr.mrrefChr5 264338 1 + 294540 C +s simCow_chr6.simCow.chr6 402606 1 + 602619 G +s simDog_chr6.simDog.chr6 393154 1 + 593897 C +s simHuman_chr6.simHuman.chr6 397674 1 + 601863 C +s simMouse_chr6.simMouse.chr6 411627 1 + 636262 C +s simRat_chr6.simRat.chr6 417927 1 + 647215 C +s simRat_chr6.simRat.chr6 420117 1 + 647215 C + +a +s simMouse_chr6.simMouse.chr6 413805 7 + 636262 AGCTGCC +s Anc0.Anc0refChr3 42608 6 + 222631 AACTAT- +s Anc1.Anc1refChr6 72976 7 + 197743 AACTATC +s Anc2.Anc2refChr13 46626 6 + 96486 TACTAT- +s mr.mrrefChr5 266490 7 + 294540 AGCTATC +s mr.mrrefChr5 264340 7 + 294540 GGCTATC +s simCow_chr6.simCow.chr6 402608 6 + 602619 TACTAT- +s simDog_chr6.simDog.chr6 393156 6 + 593897 TACCAT- +s simHuman_chr6.simHuman.chr6 397676 7 + 601863 AACAATC +s simMouse_chr6.simMouse.chr6 411629 7 + 636262 GGCTATC +s simRat_chr6.simRat.chr6 417929 7 + 647215 GGCTATC +s simRat_chr6.simRat.chr6 420119 7 + 647215 AGCTATC + +a +s simMouse_chr6.simMouse.chr6 413812 20 + 636262 AAGTTGCTATAACTCAAGCA +s Anc0.Anc0refChr3 42665 20 + 222631 AAGTTACTATAACTCAAGAT +s Anc1.Anc1refChr6 73037 20 + 197743 AAGTTACTATAACTCAAGAT +s Anc2.Anc2refChr13 46683 20 + 96486 AAGTTATTATAACTCAAGAT +s mr.mrrefChr5 266548 20 + 294540 AAGTTGCTATAACTCAAGCA +s mr.mrrefChr5 264401 20 + 294540 AAGTTACTATAACACAGGAT +s simCow_chr6.simCow.chr6 402665 20 + 602619 AAGTTATTATAACTCATAAT +s simDog_chr6.simDog.chr6 393213 20 + 593897 ATGTTATTATAACCCAAGAT +s simHuman_chr6.simHuman.chr6 397738 20 + 601863 AAGTTACCTTCACTCAGGAT +s simMouse_chr6.simMouse.chr6 411690 20 + 636262 AAGTTACTATAACACAGGAT +s simRat_chr6.simRat.chr6 417990 20 + 647215 AAGTTACTACAACCCAGGAG +s simRat_chr6.simRat.chr6 420180 19 + 647215 AAGTTGCTATAACTCAGG-G a s simMouse_chr6.simMouse.chr6 413832 2 + 636262 CA @@ -159546,11 +168886,109 @@ s simRat_chr6.simRat.chr6 420199 2 + 647215 TG a +s simMouse_chr6.simMouse.chr6 413834 12 + 636262 TGTGACGAGGTG +s Anc0.Anc0refChr3 42687 12 + 222631 CATGATGAGATC +s Anc1.Anc1refChr6 73059 12 + 197743 CATGATGAGATC +s Anc2.Anc2refChr13 46705 12 + 96486 CATGATGAGATC +s mr.mrrefChr5 266570 12 + 294540 TGTGATGAGGTG +s mr.mrrefChr5 264421 12 + 294540 CATAGTGAGGTT +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 411710 12 + 636262 CATAGTGAGGTT +s simRat_chr6.simRat.chr6 418010 12 + 647215 AATAATGGGGTT +s simRat_chr6.simRat.chr6 420201 12 + 647215 TTTGATGAGGTG + +a +s simMouse_chr6.simMouse.chr6 413846 9 + 636262 CGTTGGAAG +s Anc0.Anc0refChr3 42700 9 + 222631 CTTTGGAAG +s Anc1.Anc1refChr6 73072 9 + 197743 CTTTGGAAG +s Anc2.Anc2refChr13 46718 9 + 96486 TTTTGGACG +s mr.mrrefChr5 266582 9 + 294540 CTTTGGAAG +s mr.mrrefChr5 264433 9 + 294540 CTTCGGAAG +s simCow_chr6.simCow.chr6 402700 9 + 602619 TCTTGGATG +s simDog_chr6.simDog.chr6 393248 9 + 593897 TTTTGGACG +s simHuman_chr6.simHuman.chr6 397773 9 + 601863 CTTAGGGAG +s simMouse_chr6.simMouse.chr6 411722 9 + 636262 CTTCTGAAG +s simRat_chr6.simRat.chr6 418022 9 + 647215 CTTTGGAAG +s simRat_chr6.simRat.chr6 420213 9 + 647215 CTTTGGAAG + +a +s simMouse_chr6.simMouse.chr6 413855 4 + 636262 CCAG +s Anc0.Anc0refChr3 42709 4 + 222631 CGAG +s Anc1.Anc1refChr6 73081 4 + 197743 CGAG +s Anc2.Anc2refChr13 46727 4 + 96486 CGAG +s mr.mrrefChr5 266591 4 + 294540 CCAG +s mr.mrrefChr5 264442 4 + 294540 CTAG +s simCow_chr6.simCow.chr6 402709 4 + 602619 CTAG +s simDog_chr6.simDog.chr6 393257 4 + 593897 TGAA +s simHuman_chr6.simHuman.chr6 397782 4 + 601863 CAGG +s simMouse_chr6.simMouse.chr6 411740 4 + 636262 CTAG +s simRat_chr6.simRat.chr6 418031 4 + 647215 CTAG +s simRat_chr6.simRat.chr6 420222 4 + 647215 CCAG + +a +s simMouse_chr6.simMouse.chr6 413859 28 + 636262 GTAGATACATACCAGGGAAGAAGCGACA +s Anc0.Anc0refChr3 42722 28 + 222631 GTAGATACATAACATGAAGGAAATAACA +s Anc1.Anc1refChr6 73094 28 + 197743 GTAGATACATAACATGAAGGAAATAACA +s Anc2.Anc2refChr13 46740 28 + 96486 GAAGGGACAGAACATGAGGAAAATTACA +s mr.mrrefChr5 266595 28 + 294540 GTAGATACATACCATGGAAGAAATGACA +s mr.mrrefChr5 264455 28 + 294540 GTAAATACATGACATGGAAGAAATAAGA +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 411753 28 + 636262 GTAAATACATGACATGGAAGGAATAAGA +s simRat_chr6.simRat.chr6 418044 28 + 647215 GTAGATACATGACATGGAAGAAATAAGA +s simRat_chr6.simRat.chr6 420226 28 + 647215 GTAGATACATAACATGGAAGAAATGACA + +a +s simMouse_chr6.simMouse.chr6 413887 3 + 636262 CAT +s Anc0.Anc0refChr3 42750 3 + 222631 CAG +s Anc1.Anc1refChr6 73122 3 + 197743 CAG +s Anc2.Anc2refChr13 46768 3 + 96486 CAG +s mr.mrrefChr5 266623 3 + 294540 CAT +s mr.mrrefChr5 264483 3 + 294540 CAG +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 411781 3 + 636262 CAG +s simRat_chr6.simRat.chr6 418072 3 + 647215 CAG +s simRat_chr6.simRat.chr6 420254 3 + 647215 CAT + +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 413901 35 + 636262 TACAGTTCAAGTGAGCAATGCCTCCTCACTTAGGC +s Anc0.Anc0refChr3 42753 35 + 222631 TACAGTTCAAGTGAGCACCGCCTCCTCACTTAATT +s Anc1.Anc1refChr6 73125 35 + 197743 TACAGTTCAAGTGAGCACCGCCTCCTCACTTAATT +s Anc2.Anc2refChr13 46771 35 + 96486 TACAGTTCAAATGAGCACCGCTTCCTCACTTAATT +s mr.mrrefChr5 266637 35 + 294540 TACAGTTCAAGTGAGCAATGCCTCCTCACTTAGGC +s mr.mrrefChr5 264486 35 + 294540 TACAGTTGAAGTCAGCACTGCCTTTTCACTTCAGT +s simCow_chr6.simCow.chr6 402753 35 + 602619 TCCAGCTAAAGTGAGCACCGCTGCCTCATTTAATT +s simDog_chr6.simDog.chr6 393301 34 + 593897 AATACTTC-CATGGGTACTGCTTCCTCACTTAATT +s simHuman_chr6.simHuman.chr6 397851 35 + 601863 TACAGTTTGATTGAGCACCACCTCCTCACATAATT +s simMouse_chr6.simMouse.chr6 411784 35 + 636262 TACAGCTGAAGTCAGCACTGCCTTTTCACTTCAGG +s simRat_chr6.simRat.chr6 418077 35 + 647215 TACAGTTCAAGTCAGCAATGCCTTTTTACTTTGGT +s simRat_chr6.simRat.chr6 420268 35 + 647215 TACAGTCAGAGTGAGCAATGCCTCCTCACTTAGGC + +a +s simMouse_chr6.simMouse.chr6 413936 40 + 636262 TGAGTCAAAGCTGTGATTCACACCAGCTATGTAATACATG +s Anc0.Anc0refChr3 42791 40 + 222631 TGCATCTAAATCGTGACTCACACCAGGTGCGTAATGGGTG +s Anc1.Anc1refChr6 73163 40 + 197743 TGCATCTAAATCGTGACTCACACCAGGTGCGTAATGGGTG +s Anc2.Anc2refChr13 46809 40 + 96486 TGCATCTTAATCGTGACTCACACCAGGTGCCTAATGGTTG +s mr.mrrefChr5 266675 40 + 294540 TGAGTCTAAACTGTGATTCACACCAGCTGTGTAATTAAAG +s mr.mrrefChr5 264524 40 + 294540 TGTGTCTAAATCATGATTCACACCCGGTGTGTAATGTGTG +s simCow_chr6.simCow.chr6 402791 40 + 602619 TGTATCCGAGTTGTGGCTTACACCAGGTGCATAATGGTTG +s simDog_chr6.simDog.chr6 393338 39 + 593897 TGCATCTTAACC-TGACTCACAACAGGTGCCTAATGGTTG +s simHuman_chr6.simHuman.chr6 397889 40 + 601863 TTCATCTAAATGGTGACTCACACTGGGTGCTTAATGGGTA +s simMouse_chr6.simMouse.chr6 411822 40 + 636262 TGTGCCTAAATCATGATTCACACCCGGTGTGGAATTTGTG +s simRat_chr6.simRat.chr6 418115 40 + 647215 TATGTCTAAATTATGATTCAAATCCCGTATGTAATGTATG +s simRat_chr6.simRat.chr6 420306 39 + 647215 TGAGTCTAAACTGTGCTTCACACCAG-GGTGTAATTAAAG + +a s simMouse_chr6.simMouse.chr6 413976 210 + 636262 CAACAAGAGTGAGAGTTGAATGTTGGTCTGGGGGATGCATACATAGAATATATCAGCTGGTGACATTTGAATTGGCTCTCAGTCTGAGAGTTATCACACTCTTATTTGCGACCTTTCCCATTAGCTGATCCATAAGACTAACATGAAATTCTGCTAAATGATATGGTGTGCCACATGAGATCCCCCTCTGATCCCCCTCTACCCTTGTAA s Anc0.Anc0refChr3 43727 10 + 222631 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATATTATAA s Anc1.Anc1refChr6 74142 10 + 197743 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATATTATAA @@ -162042,12 +171480,79 @@ s simRat_chr6.simRat.chr6 426170 4 + 647215 AGAA a +s simMouse_chr6.simMouse.chr6 419954 28 + 636262 CTTAGACACATCCAGCAGCACAGCCCCC +s Anc0.Anc0refChr3 49278 28 + 222631 CTTATACACACCTAGAAGAATTGTCAGC +s Anc1.Anc1refChr6 79870 28 + 197743 CTTATACACACCTAGAAGAATTGTCAGC +s Anc2.Anc2refChr13 53683 28 + 96486 CTGATACACACCTAGAAGAATTGTCAGC +s mr.mrrefChr5 272324 28 + 294540 CTTAGACACATCCAGCAGCACAGCCCCC +s mr.mrrefChr5 272180 28 + 294540 CTCATTCACAACTGGAAGAATTGTGATC +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 419806 28 + 636262 CTCATTCACAACTGGAAGAATTGTGATC +s simRat_chr6.simRat.chr6 425880 28 + 647215 CTTACACACATCTGGAAGAATTGTGAGT +s simRat_chr6.simRat.chr6 426174 28 + 647215 CTTAGATGCGTCCAGCCGCCCAGCCCAC + +a +s simMouse_chr6.simMouse.chr6 419982 6 + 636262 CAGTCT +s Anc0.Anc0refChr3 49315 6 + 222631 CATCCT +s Anc1.Anc1refChr6 79907 6 + 197743 CATCCT +s Anc2.Anc2refChr13 53720 6 + 96486 CATCCT +s mr.mrrefChr5 272352 6 + 294540 CAGTCT +s mr.mrrefChr5 272208 6 + 294540 CATACT +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 419834 6 + 636262 CATACT +s simRat_chr6.simRat.chr6 425908 6 + 647215 GATACA +s simRat_chr6.simRat.chr6 426202 6 + 647215 CAGCCT + +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 +s simMouse_chr6.simMouse.chr6 419993 1 + 636262 A +s Anc0.Anc0refChr3 49321 1 + 222631 A +s Anc1.Anc1refChr6 79913 1 + 197743 A +s Anc2.Anc2refChr13 53726 1 + 96486 A +s mr.mrrefChr5 272363 1 + 294540 A +s mr.mrrefChr5 272214 1 + 294540 T +s simCow_chr6.simCow.chr6 409658 1 + 602619 A +s simDog_chr6.simDog.chr6 400146 1 + 593897 G +s simHuman_chr6.simHuman.chr6 405105 1 + 601863 A +s simMouse_chr6.simMouse.chr6 419840 1 + 636262 T +s simRat_chr6.simRat.chr6 425914 1 + 647215 T +s simRat_chr6.simRat.chr6 426213 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 419994 7 + 636262 AAGGAGC +s Anc0.Anc0refChr3 49322 7 + 222631 AAGGATT +s Anc1.Anc1refChr6 79914 7 + 197743 AAGGATT +s Anc2.Anc2refChr13 53727 7 + 96486 AAGGATT +s mr.mrrefChr5 272364 7 + 294540 AAGGAGC +s mr.mrrefChr5 272215 7 + 294540 AAGGATT +s simCow_chr6.simCow.chr6 409659 7 + 602619 AAAGATT +s simDog_chr6.simDog.chr6 400147 7 + 593897 AAGGATT +s simHuman_chr6.simHuman.chr6 405106 7 + 601863 AAGGATT +s simMouse_chr6.simMouse.chr6 419844 7 + 636262 GAGGATT +s simRat_chr6.simRat.chr6 425915 7 + 647215 AAGGATT +s simRat_chr6.simRat.chr6 426214 7 + 647215 AAGGAGC + +a +s simMouse_chr6.simMouse.chr6 420001 26 + 636262 AAACATGGAGCTAAGAAATATATTAT +s Anc0.Anc0refChr3 49329 23 + 222631 AGA---AAACCAAAGCCATATTTTAC +s Anc1.Anc1refChr6 79921 23 + 197743 AGA---AAACCAAAGCCATATTTTAC +s Anc2.Anc2refChr13 53734 23 + 96486 AGA---AAACCAAAGCCATATTTTAC +s mr.mrrefChr5 272371 23 + 294540 AAA---GGAGCTAAGAAATATATTAT +s mr.mrrefChr5 272222 23 + 294540 AGA---AGACCAAAGCTATATTTTGT +s simCow_chr6.simCow.chr6 409666 23 + 602619 AGA---GAACCTAAACCATATTTTAC +s simDog_chr6.simDog.chr6 400154 23 + 593897 AGA---AAACCAAAGCCAAATCTTAG +s simHuman_chr6.simHuman.chr6 405113 23 + 601863 AGA---AAACCAAGGCCATATTTTGC +s simMouse_chr6.simMouse.chr6 419852 23 + 636262 AGA---AGACCAAAGTTATACTCTGT +s simRat_chr6.simRat.chr6 425922 23 + 647215 AGA---AGACCAAAGCTCTATTTGGC +s simRat_chr6.simRat.chr6 426221 23 + 647215 AAA---GGAGCTCATAAATGTAATAT a s simMouse_chr6.simMouse.chr6 420027 2 + 636262 AG @@ -162055,11 +171560,91 @@ s simRat_chr6.simRat.chr6 426244 2 + 647215 AG a +s simMouse_chr6.simMouse.chr6 420029 15 + 636262 TTTACTCTTGTAATC +s Anc0.Anc0refChr3 49352 15 + 222631 TTCACAATTGGGCCT +s Anc1.Anc1refChr6 79944 15 + 197743 TTCACAATTGGGCCT +s Anc2.Anc2refChr13 53757 15 + 96486 TTCACAATTGGGCCT +s mr.mrrefChr5 272396 15 + 294540 TTTACTCTTGTAATC +s mr.mrrefChr5 272245 15 + 294540 TTCAGAGTAGCACCT +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 419875 15 + 636262 TTCAGAATAGCACCT +s simRat_chr6.simRat.chr6 425945 15 + 647215 TTTAGAGTAGCACCC +s simRat_chr6.simRat.chr6 426246 15 + 647215 TTTACTCTTTTAACC + +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 420050 26 + 636262 TTCTTAGGGACCTCTCAGAATGGGGT +s Anc0.Anc0refChr3 49367 26 + 222631 CAGTCAGGTACTCAGTATAATAGGGT +s Anc1.Anc1refChr6 79959 26 + 197743 CAGTCAGGTACTCAGTATAATAGGGT +s Anc2.Anc2refChr13 53772 26 + 96486 CAGTCAAGTACTCAGTATAATAGGGT +s mr.mrrefChr5 272417 26 + 294540 TTCTTAGGGACCTCTCAGAATGGGGT +s mr.mrrefChr5 272260 26 + 294540 TAGTCGCAAACTCAGTACACTAGATT +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 419890 26 + 636262 TAGTTGCAAACTCAGTACACTAGATT +s simRat_chr6.simRat.chr6 425960 26 + 647215 TAGTCACAAACTCAGTACGCTAGATT +s simRat_chr6.simRat.chr6 426267 26 + 647215 TTCTTGGGGATCTCTCTAAATGAGGT + +a +s simMouse_chr6.simMouse.chr6 420076 4 + 636262 ATAT +s Anc0.Anc0refChr3 49393 4 + 222631 AGTT +s Anc1.Anc1refChr6 79985 4 + 197743 AGTT +s Anc2.Anc2refChr13 53798 4 + 96486 AGTT +s mr.mrrefChr5 272443 4 + 294540 ATAT +s mr.mrrefChr5 272286 4 + 294540 AGTG +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 419916 4 + 636262 AGTG +s simRat_chr6.simRat.chr6 425986 4 + 647215 AGTA +s simRat_chr6.simRat.chr6 426294 4 + 647215 ATGT + +a +s simMouse_chr6.simMouse.chr6 420080 3 + 636262 TGT +s Anc0.Anc0refChr3 49398 3 + 222631 TGT +s Anc1.Anc1refChr6 79990 3 + 197743 TGT +s Anc2.Anc2refChr13 53803 3 + 96486 TGT +s mr.mrrefChr5 272447 3 + 294540 TGT +s mr.mrrefChr5 272291 3 + 294540 TCT +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 419921 3 + 636262 TCT +s simRat_chr6.simRat.chr6 425991 3 + 647215 TAT +s simRat_chr6.simRat.chr6 426298 3 + 647215 TGG + +a +s simMouse_chr6.simMouse.chr6 420083 7 + 636262 CAGTATA +s Anc0.Anc0refChr3 49410 3 + 222631 TAA---- +s Anc1.Anc1refChr6 80002 7 + 197743 TAACGTA +s Anc2.Anc2refChr13 53815 3 + 96486 TAA---- +s mr.mrrefChr5 272450 7 + 294540 CAGTATA +s mr.mrrefChr5 272303 7 + 294540 TAAGGTA +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 419933 7 + 636262 TAAGGTA +s simRat_chr6.simRat.chr6 426003 7 + 647215 TAAAGTA +s simRat_chr6.simRat.chr6 426301 7 + 647215 CATTATA + +a +s simMouse_chr6.simMouse.chr6 420090 3 + 636262 GAC +s Anc1.Anc1refChr6 80009 3 + 197743 TAC +s mr.mrrefChr5 272457 3 + 294540 GAC +s mr.mrrefChr5 272313 3 + 294540 TAC +s simHuman_chr6.simHuman.chr6 405200 3 + 601863 TAC +s simMouse_chr6.simMouse.chr6 419943 3 + 636262 TAC +s simRat_chr6.simRat.chr6 426013 3 + 647215 TAT +s simRat_chr6.simRat.chr6 426308 3 + 647215 GGC + +a s simMouse_chr6.simMouse.chr6 420093 1 + 636262 A s Anc1.Anc1refChr6 80012 1 + 197743 A s mr.mrrefChr5 272460 1 + 294540 A @@ -162067,6 +171652,34 @@ s simRat_chr6.simRat.chr6 426311 1 + 647215 G a +s simMouse_chr6.simMouse.chr6 420094 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 272461 1 + 294540 T +s mr.mrrefChr5 272316 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 419946 1 + 636262 T +s simRat_chr6.simRat.chr6 426016 1 + 647215 G +s simRat_chr6.simRat.chr6 426312 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 420095 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 272462 3 + 294540 CTG +s mr.mrrefChr5 272317 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 419947 3 + 636262 CTG +s simRat_chr6.simRat.chr6 426167 3 + 647215 CTG +s simRat_chr6.simRat.chr6 426313 3 + 647215 CTA + +a s simMouse_chr6.simMouse.chr6 420098 7 + 636262 CTCTCAG s Anc0.Anc0refChr3 49417 7 + 222631 CTCCCAG s Anc1.Anc1refChr6 80017 7 + 197743 CTCCCAG @@ -175467,52 +185080,278 @@ 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 +s simMouse_chr6.simMouse.chr6 458651 9 + 636262 GATGTGATG +s Anc0.Anc0refChr4 19468 9 + 45765 gatgtgata +s Anc1.Anc1refChr2 86554 9 - 144309 gatgtgata +s Anc2.Anc2refChr7 5764 9 - 32194 gatgtgata +s mr.mrrefChr0 51896 9 - 130230 GATGTGATA +s mr.mrrefChr3 14380 9 + 181027 GATGTGATG +s simCow_chr6.simCow.chr6 517991 9 - 602619 gatgtgata +s simDog_chr6.simDog.chr6 408036 9 - 593897 gatgtgata +s simHuman_chr6.simHuman.chr6 523431 9 - 601863 gatgtgata +s simMouse_chr6.simMouse.chr6 553483 9 - 636262 GATGTGATA +s simRat_chr6.simRat.chr6 572241 9 - 647215 GATGTGATA +s simRat_chr6.simRat.chr6 468050 9 + 647215 GATGTGATG + +a +s simMouse_chr6.simMouse.chr6 458660 15 + 636262 GACCTTGAGCAGTAG +s Anc0.Anc0refChr4 19477 13 + 45765 gagcttgagcagc-- +s Anc1.Anc1refChr2 86563 15 - 144309 gagcttgagcagcag +s Anc2.Anc2refChr7 5773 13 - 32194 aagctggaggagc-- +s mr.mrrefChr0 51905 15 - 130230 gttcttgagcagtat +s mr.mrrefChr3 14389 15 + 181027 GACCTTGAGCAGTAG +s simCow_chr6.simCow.chr6 518000 13 - 602619 gagcaaggggagt-- +s simDog_chr6.simDog.chr6 408045 13 - 593897 aagttgaaggaac-- +s simHuman_chr6.simHuman.chr6 523440 15 - 601863 cagcttgagaggcgg +s simMouse_chr6.simMouse.chr6 553492 15 - 636262 GTTCTTGAGCAGTAT +s simRat_chr6.simRat.chr6 468059 15 + 647215 GATCTTGACCAGTAC + +a +s simMouse_chr6.simMouse.chr6 458675 10 + 636262 ATTATCGAGG +s Anc0.Anc0refChr4 19493 10 + 45765 agttttaagg +s Anc1.Anc1refChr2 86581 10 - 144309 agttttaagg +s Anc2.Anc2refChr7 5789 10 - 32194 agttttaagg +s mr.mrrefChr0 51920 10 - 130230 attattgaag +s mr.mrrefChr3 14404 10 + 181027 ATTATCGAGG +s simCow_chr6.simCow.chr6 518016 10 - 602619 agtttttagg +s simDog_chr6.simDog.chr6 408061 10 - 593897 agttttaggg +s simHuman_chr6.simHuman.chr6 523458 10 - 601863 agttttaaga +s simMouse_chr6.simMouse.chr6 553507 10 - 636262 ATTATTGAAG +s simRat_chr6.simRat.chr6 468074 10 + 647215 ATTATTGAGG + +a +s simMouse_chr6.simMouse.chr6 458685 7 + 636262 CATGTGT +s Anc0.Anc0refChr4 19503 7 + 45765 cttttag +s Anc1.Anc1refChr2 86591 7 - 144309 cttttag +s Anc2.Anc2refChr7 5799 7 - 32194 ctttcag +s mr.mrrefChr0 51930 7 - 130230 CATGTGT +s mr.mrrefChr3 14414 7 + 181027 CATGTGT +s simCow_chr6.simCow.chr6 518026 7 - 602619 ctctcaa +s simDog_chr6.simDog.chr6 408071 7 - 593897 ctttcag +s simHuman_chr6.simHuman.chr6 523468 7 - 601863 cttttag +s simMouse_chr6.simMouse.chr6 553517 7 - 636262 CATGTGT +s simRat_chr6.simRat.chr6 572250 7 - 647215 CATGTGT +s simRat_chr6.simRat.chr6 468084 7 + 647215 CATCTAT + +a +s simMouse_chr6.simMouse.chr6 458692 3 + 636262 GGT +s Anc0.Anc0refChr4 19510 3 + 45765 ggt +s Anc1.Anc1refChr2 86598 3 - 144309 ggt +s Anc2.Anc2refChr7 5806 3 - 32194 ggt +s mr.mrrefChr0 51937 3 - 130230 agt +s mr.mrrefChr3 14421 3 + 181027 GGT +s simCow_chr6.simCow.chr6 518033 3 - 602619 ggt +s simDog_chr6.simDog.chr6 408078 3 - 593897 ggt +s simHuman_chr6.simHuman.chr6 523475 3 - 601863 agt +s simMouse_chr6.simMouse.chr6 553524 3 - 636262 AGT +s simRat_chr6.simRat.chr6 468091 3 + 647215 AAT + +a +s simMouse_chr6.simMouse.chr6 458695 29 + 636262 TATTAGGGAGTCAGTCAATAAACTGAGAA +s Anc0.Anc0refChr4 19516 29 + 45765 ctctagggagtcagccaataaaCtaagga +s Anc1.Anc1refChr2 86604 29 - 144309 ctctagggagtcagccaatAAaCTAAGGA +s Anc2.Anc2refChr7 5814 29 - 32194 ctctagggggttagcaaataaaTtaagga +s mr.mrrefChr0 51940 29 - 130230 CATTAGGGAGTCAGTCAAtAAACTGAGAA +s mr.mrrefChr3 14424 29 + 181027 TATTAGGGAGTCAGTCAATAAACTGAGAA +s simCow_chr6.simCow.chr6 518041 23 - 602619 ctctagggggttagcaaataaAT------ +s simDog_chr6.simDog.chr6 408086 29 - 593897 tgctagggggttagcaaataaattaagga +s simHuman_chr6.simHuman.chr6 523481 27 - 601863 ctctacggagtgagccaat--aCGAAGGA +s simMouse_chr6.simMouse.chr6 553527 28 - 636262 CATTAGGGAGTCAGTTGA-AAACTGAGAA +s simRat_chr6.simRat.chr6 572257 29 - 647215 CATTAGGGAGTCAGTCAATAAACAGAGAA +s simRat_chr6.simRat.chr6 468094 29 + 647215 CATTACGGAGTCAGTTGATAAACTGAGGA + +a +s simMouse_chr6.simMouse.chr6 458724 55 + 636262 TTAAAAATGTCCAGTGGAAAGGGAGTAATGTCAACAGCACAAGCTTATACTGAAA +s Anc0.Anc0refChr4 19545 50 + 45765 TAaaaa---tgcagtgaagagggagtaatgtcag--gcacaaccttatggtgTGA +s Anc1.Anc1refChr2 86633 55 - 144309 TAaaaaATGtgcagtgaagagggagtaatgtcagCAgcacaaccttatggtgTGA +s Anc2.Anc2refChr7 5843 50 - 32194 TAaaaa---tgcagtgaagagggagtaatgtcag--ggacaaccttatggtgGGA +s mr.mrrefChr0 51969 55 - 130230 TTAAAAATGTGCAGTGGAAAGGGAGTAATATCAACAACATAACCTTATGCTGTAA +s mr.mrrefChr3 14453 55 + 181027 TTAAAAATGTCCAGTGGAAAGGGAGTAATGTCAACAGCACAAGCTTATACTGAAA +s simCow_chr6.simCow.chr6 518064 39 - 602619 --------------TGCAGAGGGAGGAATATCAG--TGAGGAAGTTATGGTGGGA +s simDog_chr6.simDog.chr6 408116 50 - 593897 TAaaaa---tgcagtgacgagcaagtaaagtcag--ggacaaccttatggtgggg +s simHuman_chr6.simHuman.chr6 523508 52 - 601863 TAaaaa---tgcagtgaagagggagtaatgtcagcatcataaccttatggtgTGA +s simMouse_chr6.simMouse.chr6 553555 55 - 636262 TTAAAAATGTGCAGTGGAAAGGGAGTAGTATCAACAACATAACCTTATACAGTAA +s simRat_chr6.simRat.chr6 572286 55 - 647215 TTAAAAATGCGCAGTGGGAAGGGAGTAATCTCAACAGCATAGCCTCATGCTGTAA +s simRat_chr6.simRat.chr6 468123 55 + 647215 TTAAATATGTGCAGTGGAAAGGGAGTAATGTCAACAGCACAGCCTTATACTGAAA + +a +s simMouse_chr6.simMouse.chr6 458779 30 + 636262 TGTTATTCAATAAGTTGTATGGAAGCAGGA +s Anc0.Anc0refChr4 19595 30 + 45765 tgaaatttggtatggtgcaagaaagaggga +s Anc1.Anc1refChr2 86688 30 - 144309 tgaaatttggtatggtgcaagaaagaggga +s Anc2.Anc2refChr7 5894 30 - 32194 tgaaatttgctatggttcgagaaagaggga +s mr.mrrefChr0 52024 30 - 130230 TGACATTTAGTAGGGTGTATGAAAGCAGGA +s mr.mrrefChr3 14508 30 + 181027 TGTTATTCAATAAGTTGTATGGAAGCAGGA +s simCow_chr6.simCow.chr6 518104 30 - 602619 TGACGTTTGTTATAGTTCCAGGAAGAGGGA +s simDog_chr6.simDog.chr6 408167 30 - 593897 tgaaatttgctatggtttgacaaaggggga +s simHuman_chr6.simHuman.chr6 523758 30 - 601863 tgagatttggtatggtgcaagaaagaggga +s simMouse_chr6.simMouse.chr6 553610 30 - 636262 TGACATTCAATAGGGTGTATGAAATCAGGA +s simRat_chr6.simRat.chr6 572341 30 - 647215 TGACACTTAGTAGGGTGTATGGAAGCAGGA +s simRat_chr6.simRat.chr6 468178 30 + 647215 TGACATTCAATAGAGTGCATGTCAGCAGGA + +a +s simMouse_chr6.simMouse.chr6 458809 29 + 636262 ATATTAACAGTGACACAACACCTTCTAAC +s Anc0.Anc0refChr4 19625 29 + 45765 ataatattagtgacacaacACTTTCTGAC +s Anc1.Anc1refChr2 86718 29 - 144309 ataatattagtgacacaacACTTTCTGAC +s Anc2.Anc2refChr7 5924 29 - 32194 acaacattagtgacacaacACTTTCTGAC +s mr.mrrefChr0 52054 29 - 130230 ATATTATTAGTGACATGACACCTTCTGAC +s mr.mrrefChr3 14538 29 + 181027 ATATTAACAGTGACACAACACCTTCTAAC +s simCow_chr6.simCow.chr6 518134 29 - 602619 ACAACTTTAGTGACAGAACACTTTCTGAC +s simDog_chr6.simDog.chr6 408197 28 - 593897 gcaaca-tagtgacacaacacTTTCTGTC +s simHuman_chr6.simHuman.chr6 523788 29 - 601863 ataatgttagtgacacaacATTTTCTGAC +s simMouse_chr6.simMouse.chr6 553640 29 - 636262 ATATTATTAGTGACATGACGCCTTCTGAC +s simRat_chr6.simRat.chr6 572386 29 - 647215 ATATTATTAGTGACATGACACCTTCTGAC +s simRat_chr6.simRat.chr6 468208 29 + 647215 ATATTATTAGTGACACAACACCTTCTGAC + +a +s simMouse_chr6.simMouse.chr6 458838 2 + 636262 AG +s Anc0.Anc0refChr4 19661 2 + 45765 AG +s Anc1.Anc1refChr2 86754 2 - 144309 AG +s Anc2.Anc2refChr7 5960 2 - 32194 AT +s mr.mrrefChr0 52088 2 - 130230 AG +s mr.mrrefChr3 14567 2 + 181027 AG +s simCow_chr6.simCow.chr6 518170 2 - 602619 AG +s simDog_chr6.simDog.chr6 408232 2 - 593897 AT +s simHuman_chr6.simHuman.chr6 523824 2 - 601863 AA +s simMouse_chr6.simMouse.chr6 553674 2 - 636262 AG +s simRat_chr6.simRat.chr6 572420 2 - 647215 AG +s simRat_chr6.simRat.chr6 468237 2 + 647215 AG + +a +s simMouse_chr6.simMouse.chr6 458840 5 + 636262 TTGCT +s Anc0.Anc0refChr4 19663 5 + 45765 TTTCT +s Anc1.Anc1refChr2 86756 5 - 144309 TTTCT +s Anc2.Anc2refChr7 5962 5 - 32194 TTTCT +s mr.mrrefChr0 52090 5 - 130230 TCACT +s mr.mrrefChr3 14569 5 + 181027 TTGCT +s simCow_chr6.simCow.chr6 518172 5 - 602619 TTTTT +s simDog_chr6.simDog.chr6 408234 5 - 593897 TTTCT +s simHuman_chr6.simHuman.chr6 523826 5 - 601863 TTTCT +s simMouse_chr6.simMouse.chr6 553676 5 - 636262 TCACT +s simRat_chr6.simRat.chr6 572422 5 - 647215 TCACT +s simRat_chr6.simRat.chr6 468244 5 + 647215 TTGAT + +a +s simMouse_chr6.simMouse.chr6 458845 6 + 636262 TTTCCC +s Anc0.Anc0refChr4 19669 5 + 45765 TTTCC- +s Anc1.Anc1refChr2 86762 5 - 144309 TTTCC- +s Anc2.Anc2refChr7 5968 5 - 32194 TATCT- +s mr.mrrefChr0 52095 5 - 130230 TTTCC- +s mr.mrrefChr3 14574 5 + 181027 TTTCC- +s simCow_chr6.simCow.chr6 518178 5 - 602619 TTTAT- +s simDog_chr6.simDog.chr6 408240 5 - 593897 TATCT- +s simHuman_chr6.simHuman.chr6 523832 5 - 601863 TCTCC- +s simMouse_chr6.simMouse.chr6 553681 5 - 636262 TTTCC- +s simRat_chr6.simRat.chr6 572427 5 - 647215 TTTCC- +s simRat_chr6.simRat.chr6 468249 5 + 647215 TTTCT- + +a +s simMouse_chr6.simMouse.chr6 458851 38 + 636262 AGTGGTGTTTAAACATGATGAAGGCTCTCAGAATTTGA +s Anc0.Anc0refChr4 19675 37 + 45765 AATGGTCTT-AATGGTGATCTGAACTCTTGGGATATGA +s Anc1.Anc1refChr2 86768 37 - 144309 AATGGTCTT-AATGGTGATCTGAACTCTTGGGATATGA +s Anc2.Anc2refChr7 5974 37 - 32194 AATGGTCTT-AATGGTGATCTGAACTCTTGGGATATGA +s mr.mrrefChr0 52101 37 - 130230 AGTGGTGTT-AAACGTAATGTGAGCTCTAAGAATTTGA +s mr.mrrefChr3 14579 37 + 181027 AGTGGTGTT-AAACATGATGAAGGCTCTCAGAATTTGA +s simCow_chr6.simCow.chr6 518184 35 - 602619 GATTGTC-T-AATGGTGATTTGTACT-TTGTGATATGG +s simDog_chr6.simDog.chr6 408246 37 - 593897 AATGGACTC-AATGGTGATCTGAGCTCTTGGGATCTGA +s simHuman_chr6.simHuman.chr6 523838 37 - 601863 TATGGTCTT-AATGGTAATCTGAACTCTTGCGATATCA +s simMouse_chr6.simMouse.chr6 553687 36 - 636262 AGTGGTGTT-AAACGTAA-GTGAGCTCTAAGAATTTGA +s simRat_chr6.simRat.chr6 572433 37 - 647215 AGTGGTATT-AAACGTGATGTAAGCTCTCAGAATTTGA +s simRat_chr6.simRat.chr6 468254 37 + 647215 AGTGGTGTT-AAAAATGATGTAAGCTCTCAGAATTTGA + +a +s simMouse_chr6.simMouse.chr6 458889 21 + 636262 ATATGCCGAACTATCTGATCA +s Anc0.Anc0refChr4 19712 10 + 45765 ACATGTGGAC----------- +s Anc1.Anc1refChr2 86805 10 - 144309 ACATGTGGAC----------- +s Anc2.Anc2refChr7 6011 10 - 32194 ACATGTGGAC----------- +s mr.mrrefChr0 52138 10 - 130230 GCATGCAGAC----------- +s mr.mrrefChr3 14616 10 + 181027 ATATGCCGAA----------- +s simCow_chr6.simCow.chr6 518219 10 - 602619 ACATGTGGAC----------- +s simDog_chr6.simDog.chr6 408283 10 - 593897 GTATGTCAAC----------- +s simHuman_chr6.simHuman.chr6 523875 10 - 601863 ACATGTGGAC----------- +s simMouse_chr6.simMouse.chr6 553723 10 - 636262 GCATGCAGAC----------- +s simRat_chr6.simRat.chr6 468291 10 + 647215 ACATACAGAA----------- + +a +s simMouse_chr6.simMouse.chr6 458910 5 + 636262 TGAGC +s Anc0.Anc0refChr4 19727 5 + 45765 CAATC +s Anc1.Anc1refChr2 86820 5 - 144309 CAATC +s Anc2.Anc2refChr7 6028 5 - 32194 CAATC +s mr.mrrefChr0 52148 5 - 130230 CGATC +s mr.mrrefChr3 14626 5 + 181027 TGAGC +s simCow_chr6.simCow.chr6 518236 5 - 602619 CAATC +s simDog_chr6.simDog.chr6 408300 5 - 593897 CAATC +s simHuman_chr6.simHuman.chr6 523890 5 - 601863 CAATC +s simMouse_chr6.simMouse.chr6 553733 5 - 636262 CGATC +s simRat_chr6.simRat.chr6 468301 5 + 647215 TCAGC + +a +s simMouse_chr6.simMouse.chr6 458915 1 + 636262 A +s Anc0.Anc0refChr4 19737 1 + 45765 A +s Anc1.Anc1refChr2 86830 1 - 144309 A +s Anc2.Anc2refChr7 6038 1 - 32194 A +s mr.mrrefChr0 52153 1 - 130230 A +s mr.mrrefChr3 14631 1 + 181027 A +s simCow_chr6.simCow.chr6 518246 1 - 602619 A +s simDog_chr6.simDog.chr6 408310 1 - 593897 A +s simHuman_chr6.simHuman.chr6 523900 1 - 601863 A +s simMouse_chr6.simMouse.chr6 553738 1 - 636262 A +s simRat_chr6.simRat.chr6 572470 1 - 647215 A +s simRat_chr6.simRat.chr6 468306 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 458916 2 + 636262 TT +s Anc0.Anc0refChr4 19741 2 + 45765 TT +s Anc1.Anc1refChr2 86834 2 - 144309 TT +s Anc2.Anc2refChr7 6042 2 - 32194 TT +s mr.mrrefChr0 52157 2 - 130230 TA +s mr.mrrefChr3 14632 2 + 181027 TT +s simCow_chr6.simCow.chr6 518250 2 - 602619 TT +s simDog_chr6.simDog.chr6 408314 2 - 593897 TT +s simHuman_chr6.simHuman.chr6 523904 2 - 601863 TT +s simMouse_chr6.simMouse.chr6 553742 2 - 636262 TA +s simRat_chr6.simRat.chr6 572474 2 - 647215 TA +s simRat_chr6.simRat.chr6 468307 2 + 647215 TT + +a +s simMouse_chr6.simMouse.chr6 458918 1 + 636262 G +s Anc0.Anc0refChr4 19743 1 + 45765 G +s Anc1.Anc1refChr2 86836 1 - 144309 G +s Anc2.Anc2refChr7 6044 1 - 32194 G +s mr.mrrefChr0 52159 1 - 130230 G +s mr.mrrefChr3 14634 1 + 181027 G +s simCow_chr6.simCow.chr6 518252 1 - 602619 G +s simDog_chr6.simDog.chr6 408316 1 - 593897 G +s simHuman_chr6.simHuman.chr6 523906 1 - 601863 G +s simMouse_chr6.simMouse.chr6 553744 1 - 636262 G +s simRat_chr6.simRat.chr6 468309 1 + 647215 G + +a +s simMouse_chr6.simMouse.chr6 458919 37 + 636262 GTACTCAAGTAACTTTGATTAATGTTCCCATTATTAT +s Anc0.Anc0refChr4 19744 36 + 45765 GCACTCAAACCGCTTTG-TTAATATTCTCAATGTTAC +s Anc1.Anc1refChr2 86837 37 - 144309 GCACTCAAACCGCTTTGATTAATATTCTCAATGTTAC +s Anc2.Anc2refChr7 6045 36 - 32194 ACACTTAAACCGCTTTG-TTAATATTCTCAATGTTAC +s mr.mrrefChr0 52160 37 - 130230 GTACCCAAGTAGCTTTGATTAATGTTCCCATTATTAT +s mr.mrrefChr3 14635 37 + 181027 GTACTCAAGTAACTTTGATTAATGTTCCCATTATTAT +s simCow_chr6.simCow.chr6 518253 36 - 602619 ACACTTAAACTGCTTTA-TTAAGATTCTCAATCCTAC +s simDog_chr6.simDog.chr6 408317 36 - 593897 ACACTTAAGTCCCTTTG-TTAGTATTCTCAATGTCAC +s simHuman_chr6.simHuman.chr6 523907 32 - 601863 GCATTCTAACCGC-----TTAACATTCTCAATGTTAC +s simMouse_chr6.simMouse.chr6 553745 35 - 636262 GTACCCAAGTAGCTTTGATT--TGTTCCTATTATTAT +s simRat_chr6.simRat.chr6 572476 37 - 647215 GTACCCAAGTAGCTTTGATTAATGTTCCCATCATTAT +s simRat_chr6.simRat.chr6 468310 37 + 647215 GTACTCAAGTAGCTTTGATTAATGTTCCCATCATTCT + +a +s simMouse_chr6.simMouse.chr6 458956 2 + 636262 AT +s Anc0.Anc0refChr4 19780 2 + 45765 AT +s Anc1.Anc1refChr2 86874 2 - 144309 AT +s Anc2.Anc2refChr7 6081 2 - 32194 AT +s mr.mrrefChr0 52197 2 - 130230 AT +s mr.mrrefChr3 14672 2 + 181027 AT +s simCow_chr6.simCow.chr6 518289 2 - 602619 AC +s simDog_chr6.simDog.chr6 408353 2 - 593897 AT +s simHuman_chr6.simHuman.chr6 523940 2 - 601863 AT +s simMouse_chr6.simMouse.chr6 553780 2 - 636262 AT +s simRat_chr6.simRat.chr6 572513 2 - 647215 AT +s simRat_chr6.simRat.chr6 468347 2 + 647215 AT a s simMouse_chr6.simMouse.chr6 458958 3 + 636262 TGA @@ -175526,6 +185365,20 @@ s simRat_chr6.simRat.chr6 468349 3 + 647215 TCA a +s simMouse_chr6.simMouse.chr6 458961 5 + 636262 GCTGG +s Anc0.Anc0refChr4 19785 5 + 45765 GCTGA +s Anc1.Anc1refChr2 86879 5 - 144309 GCTGA +s Anc2.Anc2refChr7 6086 5 - 32194 GCTGA +s mr.mrrefChr0 52199 5 - 130230 GCTGG +s mr.mrrefChr3 14677 5 + 181027 GCTGG +s simCow_chr6.simCow.chr6 518294 4 - 602619 -CTGA +s simDog_chr6.simDog.chr6 408358 5 - 593897 GCTGA +s simHuman_chr6.simHuman.chr6 523945 5 - 601863 GCTGA +s simMouse_chr6.simMouse.chr6 553782 5 - 636262 GCTGG +s simRat_chr6.simRat.chr6 572515 5 - 647215 GCTGG +s simRat_chr6.simRat.chr6 468352 5 + 647215 GCTGG + +a s simMouse_chr6.simMouse.chr6 458966 1 + 636262 T s Anc0.Anc0refChr4 19790 1 + 45765 T s Anc1.Anc1refChr2 86884 1 - 144309 T @@ -175537,6 +185390,132 @@ s simRat_chr6.simRat.chr6 468357 1 + 647215 T a +s simMouse_chr6.simMouse.chr6 458967 26 + 636262 ATGATCAGGCTAAGCAATGATATGTG +s Anc0.Anc0refChr4 19791 26 + 45765 ATACCCAGGCTAAGGAAACATACATG +s Anc1.Anc1refChr2 86885 26 - 144309 ATACCCAGGCTAAGGAAACATACATG +s Anc2.Anc2refChr7 6092 26 - 32194 ACACCCAGGCCAAGGAAACATACATC +s mr.mrrefChr0 52204 26 - 130230 ATACTCAGGTTAAGGAAAGATATGTG +s mr.mrrefChr3 14683 26 + 181027 ATGATCAGGCTAAGCAATGATATGTG +s simCow_chr6.simCow.chr6 518299 26 - 602619 TCACCCAGGCCAAGGAAACATACATA +s simDog_chr6.simDog.chr6 408364 26 - 593897 ACACCCAGAGCCAGGAAACATGCATC +s simHuman_chr6.simHuman.chr6 523951 26 - 601863 AAACCCAGGCTAAAGAAGCATACATG +s simMouse_chr6.simMouse.chr6 553787 26 - 636262 ATACTCAGGTTAAGGAAAGATAAGTG +s simRat_chr6.simRat.chr6 572520 26 - 647215 ATACTCAGGTTAAGGAAAGATATGTG +s simRat_chr6.simRat.chr6 468358 26 + 647215 ATGCTTAGGTTATGGAAAGATATGTG + +a +s simMouse_chr6.simMouse.chr6 458993 8 + 636262 AGATGGCC +s Anc0.Anc0refChr4 19821 8 + 45765 GTGTGGTT +s Anc1.Anc1refChr2 86915 8 - 144309 GTGTGGTT +s Anc2.Anc2refChr7 6122 8 - 32194 GTGTGGTT +s mr.mrrefChr0 52230 8 - 130230 GCATGGTT +s mr.mrrefChr3 14709 8 + 181027 AGATGGCC +s simCow_chr6.simCow.chr6 518329 8 - 602619 GTATGGTT +s simDog_chr6.simDog.chr6 408394 8 - 593897 ATGTGGTT +s simHuman_chr6.simHuman.chr6 523981 8 - 601863 GTGTGGTT +s simMouse_chr6.simMouse.chr6 553813 8 - 636262 GCATGGTT +s simRat_chr6.simRat.chr6 572546 8 - 647215 GCACGGTC +s simRat_chr6.simRat.chr6 468384 8 + 647215 ACATGGTT + +a +s simMouse_chr6.simMouse.chr6 459001 6 + 636262 AAAGTA +s Anc0.Anc0refChr4 19831 6 + 45765 ATAGTA +s Anc1.Anc1refChr2 86925 6 - 144309 ATAGTA +s Anc2.Anc2refChr7 6132 6 - 32194 ATAGTA +s mr.mrrefChr0 52240 6 - 130230 AAAGTA +s mr.mrrefChr3 14717 6 + 181027 AAAGTA +s simCow_chr6.simCow.chr6 518339 6 - 602619 ATAGTA +s simDog_chr6.simDog.chr6 408405 6 - 593897 ATAGTA +s simHuman_chr6.simHuman.chr6 523991 6 - 601863 ATAGTA +s simMouse_chr6.simMouse.chr6 553823 6 - 636262 AAAGGA +s simRat_chr6.simRat.chr6 572556 6 - 647215 AAAGTA +s simRat_chr6.simRat.chr6 468392 6 + 647215 AAAGTA + +a +s simMouse_chr6.simMouse.chr6 459007 13 + 636262 ATATGCACTTTGC +s Anc0.Anc0refChr4 19838 13 + 45765 ATGCACACTTTGC +s Anc1.Anc1refChr2 86932 13 - 144309 ATGCACACTTTGC +s Anc2.Anc2refChr7 6139 13 - 32194 ATGCACATTTTGC +s mr.mrrefChr0 52246 13 - 130230 ATATGTGCTTTGC +s mr.mrrefChr3 14723 13 + 181027 ATATGCACTTTGC +s simCow_chr6.simCow.chr6 518345 12 - 602619 AGGCACAATTTG- +s simDog_chr6.simDog.chr6 408412 13 - 593897 ATAAACATTTTGC +s simHuman_chr6.simHuman.chr6 523998 13 - 601863 ATGCACAGTGTGC +s simMouse_chr6.simMouse.chr6 553829 13 - 636262 ATATGTGCTTTGC +s simRat_chr6.simRat.chr6 572562 13 - 647215 ATATGTGCTCTGC +s simRat_chr6.simRat.chr6 468398 13 + 647215 ATATGTGCTTTGC + +a +s simMouse_chr6.simMouse.chr6 459020 1 + 636262 T +s Anc0.Anc0refChr4 19851 1 + 45765 C +s Anc1.Anc1refChr2 86945 1 - 144309 C +s Anc2.Anc2refChr7 6152 1 - 32194 C +s mr.mrrefChr0 52259 1 - 130230 C +s mr.mrrefChr3 14736 1 + 181027 T +s simCow_chr6.simCow.chr6 518357 1 - 602619 C +s simDog_chr6.simDog.chr6 408426 1 - 593897 C +s simHuman_chr6.simHuman.chr6 524011 1 - 601863 T +s simMouse_chr6.simMouse.chr6 553842 1 - 636262 C +s simRat_chr6.simRat.chr6 572575 1 - 647215 T +s simRat_chr6.simRat.chr6 468411 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 459021 35 + 636262 CCAGGTGTCTATTTTTGGAACTGAACCTGATGGCA +s Anc0.Anc0refChr4 19852 35 + 45765 CTAGATGTCTATTGATGGATCTGAATCCGATGGCA +s Anc1.Anc1refChr2 86946 35 - 144309 CTAGATGTCTATTGATGGATCTGAATCCGATGGCA +s Anc2.Anc2refChr7 6154 35 - 32194 CTTGATATGTATTGATGGGTCTGGATCCAATGGAA +s mr.mrrefChr0 52260 35 - 130230 CTAGATGTCTATTTATGGATCTGAATGCGATGGCA +s mr.mrrefChr3 14737 35 + 181027 CCAGGTGTCTATTTTTGGAACTGAACCTGATGGCA +s simCow_chr6.simCow.chr6 518359 35 - 602619 CTTGATGTCTATTTATGGGCCTGGATCCAGTGGAA +s simDog_chr6.simDog.chr6 408428 35 - 593897 CTTGATATGCATTGATGGGTCTGGATACAATGGAG +s simHuman_chr6.simHuman.chr6 524012 26 - 601863 ---------TATTGATGGATCTGAATCAGATGGGA +s simMouse_chr6.simMouse.chr6 553843 35 - 636262 CTAGATGTCTACTTATGGATCTGAATGCGATGGCA +s simRat_chr6.simRat.chr6 572576 35 - 647215 CTAGATGTCTATTTATGGATCTGAATTTGATGGCA +s simRat_chr6.simRat.chr6 468412 35 + 647215 CTAGAGATCTATTTTTAGATCTGAATGTGATGGCA + +a +s simMouse_chr6.simMouse.chr6 459056 1 + 636262 G +s Anc0.Anc0refChr4 19887 1 + 45765 G +s Anc1.Anc1refChr2 86981 1 - 144309 G +s Anc2.Anc2refChr7 6189 1 - 32194 G +s mr.mrrefChr0 52295 1 - 130230 G +s mr.mrrefChr3 14772 1 + 181027 G +s simCow_chr6.simCow.chr6 518394 1 - 602619 G +s simDog_chr6.simDog.chr6 408463 1 - 593897 A +s simHuman_chr6.simHuman.chr6 524038 1 - 601863 G +s simMouse_chr6.simMouse.chr6 553878 1 - 636262 G +s simRat_chr6.simRat.chr6 468447 1 + 647215 G + +a +s simMouse_chr6.simMouse.chr6 459057 3 + 636262 CAT +s Anc0.Anc0refChr4 19888 3 + 45765 TAC +s Anc1.Anc1refChr2 86982 3 - 144309 TAC +s Anc2.Anc2refChr7 6190 3 - 32194 TAC +s mr.mrrefChr0 52296 3 - 130230 TAT +s mr.mrrefChr3 14773 3 + 181027 CAT +s simCow_chr6.simCow.chr6 518395 2 - 602619 TA- +s simDog_chr6.simDog.chr6 408464 3 - 593897 TAC +s simHuman_chr6.simHuman.chr6 524039 3 - 601863 CAC +s simMouse_chr6.simMouse.chr6 553879 3 - 636262 TGT +s simRat_chr6.simRat.chr6 572611 3 - 647215 CAT +s simRat_chr6.simRat.chr6 468448 3 + 647215 CAT + +a +s simMouse_chr6.simMouse.chr6 459060 3 + 636262 TTG +s Anc0.Anc0refChr4 19891 3 + 45765 TTG +s Anc1.Anc1refChr2 86985 3 - 144309 TTG +s Anc2.Anc2refChr7 6193 3 - 32194 TTC +s mr.mrrefChr0 52299 3 - 130230 TTG +s mr.mrrefChr3 14776 3 + 181027 TTG +s simCow_chr6.simCow.chr6 518397 3 - 602619 TCT +s simDog_chr6.simDog.chr6 408467 3 - 593897 TTC +s simHuman_chr6.simHuman.chr6 524042 3 - 601863 TTT +s simMouse_chr6.simMouse.chr6 553882 3 - 636262 TTG +s simMouse_chr6.simMouse.chr6 459188 3 + 636262 TTG +s simRat_chr6.simRat.chr6 572614 3 - 647215 TTG +s simRat_chr6.simRat.chr6 468451 3 + 647215 TTG + +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 @@ -175615,15 +185594,109 @@ 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 +s simMouse_chr6.simMouse.chr6 459188 3 + 636262 TTG +s Anc0.Anc0refChr4 19891 3 + 45765 TTG +s Anc1.Anc1refChr2 86985 3 - 144309 TTG +s Anc2.Anc2refChr7 6193 3 - 32194 TTC +s mr.mrrefChr0 52299 3 - 130230 TTG +s mr.mrrefChr3 14776 3 + 181027 TTG +s simCow_chr6.simCow.chr6 518397 3 - 602619 TCT +s simDog_chr6.simDog.chr6 408467 3 - 593897 TTC +s simHuman_chr6.simHuman.chr6 524042 3 - 601863 TTT +s simMouse_chr6.simMouse.chr6 553882 3 - 636262 TTG +s simMouse_chr6.simMouse.chr6 459060 3 + 636262 TTG +s simRat_chr6.simRat.chr6 572614 3 - 647215 TTG +s simRat_chr6.simRat.chr6 468451 3 + 647215 TTG + +a +s simMouse_chr6.simMouse.chr6 459191 47 + 636262 ATATGCGTCCACTTTAAGGTTGTGTCTTATCTAGGAGTCAAATTTGT +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 459063 47 + 636262 ATATAGGGTCACTTTAAGGTTGTGTTTTATCTAGGAGTCAAATTTGT +s simRat_chr6.simRat.chr6 468454 45 + 647215 GTATAGGGTCACTTTAAGGTTGT--CTAATCTAGGAGTCAAATTTGT + +a +s simMouse_chr6.simMouse.chr6 459238 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 459110 12 + 636262 CGACTTGTAAGT +s simRat_chr6.simRat.chr6 468499 12 + 647215 CGATTTGTAAGT + +a +s simMouse_chr6.simMouse.chr6 459250 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 459122 1 + 636262 T +s simRat_chr6.simRat.chr6 468511 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 459251 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 459123 9 + 636262 GTACAGATG +s simRat_chr6.simRat.chr6 468536 9 + 647215 GTATAAATG + +a +s simMouse_chr6.simMouse.chr6 459260 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 459132 1 + 636262 C +s simRat_chr6.simRat.chr6 468545 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 459261 16 + 636262 TATTGGCGCTGCCCAA +s Anc0.Anc0refChr3 80731 12 + 222631 TGTTGGTCTTGT---- +s Anc1.Anc1refChr6 112956 12 + 197743 TGTTGGTCTTGT---- +s Anc2.Anc2refChr13 87225 12 + 96486 TGTTGGTCTTGT---- +s mr.mrrefChr3 14849 16 + 181027 TATTGGTGCTGCCCAA +s simCow_chr6.simCow.chr6 443541 12 + 602619 TGTTTGTCTTGT---- +s simDog_chr6.simDog.chr6 435498 12 + 593897 TGTTGGTCTTGT---- +s simMouse_chr6.simMouse.chr6 459133 16 + 636262 TATTGGTGCTGTCCCA +s simRat_chr6.simRat.chr6 468546 15 + 647215 TATTGGTG-GACTCAA + +a +s simMouse_chr6.simMouse.chr6 459277 30 + 636262 CGCACAAGCTTGAGATCTCATTTTACAAGC +s Anc0.Anc0refChr3 80743 23 + 222631 -------GCATGGAATCATATATCTCAAGC +s Anc1.Anc1refChr6 112968 23 + 197743 -------GCATGGAATCATATATCTCAAGC +s Anc2.Anc2refChr13 87237 23 + 96486 -------GCATGGAATCATATATCTCAAGC +s mr.mrrefChr3 14865 30 + 181027 CGCACAAGCCTGAGATCACATTTTACAAGC +s simCow_chr6.simCow.chr6 443553 23 + 602619 -------GCATGAGCTCGTACATCTCAATC +s simDog_chr6.simDog.chr6 435510 23 + 593897 -------GCATGGAATCATATATCTCAAGC +s simMouse_chr6.simMouse.chr6 459154 30 + 636262 CACACAAGCCTGAGATCACATTTTGCAAGC +s simRat_chr6.simRat.chr6 468561 29 + 647215 TGC-CAAGCCTGAGTGCACATGTCTCAAGC + +a +s simMouse_chr6.simMouse.chr6 459307 61 + 636262 ATTACTCAGTACACCTTGATTTCTAAACTATGCAGCATCCAGACCATATCACCCAGCATGA +s Anc0.Anc0refChr3 80766 50 + 222631 CTTACTTGGTATGCCTTAATGGCTAAACTAT----A--CCATACCT-----CCCACCATGA +s Anc1.Anc1refChr6 112991 54 + 197743 CTTACTTGGTATGCCTTAATGGCTAAACTATCTAGA--CCATACCT-----CCCACCATGA +s Anc2.Anc2refChr13 87260 50 + 96486 CTTACTTGGTATGCCTTAATGGCTAAACTAT----A--CCATATCT-----CTCACCATGA +s mr.mrrefChr3 14895 56 + 181027 ATTACTCAGTACACCTTGATTTCTAAACTATGCAGCATCCAGACCA-----CCCAGCATGA +s simCow_chr6.simCow.chr6 443581 50 + 602619 TTTATTCGATATGCCTTGATAACTGAACTTG----A--CCGTGCCT-----CTCACTATGA +s simDog_chr6.simDog.chr6 435533 50 + 593897 CTTACTTGGTATGCCTTAATGGCTAAACTAT----A--CCATATCT-----CTCACCATGA +s simHuman_chr6.simHuman.chr6 443793 32 + 601863 ----------------------TGAAAATAACTAGA--CCATACCT-----CCCACCATGA +s simMouse_chr6.simMouse.chr6 459184 4 + 636262 ATGT--------------------------------------------------------- +s simRat_chr6.simRat.chr6 468590 56 + 647215 ATTACCCAATATATCTAGATATCTAAACTATGCAACATCCAGACTG-----CCCAGCATGA a s simMouse_chr6.simMouse.chr6 459368 16 + 636262 GATATAACATTTAGAG @@ -177333,11 +187406,120 @@ s simRat_chr6.simRat.chr6 472754 34 + 647215 GAATTCAAGAATAACTGGAGTAGCCTGCAATATG a +s simMouse_chr6.simMouse.chr6 463095 14 + 636262 AGCAACTGGGGAAT +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 18882 14 + 181027 AGCAACTGGGGAAT +s mr.mrrefChr3 18670 14 + 181027 TGAAACTGTTGAAT +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 462864 14 + 636262 TGAAACTGCTGAAT +s simRat_chr6.simRat.chr6 472539 14 + 647215 TGAAACTGTTGAAT +s simRat_chr6.simRat.chr6 472790 14 + 647215 AGCAGTTGAGGTAT + +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 463118 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 18905 5 + 181027 AAAGA +s mr.mrrefChr3 18684 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 462878 5 + 636262 AAAGA +s simRat_chr6.simRat.chr6 472553 5 + 647215 AAAGA +s simRat_chr6.simRat.chr6 472813 5 + 647215 TAAGA + +a +s simMouse_chr6.simMouse.chr6 463123 12 + 636262 CTCTAGATTGTG +s Anc0.Anc0refChr3 84370 12 + 222631 TTGTAGATACTG +s Anc1.Anc1refChr6 116692 12 + 197743 TTGTAGATACTG +s Anc2.Anc2refChr13 91787 12 + 96486 TTATAGATACTG +s mr.mrrefChr3 18910 12 + 181027 CTCTAGATTGTG +s mr.mrrefChr3 18758 12 + 181027 TTGTAGATAGGG +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 462952 12 + 636262 TTGTAGATAGGG +s simRat_chr6.simRat.chr6 472667 12 + 647215 TTGTAGGTAGGG +s simRat_chr6.simRat.chr6 472818 12 + 647215 CTCTAGCTTATG + +a +s simMouse_chr6.simMouse.chr6 463135 11 + 636262 TCCAGAAAGCA +s Anc0.Anc0refChr3 84383 11 + 222631 TCTGTAAAGCA +s Anc1.Anc1refChr6 116705 11 + 197743 TCTGTAAAGCA +s Anc2.Anc2refChr13 91800 11 + 96486 TCTGTAAAGCA +s mr.mrrefChr3 18922 11 + 181027 TCCAGAAAGCA +s mr.mrrefChr3 18771 11 + 181027 TGTGTAAACCA +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 462965 11 + 636262 TGTGTAAACCA +s simRat_chr6.simRat.chr6 472680 11 + 647215 TTTGTCATCCA +s simRat_chr6.simRat.chr6 472830 11 + 647215 TCCAGAAAGCA + +a +s simMouse_chr6.simMouse.chr6 463146 4 + 636262 TTAC +s Anc0.Anc0refChr3 84394 4 + 222631 TCAC +s Anc1.Anc1refChr6 116716 4 + 197743 TCAC +s Anc2.Anc2refChr13 91811 4 + 96486 CCAC +s mr.mrrefChr3 18933 4 + 181027 TTAC +s mr.mrrefChr3 18782 4 + 181027 TCAT +s simCow_chr6.simCow.chr6 448199 4 + 602619 CCAT +s simDog_chr6.simDog.chr6 440899 4 + 593897 CCAC +s simHuman_chr6.simHuman.chr6 448826 4 + 601863 TCAC +s simMouse_chr6.simMouse.chr6 462976 4 + 636262 TCAT +s simRat_chr6.simRat.chr6 472841 4 + 647215 TTAC + +a +s simMouse_chr6.simMouse.chr6 463150 6 + 636262 AAAATC +s Anc0.Anc0refChr3 84398 6 + 222631 ATAATT +s Anc1.Anc1refChr6 116720 6 + 197743 ATAATT +s Anc2.Anc2refChr13 91815 6 + 96486 ATAATT +s mr.mrrefChr3 18937 6 + 181027 AAAATC +s mr.mrrefChr3 18786 6 + 181027 AGAATT +s simCow_chr6.simCow.chr6 448203 6 + 602619 TTAATT +s simDog_chr6.simDog.chr6 440903 6 + 593897 ATAATT +s simHuman_chr6.simHuman.chr6 448830 6 + 601863 ATAACT +s simMouse_chr6.simMouse.chr6 462980 6 + 636262 AGAATT +s simRat_chr6.simRat.chr6 472691 6 + 647215 AGGATT +s simRat_chr6.simRat.chr6 472845 6 + 647215 AAAAAG + +a +s simMouse_chr6.simMouse.chr6 463156 2 + 636262 AA +s Anc0.Anc0refChr3 84410 1 + 222631 -A +s Anc1.Anc1refChr6 116732 2 + 197743 CA +s Anc2.Anc2refChr13 91827 1 + 96486 -A +s mr.mrrefChr3 18943 2 + 181027 AA +s mr.mrrefChr3 18800 2 + 181027 CA +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 462994 2 + 636262 CA +s simRat_chr6.simRat.chr6 472705 2 + 647215 CA +s simRat_chr6.simRat.chr6 472851 2 + 647215 AG + +a +s simMouse_chr6.simMouse.chr6 463158 12 + 636262 TGTGATGACACC +s Anc0.Anc0refChr3 84411 12 + 222631 TGTGATGATTCC +s Anc1.Anc1refChr6 116734 12 + 197743 TGTGATGATTCC +s Anc2.Anc2refChr13 91828 12 + 96486 TGTGATGATTCC +s mr.mrrefChr3 18945 12 + 181027 TGTGATGACCCC +s mr.mrrefChr3 18802 12 + 181027 TGTGGTGAATCC +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 462996 12 + 636262 TGTGGTGAATCC +s simRat_chr6.simRat.chr6 472708 12 + 647215 TATGGTGAATCC +s simRat_chr6.simRat.chr6 472853 12 + 647215 TGCGATGACCCC + +a s simMouse_chr6.simMouse.chr6 463170 6 + 636262 ATAAGG s Anc0.Anc0refChr3 84423 6 + 222631 ATAAAG s Anc1.Anc1refChr6 116746 6 + 197743 ATAAAG @@ -177349,6 +187531,48 @@ s simRat_chr6.simRat.chr6 472865 6 + 647215 ATAAGC a +s simMouse_chr6.simMouse.chr6 463176 8 + 636262 AAAAGGTC +s Anc0.Anc0refChr3 84429 8 + 222631 AAAAAAAG +s Anc1.Anc1refChr6 116752 8 + 197743 AAAAAAAG +s Anc2.Anc2refChr13 91846 8 + 96486 AAAAAAAG +s mr.mrrefChr3 18963 8 + 181027 AAAAGGTG +s mr.mrrefChr3 18814 8 + 181027 TGAAATAG +s simCow_chr6.simCow.chr6 448239 8 + 602619 AAAAAGAG +s simDog_chr6.simDog.chr6 441001 8 + 593897 AATAGATG +s simHuman_chr6.simHuman.chr6 448861 8 + 601863 ATAGAAAG +s simMouse_chr6.simMouse.chr6 463008 8 + 636262 TGAAATAG +s simRat_chr6.simRat.chr6 472720 8 + 647215 TAAAATAG +s simRat_chr6.simRat.chr6 472871 8 + 647215 AAAAGGTG + +a +s simMouse_chr6.simMouse.chr6 463184 1 + 636262 C +s Anc0.Anc0refChr3 84437 1 + 222631 T +s Anc1.Anc1refChr6 116760 1 + 197743 T +s Anc2.Anc2refChr13 91854 1 + 96486 T +s mr.mrrefChr3 18971 1 + 181027 C +s mr.mrrefChr3 18822 1 + 181027 T +s simCow_chr6.simCow.chr6 448247 1 + 602619 T +s simDog_chr6.simDog.chr6 441009 1 + 593897 T +s simHuman_chr6.simHuman.chr6 448869 1 + 601863 T +s simMouse_chr6.simMouse.chr6 463022 1 + 636262 T +s simRat_chr6.simRat.chr6 472728 1 + 647215 T +s simRat_chr6.simRat.chr6 472879 1 + 647215 C + +a +s simMouse_chr6.simMouse.chr6 463185 4 + 636262 TCTG +s Anc0.Anc0refChr3 84441 4 + 222631 TCTG +s Anc1.Anc1refChr6 116764 4 + 197743 TCTG +s Anc2.Anc2refChr13 91858 4 + 96486 TCTG +s mr.mrrefChr3 18975 4 + 181027 TCTG +s mr.mrrefChr3 18826 4 + 181027 TCTT +s simCow_chr6.simCow.chr6 448251 4 + 602619 TATT +s simDog_chr6.simDog.chr6 441013 4 + 593897 TCTG +s simHuman_chr6.simHuman.chr6 448873 4 + 601863 TCTG +s simMouse_chr6.simMouse.chr6 463026 4 + 636262 TCTT +s simRat_chr6.simRat.chr6 472732 4 + 647215 TCCT +s simRat_chr6.simRat.chr6 472883 4 + 647215 TCTG + +a s simMouse_chr6.simMouse.chr6 463189 3 + 636262 TTA s Anc0.Anc0refChr3 84445 3 + 222631 TTA s Anc1.Anc1refChr6 116768 3 + 197743 TTA @@ -177371,6 +187595,62 @@ s simRat_chr6.simRat.chr6 472890 8 + 647215 GAACAGCT a +s simMouse_chr6.simMouse.chr6 463200 1 + 636262 G +s Anc0.Anc0refChr3 84462 1 + 222631 G +s Anc1.Anc1refChr6 116785 1 + 197743 G +s Anc2.Anc2refChr13 91879 1 + 96486 G +s mr.mrrefChr3 18990 1 + 181027 G +s mr.mrrefChr3 18830 1 + 181027 A +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 463038 1 + 636262 A +s simRat_chr6.simRat.chr6 472736 1 + 647215 A +s simRat_chr6.simRat.chr6 472898 1 + 647215 G + +a +s simMouse_chr6.simMouse.chr6 463201 8 + 636262 CTAGGCGG +s Anc0.Anc0refChr3 84464 8 + 222631 CTAGGCAG +s Anc1.Anc1refChr6 116787 8 + 197743 CTAGGCAG +s Anc2.Anc2refChr13 91881 8 + 96486 CTTGGTAG +s mr.mrrefChr3 18991 8 + 181027 CTAGGCGG +s mr.mrrefChr3 18831 8 + 181027 CTAGACTG +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 463039 8 + 636262 CTAGACTG +s simRat_chr6.simRat.chr6 472737 8 + 647215 AAAGACTA +s simRat_chr6.simRat.chr6 472899 8 + 647215 CTAGGCGG + +a +s simMouse_chr6.simMouse.chr6 463209 1 + 636262 C +s Anc0.Anc0refChr3 84472 1 + 222631 C +s Anc1.Anc1refChr6 116795 1 + 197743 C +s Anc2.Anc2refChr13 91889 1 + 96486 C +s mr.mrrefChr3 18999 1 + 181027 C +s mr.mrrefChr3 18841 1 + 181027 C +s simCow_chr6.simCow.chr6 448278 1 + 602619 C +s simDog_chr6.simDog.chr6 441044 1 + 593897 C +s simHuman_chr6.simHuman.chr6 448904 1 + 601863 C +s simMouse_chr6.simMouse.chr6 463049 1 + 636262 C +s simRat_chr6.simRat.chr6 472747 1 + 647215 C +s simRat_chr6.simRat.chr6 472907 1 + 647215 C + +a +s simMouse_chr6.simMouse.chr6 463210 34 + 636262 GAGTCCAGCAATGACCTGAGTAACTTACACGATG +s Anc0.Anc0refChr3 84477 34 + 222631 GAATTCAACAATGACCTGAGTAACTTATACAATG +s Anc1.Anc1refChr6 116800 34 + 197743 GAATTCAACAATGACCTGAGTAACTTATACAATG +s Anc2.Anc2refChr13 91894 34 + 96486 GAATTCAACAATGACCTGAGTAACTTATACAATG +s mr.mrrefChr3 19004 34 + 181027 GAGTCCAGCAATGACCTGAGTAACTTACACGATG +s mr.mrrefChr3 18848 34 + 181027 GAACTCAACAATAACTGGAGTACCTTAGGTAATG +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 463061 34 + 636262 GAACTCAACAATAACTGGAGTACCTTAGGTAATG +s simRat_chr6.simRat.chr6 472754 34 + 647215 GAATTCAAGAATAACTGGAGTAGCCTGCAATATG +s simRat_chr6.simRat.chr6 472912 34 + 647215 GGGTCCAGAAATGGCCTGAGCAACTTACATGATG + +a s simMouse_chr6.simMouse.chr6 463244 8 + 636262 ATTTGAGT s Anc0.Anc0refChr3 84511 8 + 222631 ACCTGAGT s Anc1.Anc1refChr6 116834 8 + 197743 ACCTGAGT @@ -179799,7 +190079,173 @@ s simRat_chr6.simRat.chr6 478782 1 + 647215 G a -s simMouse_chr6.simMouse.chr6 468845 1 + 636262 G +s simMouse_chr6.simMouse.chr6 468843 3 + 636262 GGG +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 242718 2 + 636262 GA- +s simMouse_chr6.simMouse.chr6 697 2 - 636262 GA- +s simRat_chr6.simRat.chr6 352588 2 + 647215 GG- +s simRat_chr6.simRat.chr6 66883 2 - 647215 GG- +s simRat_chr6.simRat.chr6 478783 2 + 647215 GG- + +a +s simMouse_chr6.simMouse.chr6 468846 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 242720 4 + 636262 CTTC +s simMouse_chr6.simMouse.chr6 699 4 - 636262 CTTC +s simRat_chr6.simRat.chr6 352590 4 + 647215 CTTC +s simRat_chr6.simRat.chr6 478785 4 + 647215 CTTC + +a +s simMouse_chr6.simMouse.chr6 468850 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 609224 1 + 636262 G +s simMouse_chr6.simMouse.chr6 242724 1 + 636262 A +s simMouse_chr6.simMouse.chr6 703 1 - 636262 G +s simRat_chr6.simRat.chr6 83776 1 - 647215 G +s simRat_chr6.simRat.chr6 352594 1 + 647215 T +s simRat_chr6.simRat.chr6 478789 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 468851 17 + 636262 AAGTTGCAAACAGAGCA +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 609225 17 + 636262 AAGCCGCAAACAAAGCA +s simMouse_chr6.simMouse.chr6 242725 17 + 636262 AATTCACAAACAAAGCG +s simMouse_chr6.simMouse.chr6 704 17 - 636262 AAGTCGTGAACAAAGCG +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 +s simRat_chr6.simRat.chr6 478790 17 + 647215 AAGTTGCAAGCAAAGTA + +a +s simMouse_chr6.simMouse.chr6 468868 4 + 636262 TACG +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 609242 4 + 636262 TACG +s simMouse_chr6.simMouse.chr6 242742 4 + 636262 TACA +s simMouse_chr6.simMouse.chr6 721 4 - 636262 TACG +s simRat_chr6.simRat.chr6 83794 4 - 647215 TACA +s simRat_chr6.simRat.chr6 66902 4 - 647215 TATG +s simRat_chr6.simRat.chr6 478807 4 + 647215 TACA + +a +s simMouse_chr6.simMouse.chr6 468872 61 + 636262 CAAGTCAATTGCATACCGGAGCCCTCAAATGGCAATTAGTCCCAAGCCAACAATGATTGTG +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 609246 61 + 636262 CAAGGCAATTGCATACTAGAGCACTCAAATGGCAAATAGTCTTGAGTTAATAATGACTGTG +s simMouse_chr6.simMouse.chr6 242746 61 + 636262 CGAGGCAGTCGTATACAAGAGTGTTCAGTTAGCAAATCGTCTCGAGCGAGTCATGACCGTG +s simMouse_chr6.simMouse.chr6 725 61 - 636262 CAAGGCGGTCGCATACCAGAGCGCTCAGTTAGCAAATCGTCTTGAGCGAATCATGACCGTG +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 +s simRat_chr6.simRat.chr6 478811 61 + 647215 CAAAGCAATTGCATACTGGAGCACTCAAATGGCAGATAGCCCCAAGCCAATAATGACTGTG + +a +s simMouse_chr6.simMouse.chr6 468933 13 + 636262 GGCCCACACGTTA +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 609307 13 + 636262 GGCCCACACATTA +s simMouse_chr6.simMouse.chr6 242807 13 + 636262 GGCCCAGACAGTA +s simMouse_chr6.simMouse.chr6 786 13 - 636262 GGCCCAGACAGTA +s simRat_chr6.simRat.chr6 83859 13 - 647215 GGCCCACACATTA +s simRat_chr6.simRat.chr6 66967 13 - 647215 GGGCCACACAATT +s simRat_chr6.simRat.chr6 478872 13 + 647215 GGCCCACCCGTTA + +a +s simMouse_chr6.simMouse.chr6 468946 2 + 636262 TG +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 242820 2 + 636262 TA +s simMouse_chr6.simMouse.chr6 799 2 - 636262 CG +s simRat_chr6.simRat.chr6 66980 2 - 647215 CG +s simRat_chr6.simRat.chr6 478885 2 + 647215 TG + +a +s simMouse_chr6.simMouse.chr6 468948 4 + 636262 TTGT +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 609320 4 + 636262 ATGT +s simMouse_chr6.simMouse.chr6 242822 4 + 636262 ATGT +s simMouse_chr6.simMouse.chr6 801 4 - 636262 ATGT +s simRat_chr6.simRat.chr6 83874 4 - 647215 ATTT +s simRat_chr6.simRat.chr6 66982 4 - 647215 ATGT +s simRat_chr6.simRat.chr6 478887 4 + 647215 ATGT + +a +s simMouse_chr6.simMouse.chr6 468952 12 + 636262 AGAATTCATTGG +s Anc1.Anc1refChr6 122046 12 + 197743 AGCACTCACTGG +s mr.mrrefChr3 24659 12 + 181027 AGAATTCATTGG +s mr.mrrefChr3 157248 12 + 181027 AGCACTCACTGG +s mr.mrrefChr5 95921 12 + 294540 AGCACTCACTGG +s simMouse_chr6.simMouse.chr6 609324 12 + 636262 AGCACTCACTGG +s simMouse_chr6.simMouse.chr6 242826 12 + 636262 AGCACTCACTGG +s simMouse_chr6.simMouse.chr6 805 12 - 636262 AGCACTCACTGG +s simRat_chr6.simRat.chr6 83878 12 - 647215 AGGACTCACTGG +s simRat_chr6.simRat.chr6 67036 12 - 647215 AGCACTCATTAG +s simRat_chr6.simRat.chr6 478891 12 + 647215 AGCACTGACTGG + +a +s simMouse_chr6.simMouse.chr6 468964 3 + 636262 TTA +s Anc1.Anc1refChr6 122058 3 + 197743 TTA +s mr.mrrefChr3 24671 3 + 181027 TTA +s mr.mrrefChr3 157260 3 + 181027 TTA +s mr.mrrefChr5 95933 3 + 294540 TTA +s simMouse_chr6.simMouse.chr6 609336 3 + 636262 TTA +s simMouse_chr6.simMouse.chr6 242838 3 + 636262 TTA +s simMouse_chr6.simMouse.chr6 817 3 - 636262 TTA +s simRat_chr6.simRat.chr6 83890 3 - 647215 TTA +s simRat_chr6.simRat.chr6 478903 3 + 647215 TTA + +a +s simMouse_chr6.simMouse.chr6 468967 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 242841 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 468968 3 + 636262 AAC +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 609339 3 + 636262 TAA +s simMouse_chr6.simMouse.chr6 242842 3 + 636262 TAA +s simMouse_chr6.simMouse.chr6 821 3 - 636262 AAC +s simRat_chr6.simRat.chr6 83893 3 - 647215 TAG +s simRat_chr6.simRat.chr6 478907 3 + 647215 AAC + +a +s simMouse_chr6.simMouse.chr6 468971 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 609343 5 + 636262 CACTC +s simMouse_chr6.simMouse.chr6 242845 5 + 636262 GACTT +s simMouse_chr6.simMouse.chr6 824 5 - 636262 GACTT +s simRat_chr6.simRat.chr6 83896 5 - 647215 TGCTC +s simRat_chr6.simRat.chr6 478910 5 + 647215 GACTT a s simMouse_chr6.simMouse.chr6 468976 20 + 636262 GAGTACCCAGACCTGACTTA @@ -179807,20 +190253,99 @@ 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 +s simMouse_chr6.simMouse.chr6 468996 7 + 636262 TCACACC +s Anc1.Anc1refChr6 122070 7 + 197743 TCATACC +s mr.mrrefChr3 24695 7 + 181027 TCACACC +s mr.mrrefChr3 157271 7 + 181027 ACATACC +s mr.mrrefChr5 95945 7 + 294540 TCGTGCC +s simMouse_chr6.simMouse.chr6 609348 7 + 636262 ACATACC +s simMouse_chr6.simMouse.chr6 242850 7 + 636262 TCGTGCC +s simMouse_chr6.simMouse.chr6 829 7 - 636262 TCGTGCC +s simRat_chr6.simRat.chr6 83901 7 - 647215 ACATACC +s simRat_chr6.simRat.chr6 478927 7 + 647215 TCACACT + +a +s simMouse_chr6.simMouse.chr6 469003 5 + 636262 CCATG +s Anc1.Anc1refChr6 122077 4 + 197743 CA-TG +s mr.mrrefChr3 24702 4 + 181027 CC-TG +s mr.mrrefChr3 157278 4 + 181027 CA-GA +s mr.mrrefChr5 95952 4 + 294540 CA-TG +s simMouse_chr6.simMouse.chr6 609355 4 + 636262 CA-GA +s simMouse_chr6.simMouse.chr6 242877 4 + 636262 CA-TG +s simMouse_chr6.simMouse.chr6 836 4 - 636262 CA-CT +s simRat_chr6.simRat.chr6 83908 4 - 647215 GG-GA +s simRat_chr6.simRat.chr6 478934 4 + 647215 AT-TG + +a +s simMouse_chr6.simMouse.chr6 469008 12 + 636262 ATTACCAATGAA +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 609374 12 + 636262 GTTACCAACGAA +s simMouse_chr6.simMouse.chr6 242881 12 + 636262 GTTACCAACGAA +s simMouse_chr6.simMouse.chr6 840 12 - 636262 ATTTGCAAAGAA +s simRat_chr6.simRat.chr6 83932 12 - 647215 GTTACCAACAAA +s simRat_chr6.simRat.chr6 478938 12 + 647215 GTTACCAACAAA + +a +s simMouse_chr6.simMouse.chr6 469020 8 + 636262 TGTGGATT +s Anc1.Anc1refChr6 122094 8 + 197743 TGTGGATT +s mr.mrrefChr3 24719 8 + 181027 TGTGGATT +s mr.mrrefChr3 157310 8 + 181027 TGCGGATT +s mr.mrrefChr5 95969 8 + 294540 TTTATATT +s simMouse_chr6.simMouse.chr6 609387 8 + 636262 TGCGGATT +s simMouse_chr6.simMouse.chr6 242894 8 + 636262 TTTGTATT +s simMouse_chr6.simMouse.chr6 853 8 - 636262 TTTAGATT +s simRat_chr6.simRat.chr6 83945 8 - 647215 TGCAGATT +s simRat_chr6.simRat.chr6 478951 6 + 647215 TGTGGA-- + +a +s simMouse_chr6.simMouse.chr6 469028 9 + 636262 TACTGATCA +s Anc1.Anc1refChr6 122102 8 + 197743 TACCCA-CA +s mr.mrrefChr3 24727 9 + 181027 TACTGATCA +s mr.mrrefChr3 157318 8 + 181027 TACCCA-TC +s mr.mrrefChr5 95977 8 + 294540 TCCCCA-CA +s simMouse_chr6.simMouse.chr6 609395 8 + 636262 TACCCA-TC +s simMouse_chr6.simMouse.chr6 242902 8 + 636262 TCCCCA-CA +s simMouse_chr6.simMouse.chr6 958 8 - 636262 TCTCCA-AT +s simRat_chr6.simRat.chr6 83953 8 - 647215 TACCCA-TC + +a +s simMouse_chr6.simMouse.chr6 469037 11 + 636262 CTATACAGCAC +s Anc1.Anc1refChr6 122110 11 + 197743 CAATGCAGCAC +s mr.mrrefChr3 24736 11 + 181027 CTATACAGCAC +s mr.mrrefChr3 157326 11 + 181027 CATTGCAGCAC +s mr.mrrefChr5 95985 11 + 294540 CAAGGCACAAG +s simMouse_chr6.simMouse.chr6 609404 11 + 636262 CATTGCAGCAC +s simMouse_chr6.simMouse.chr6 242910 11 + 636262 CAAAGCACCAG +s simMouse_chr6.simMouse.chr6 966 11 - 636262 CAAGAAACAAG +s simRat_chr6.simRat.chr6 83961 11 - 647215 CAATGCACAAC +s simRat_chr6.simRat.chr6 478957 6 + 647215 -----CAGCAC + +a +s simMouse_chr6.simMouse.chr6 469048 5 + 636262 TCATT +s Anc1.Anc1refChr6 122121 5 + 197743 TCATT +s mr.mrrefChr3 24747 5 + 181027 TCATT +s mr.mrrefChr3 157337 5 + 181027 TCATT +s mr.mrrefChr5 95996 3 + 294540 GC--C +s simMouse_chr6.simMouse.chr6 609415 5 + 636262 TCATT +s simMouse_chr6.simMouse.chr6 242921 3 + 636262 GC--C +s simMouse_chr6.simMouse.chr6 987 3 - 636262 GC--C +s simRat_chr6.simRat.chr6 83972 5 - 647215 TCATT +s simRat_chr6.simRat.chr6 478963 5 + 647215 TCACT + +a +s simMouse_chr6.simMouse.chr6 469053 1 + 636262 G +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 609421 1 + 636262 G +s simMouse_chr6.simMouse.chr6 242924 1 + 636262 A +s simMouse_chr6.simMouse.chr6 990 1 - 636262 A +s simRat_chr6.simRat.chr6 83977 1 - 647215 G +s simRat_chr6.simRat.chr6 478968 1 + 647215 G a s simMouse_chr6.simMouse.chr6 469054 1 + 636262 C @@ -179841,6 +190366,20 @@ s simRat_chr6.simRat.chr6 478970 2 + 647215 CT a +s simMouse_chr6.simMouse.chr6 469057 10 + 636262 TGTTTATCAT +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 609424 10 + 636262 CATTTATCAT +s simMouse_chr6.simMouse.chr6 242925 10 + 636262 CGTTAGTCAC +s simMouse_chr6.simMouse.chr6 996 7 - 636262 TGCTTTT--- +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 +s simRat_chr6.simRat.chr6 478972 10 + 647215 CGTTTATCAC + +a s simMouse_chr6.simMouse.chr6 469067 4 + 636262 GGCC s Anc0.Anc0refChr3 89351 4 + 222631 AATA s Anc1.Anc1refChr6 122206 4 + 197743 AATA @@ -182894,11 +193433,12 @@ 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 +s simMouse_chr6.simMouse.chr6 477830 125 + 636262 AACCATTGTAACTGTCTCAAACAAGTGTAACTGTGGCAGGGTAACCTGAACTCACACAATCTTGGCCGTAGCAAGCAGATTCATAGAACGATCCAACTCACATGAACGGGTTCAGCCCCCTGGCT +s Anc1.Anc1refChr6 129428 17 + 197743 -------------------------------------------------------------------------AACA-------------------------------GG----GTTCTCTGACT +s mr.mrrefChr3 32152 94 + 181027 AACTATTGTAACTGTCTCAAACGAGTGTAACTGTGGCGGGGTAACCTGAACTCAAATAATCTTTGCCGGACCAAGCA-------------------------------GGTTCAGCCCCCTGGCT +s simHuman_chr6.simHuman.chr6 461344 17 + 601863 -------------------------------------------------------------------------AACA-------------------------------GG----GTTCTCTGACT +s simMouse_chr6.simMouse.chr6 477753 77 + 636262 AACTATTGTAACTGTCTCAAACGAATGTAACTGTGGCGGGGTAACCTGAACTCAAATGATCTTTGCTGGACCAATCA------------------------------------------------ +s simRat_chr6.simRat.chr6 486444 17 + 647215 ------------------------------------------------------------------------------------------------------------GGTTCAGACCCCTGGCT a s simMouse_chr6.simMouse.chr6 477955 6 + 636262 GTAAAG @@ -183519,30 +194059,50 @@ 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 +s simMouse_chr6.simMouse.chr6 479721 24 + 636262 AAACTCACCTTTATTTCATGGTGC +s Anc0.Anc0refChr3 97660 22 + 222631 AATCTTAGTCTTATT--GAATTTG +s Anc1.Anc1refChr6 130745 22 + 197743 AATCTTAGTCTTATT--GAATTTG +s Anc2.Anc2refChr1 9009 22 + 142988 AATCTTAGTCTTATT--GAATGTG +s mr.mrrefChr3 33934 24 + 181027 AAACTCACCTTTATTTCATGGTGC +s mr.mrrefChr3 33712 22 + 181027 AATTTCAGTCTTATT--GGGTTTG +s simCow_chr6.simCow.chr6 465713 22 + 602619 AATCTTAGTCTTATT--GAATGTG +s simHuman_chr6.simHuman.chr6 462656 22 + 601863 AATTTTAGTCTTATT--GAATCTG +s simMouse_chr6.simMouse.chr6 479492 22 + 636262 AATTTCAGTCTTATT--GGGTTTG +s simRat_chr6.simRat.chr6 487995 24 + 647215 AAGCTCACTTTTATTTCATGATGC + +a +s simMouse_chr6.simMouse.chr6 479745 42 + 636262 CCATGTCCACTACTTATTGCAGATTCTGACCAAAGTGCATAA +s Anc0.Anc0refChr3 97683 38 + 222631 ACATATTAGCTATTAGTAGCATGTTCTGAAC----TTCAAAG +s Anc1.Anc1refChr6 130768 38 + 197743 ACATATTAGCTATTAGTAGCATGTTCTGAAC----TTCAAAG +s Anc2.Anc2refChr1 9032 38 + 142988 ACATATTTCCTATTAGTAGCTTGTTCTGAAT----TTCTAAG +s mr.mrrefChr3 33958 42 + 181027 CCATGTCCACTACTTATTGCAGATTCTGACCAAAGTGCATAA +s mr.mrrefChr3 33734 38 + 181027 ACATATTAGTGTCTCAAAGTATCGTTTGCAC----TTTAAAG +s simCow_chr6.simCow.chr6 465736 38 + 602619 ACATATTTCCTATTAGTAGCTTGTTCTGAAT----TTCTAAG +s simHuman_chr6.simHuman.chr6 462679 38 + 601863 ACATATTAGCAGTTAGTAGCATTAGTTGCAC----TGCAAAG +s simMouse_chr6.simMouse.chr6 479514 38 + 636262 ACATATTAGTGTCTCAAAGTATCGTTTGCAC----TTTAAAG +s simRat_chr6.simRat.chr6 488019 42 + 647215 CCATGTCCACAAATCATTGCAGATTCCAGCCAAAGTGCATAA + +a +s simMouse_chr6.simMouse.chr6 479787 56 + 636262 GTCCACTAATCAAACTTAAGAAATACTGCCATAATGTTAGTGTGTCACTGTCTCTT +s Anc0.Anc0refChr3 97734 52 + 222631 GTGTACTATGTAGAC----AAGCAACAGGTAAAAAGCTGTTGAGTTTCTGCCTCTT +s Anc1.Anc1refChr6 130819 52 + 197743 GTGTACTATGTAGAC----AAGCAACAGGTAAAAAGCTGTTGAGTTTCTGCCTCTT +s Anc2.Anc2refChr1 9083 52 + 142988 GCGTACTATGTAGAC----AAGCAACAGGTAAAAAGCTCTTGAGTTTCTGCCTCTT +s mr.mrrefChr3 34000 56 + 181027 GTCCACTAATCAAACTTAAGAAATACTGCCATAATGTTAGTGTGTCACTGTCTCTT +s mr.mrrefChr3 33772 51 + 181027 ATGTACCATGTGGCC----GATCAACTGGCA-ACCACTGTGAGGCTTCTGCCTTTT +s simCow_chr6.simCow.chr6 465788 52 + 602619 GCGTACTATGTGGTC----AATTAACAGGCAATACACTCTTGAGTCTCCGCCCCTT +s simDog_chr6.simDog.chr6 455791 34 + 593897 -----------AGAG----AGGCACAGACTCAAGAGC-------TTTTTGTCTGTT +s simHuman_chr6.simHuman.chr6 462730 52 + 601863 ATGTTCTATGTAGAC----AAGCAACAGGTAAAAGGCTGTGGAGTTTCTGCCACTT +s simMouse_chr6.simMouse.chr6 479552 51 + 636262 ATGTACCATGTGGCC----GATCAACTGGCA-ACCACTGTGAGGCTTCTGCCTTTT +s simRat_chr6.simRat.chr6 488061 56 + 647215 GTCCCCTAATCAAATTTAAGAAGTACTGCCAAAATGTTAATGTGTCACTATATCTT + +a +s simMouse_chr6.simMouse.chr6 479843 5 + 636262 CAATC +s Anc1.Anc1refChr6 130929 5 + 197743 CAATC +s mr.mrrefChr3 34056 5 + 181027 CAATC +s mr.mrrefChr3 33908 5 + 181027 CAAGC +s simMouse_chr6.simMouse.chr6 479688 5 + 636262 CAAGC +s simRat_chr6.simRat.chr6 487969 5 + 647215 CAAGC +s simRat_chr6.simRat.chr6 488117 5 + 647215 CGATC a s simMouse_chr6.simMouse.chr6 479848 95 + 636262 TGCACGTCTGGTAGATACATGTCATTCTTGACCTTGAGCAGTTGATGACTTTATGTATAAAAAGCTTTTACTGATTAATTGATTTTGCTGATTAG @@ -185037,6 +195597,34 @@ s simRat_chr6.simRat.chr6 490570 1 + 647215 C a +s simMouse_chr6.simMouse.chr6 482305 7 + 636262 TGCCCCA +s Anc0.Anc0refChr3 99268 7 + 222631 TGCCCCT +s Anc1.Anc1refChr6 132464 7 + 197743 TGCCCCT +s Anc2.Anc2refChr1 10647 7 + 142988 TGCCCCT +s mr.mrrefChr3 36515 7 + 181027 TGCCCCA +s mr.mrrefChr3 35772 7 + 181027 TGCCCAT +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 481506 7 + 636262 TGCCGAT +s simRat_chr6.simRat.chr6 489823 7 + 647215 TGCCCAC +s simRat_chr6.simRat.chr6 490571 7 + 647215 TGCCCCA + +a +s simMouse_chr6.simMouse.chr6 482312 13 + 636262 TAATTTTATCACA +s Anc0.Anc0refChr3 99275 13 + 222631 TAATTTCACTATC +s Anc1.Anc1refChr6 132471 13 + 197743 TAATTTCACTATC +s Anc2.Anc2refChr1 10654 13 + 142988 TATTTTCGCTATG +s mr.mrrefChr3 36522 13 + 181027 TAATTTTATCACC +s mr.mrrefChr3 35779 13 + 181027 TAAGTCCACCATC +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 481513 13 + 636262 TAAGTCCACCATC +s simRat_chr6.simRat.chr6 489830 13 + 647215 TAAGTCCACCAGC +s simRat_chr6.simRat.chr6 490579 13 + 647215 TAATTTTATCACC + +a s simMouse_chr6.simMouse.chr6 482325 1 + 636262 T s Anc0.Anc0refChr3 99288 1 + 222631 T s Anc1.Anc1refChr6 132484 1 + 197743 T @@ -185081,6 +195669,117 @@ s simRat_chr6.simRat.chr6 490597 1 + 647215 C a +s simMouse_chr6.simMouse.chr6 482331 44 + 636262 CATCAAATGATATCATGCTAGCAGGAAAACGACTTAACAGACTG +s Anc0.Anc0refChr3 99304 44 + 222631 CATTGAATGACATCTTGATAGTAGGAAAATTACTGAGTTGAGTG +s Anc1.Anc1refChr6 132500 44 + 197743 CATTGAATGACATCTTGATAGTAGGAAAATTACTGAGTTGAGTG +s Anc2.Anc2refChr1 10689 44 + 142988 CATTGAATGACATCTTGATAGTAAGAAAATTACTGAGTTGAGTT +s mr.mrrefChr3 36541 44 + 181027 CATCAAATGATATCATGCTAGTAGGAAAACTATTTAACAGACTG +s mr.mrrefChr3 35792 44 + 181027 CATGAATATATATACTGATAGTAGAGAAATAACTGAGTTCAGTG +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 481526 44 + 636262 CATGGATATATATACTGATAGTAGAGAAATAACTGAGTTCAGTG +s simRat_chr6.simRat.chr6 489843 44 + 647215 CATGAATATATATGTTAATAGTGGGAAAATTACCGAGTTTGCTG +s simRat_chr6.simRat.chr6 490598 44 + 647215 CATCAAATGATATCATCCTATTAGGAAAACTATTTAACAGCCTG + +a +s simMouse_chr6.simMouse.chr6 482375 3 + 636262 AGC +s Anc0.Anc0refChr3 99354 3 + 222631 AGC +s Anc1.Anc1refChr6 132550 3 + 197743 AGC +s Anc2.Anc2refChr1 10740 3 + 142988 AGC +s mr.mrrefChr3 36585 3 + 181027 AGC +s mr.mrrefChr3 35842 3 + 181027 ACC +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 481576 3 + 636262 ACC +s simRat_chr6.simRat.chr6 489893 3 + 647215 ACG +s simRat_chr6.simRat.chr6 490642 3 + 647215 AGC + +a +s simMouse_chr6.simMouse.chr6 482378 4 + 636262 AATG +s Anc0.Anc0refChr3 99357 4 + 222631 CATG +s Anc1.Anc1refChr6 132553 4 + 197743 CATG +s Anc2.Anc2refChr1 10747 4 + 142988 CATG +s mr.mrrefChr3 36588 4 + 181027 AATG +s mr.mrrefChr3 35845 4 + 181027 CATG +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 481579 4 + 636262 CATG +s simRat_chr6.simRat.chr6 489896 4 + 647215 CATG +s simRat_chr6.simRat.chr6 490645 4 + 647215 AATG + +a +s simMouse_chr6.simMouse.chr6 482382 31 + 636262 TTTTGATTGGGTTGATGATAGTTATAACTAA +s Anc0.Anc0refChr3 99362 31 + 222631 TTTTGATGTGGTTGACGATAATCATACCTAA +s Anc1.Anc1refChr6 132558 31 + 197743 TTTTGATGTGGTTGACGATAATCATACCTAA +s Anc2.Anc2refChr1 10752 31 + 142988 TTTTGATGTGGTTTACGATAATCATACCCAA +s mr.mrrefChr3 36592 31 + 181027 TTTTGATTTGGTTGATGATAATTATACCTAA +s mr.mrrefChr3 35850 31 + 181027 GTTTGATGTGGATCACGATAATAATACCTAA +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 481584 31 + 636262 GTTTGATGTGGATCACGATAATAATACCTAA +s simRat_chr6.simRat.chr6 489901 31 + 647215 ATTTGATGTGGTTAATGATAACAATACCTAA +s simRat_chr6.simRat.chr6 490649 31 + 647215 TTATGATCTGGTTGATAATAATTATACCTAA + +a +s simMouse_chr6.simMouse.chr6 482413 22 + 636262 TGGTCAACATGAAATTATAGGG +s Anc0.Anc0refChr3 99403 22 + 222631 TAGTTAACATGCAATTATTAGG +s Anc1.Anc1refChr6 132599 22 + 197743 TAGTTAACATGCAATTATTAGG +s Anc2.Anc2refChr1 10793 22 + 142988 TAGTTAACATTCAATTGTGAGG +s mr.mrrefChr3 36623 22 + 181027 TGGTCAACATGAAATTATAGGG +s mr.mrrefChr3 35881 22 + 181027 TGGATAACGTGCAATCATTACA +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 481615 22 + 636262 TGGATAACGTGCAATCATTACA +s simRat_chr6.simRat.chr6 489932 22 + 647215 TGGATAACTTGCAATCATTAGA +s simRat_chr6.simRat.chr6 490680 22 + 647215 TGGTCAACATGAAATTATGGGG + +a +s simMouse_chr6.simMouse.chr6 482435 5 + 636262 TAGAA +s Anc0.Anc0refChr3 99425 5 + 222631 TAAAA +s Anc1.Anc1refChr6 132621 5 + 197743 TAAAA +s Anc2.Anc2refChr1 10815 5 + 142988 TAAGC +s mr.mrrefChr3 36645 5 + 181027 TAGAA +s mr.mrrefChr3 35903 5 + 181027 TAAAA +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 481637 5 + 636262 TAAAA +s simRat_chr6.simRat.chr6 489955 5 + 647215 TAACA +s simRat_chr6.simRat.chr6 490702 5 + 647215 TAGAA + +a +s simMouse_chr6.simMouse.chr6 482440 28 + 636262 ATCTATAATGCTCTTATAGAGCAGGGCA +s Anc0.Anc0refChr3 99436 28 + 222631 ATCTATAATGCTCTTGTAGAAAGGGGCA +s Anc1.Anc1refChr6 132632 28 + 197743 ATCTATAATGCTCTTGTAGAAAGGGGCA +s Anc2.Anc2refChr1 10826 28 + 142988 ATCTAGAATGCTCTTGTAGAAAGGGGCA +s mr.mrrefChr3 36650 28 + 181027 ATCTATAATGCTCTTGTAGAGCAGGGCA +s mr.mrrefChr3 35908 28 + 181027 ATTTATTAAGCTCTTGTAGTAAGGGGCA +s simCow_chr6.simCow.chr6 467583 19 + 602619 ATCTAATATGCTCTCCTAG--------- +s simDog_chr6.simDog.chr6 457509 28 + 593897 ATTTAGAATGCTCTTGTAGAAAGGGGCA +s simHuman_chr6.simHuman.chr6 464828 28 + 601863 ATCTACAATGCTCTTGTAGCAAGGGGCA +s simMouse_chr6.simMouse.chr6 481642 28 + 636262 ATTTATTAAGCTCTTGTAGTAAGGGGCA +s simRat_chr6.simRat.chr6 489960 28 + 647215 ACCTATTATACTGGTGTAGCAAGGAGCA +s simRat_chr6.simRat.chr6 490707 27 + 647215 ATCTATAATGCCCT-GCAGAGCAGGGCA + +a +s simMouse_chr6.simMouse.chr6 482468 4 + 636262 TGGA +s Anc0.Anc0refChr3 99464 4 + 222631 CTGA +s Anc1.Anc1refChr6 132660 4 + 197743 CTGA +s Anc2.Anc2refChr1 10854 4 + 142988 CTGT +s mr.mrrefChr3 36678 4 + 181027 TGGA +s mr.mrrefChr3 35938 4 + 181027 TGCA +s simDog_chr6.simDog.chr6 457537 4 + 593897 CTGT +s simHuman_chr6.simHuman.chr6 464856 4 + 601863 CTGA +s simMouse_chr6.simMouse.chr6 481672 4 + 636262 TGCA +s simRat_chr6.simRat.chr6 489990 4 + 647215 TGCA +s simRat_chr6.simRat.chr6 490734 4 + 647215 TGGA + +a s simMouse_chr6.simMouse.chr6 482472 12 + 636262 ATGTTTTATTGT s Anc0.Anc0refChr3 99468 12 + 222631 ATGTCTTCTGAT s Anc1.Anc1refChr6 132664 12 + 197743 ATGTCTTCTGAT @@ -185091,6 +195790,104 @@ s simRat_chr6.simRat.chr6 490738 12 + 647215 ATTTCTTATTGC a +s simMouse_chr6.simMouse.chr6 482484 28 + 636262 AGTATGTAGCCCTCTTATTCAGATGCCA +s Anc0.Anc0refChr3 99480 28 + 222631 AGTATGTTGCCTTCTTATTCAGCTGCCC +s Anc1.Anc1refChr6 132676 28 + 197743 AGTATGTTGCCTTCTTATTCAGCTGCCC +s Anc2.Anc2refChr1 10870 28 + 142988 AGTATGTTGCCTTCTTATTCAGCTACCC +s mr.mrrefChr3 36694 28 + 181027 AGTATGTTGCCTTCTTATTCAGATGCCC +s mr.mrrefChr3 35942 28 + 181027 CAGATGTTGCCTTCTCACTTAGTTGTCC +s simCow_chr6.simCow.chr6 467602 26 + 602619 --TATGTCACCTTCTTATTCAACTACCT +s simDog_chr6.simDog.chr6 457553 28 + 593897 AGCATGTTGCCTTCTGATACAGCTACCC +s simHuman_chr6.simHuman.chr6 464872 28 + 601863 AATATCTTGCCTTCTTTTTCAGCTGCCC +s simMouse_chr6.simMouse.chr6 481676 28 + 636262 CAGATGTTGCCTTCTCACTTAGTTGTCC +s simRat_chr6.simRat.chr6 489994 28 + 647215 AGGATGCTGCCTTCTCATTCAGTTGTGA +s simRat_chr6.simRat.chr6 490750 26 + 647215 AGTATGTTGTCTT--TATTCGGATGCCC + +a +s simMouse_chr6.simMouse.chr6 482512 3 + 636262 TGT +s Anc0.Anc0refChr3 99508 3 + 222631 TAT +s Anc1.Anc1refChr6 132704 3 + 197743 TAT +s Anc2.Anc2refChr1 10898 3 + 142988 TAT +s mr.mrrefChr3 36722 3 + 181027 TGT +s mr.mrrefChr3 35970 3 + 181027 TGC +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 481704 3 + 636262 TGC +s simRat_chr6.simRat.chr6 490022 3 + 647215 TGT +s simRat_chr6.simRat.chr6 490776 3 + 647215 TGT + +a +s simMouse_chr6.simMouse.chr6 482515 3 + 636262 ATC +s Anc0.Anc0refChr3 99511 3 + 222631 GTC +s Anc1.Anc1refChr6 132707 3 + 197743 GTC +s Anc2.Anc2refChr1 10902 3 + 142988 GTC +s mr.mrrefChr3 36725 3 + 181027 GTC +s mr.mrrefChr3 35973 3 + 181027 ATT +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 481707 3 + 636262 ATT +s simRat_chr6.simRat.chr6 490025 3 + 647215 GTT +s simRat_chr6.simRat.chr6 490779 3 + 647215 GTC + +a +s simMouse_chr6.simMouse.chr6 482518 2 + 636262 TG +s Anc0.Anc0refChr3 99516 2 + 222631 AC +s Anc1.Anc1refChr6 132712 2 + 197743 AC +s Anc2.Anc2refChr1 10907 2 + 142988 AC +s mr.mrrefChr3 36728 2 + 181027 TG +s mr.mrrefChr3 35976 2 + 181027 AC +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 481710 2 + 636262 AC +s simRat_chr6.simRat.chr6 490028 2 + 647215 AC +s simRat_chr6.simRat.chr6 490782 2 + 647215 AG + +a +s simMouse_chr6.simMouse.chr6 482520 6 + 636262 AAATAC +s Anc0.Anc0refChr3 99518 6 + 222631 ATATTT +s Anc1.Anc1refChr6 132714 6 + 197743 ATATTT +s Anc2.Anc2refChr1 10909 6 + 142988 ATATTT +s mr.mrrefChr3 36730 6 + 181027 AAATAT +s mr.mrrefChr3 35978 6 + 181027 ATGTAT +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 481712 6 + 636262 ATGTAT +s simRat_chr6.simRat.chr6 490030 6 + 647215 ATGTAT +s simRat_chr6.simRat.chr6 490784 6 + 647215 AAATAT + +a +s simMouse_chr6.simMouse.chr6 482526 30 + 636262 TTCTCCAATCAGATAAGCTGTATCTAAACT +s Anc0.Anc0refChr3 99528 30 + 222631 TTCTCCCAGCTGACAAACTGTATCAAAACT +s Anc1.Anc1refChr6 132724 30 + 197743 TTCTCCCAGCTGACAAACTGTATCAAAACT +s Anc2.Anc2refChr1 10919 30 + 142988 TTCTCTCAGCTGACAAACTGTATCAAAACT +s mr.mrrefChr3 36736 30 + 181027 TTCTCCAATCAGATAAGCTGTATCTAAACT +s mr.mrrefChr3 35988 30 + 181027 TTCTCCTTACAGATGAGTTGGATCAAAACC +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 481722 30 + 636262 TTCTCCTTACAGATGAGTTGGATCAAAACC +s simRat_chr6.simRat.chr6 490040 30 + 647215 TTCCCCTTACAGATGAGTTGGATCAAAGCC +s simRat_chr6.simRat.chr6 490790 30 + 647215 TTCTCCAATCAAATAAGCTGTATCTATACT + +a +s simMouse_chr6.simMouse.chr6 482556 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 36766 2 + 181027 TG +s mr.mrrefChr3 36018 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 481752 2 + 636262 TG +s simRat_chr6.simRat.chr6 490070 2 + 647215 TG +s simRat_chr6.simRat.chr6 490820 2 + 647215 TG + +a s simMouse_chr6.simMouse.chr6 482558 9 + 636262 GTCACTGAA s Anc0.Anc0refChr3 99568 4 + 222631 GACA----- s Anc1.Anc1refChr6 132764 9 + 197743 GACACTCAA @@ -185109,6 +195906,44 @@ s simRat_chr6.simRat.chr6 490831 1 + 647215 A a +s simMouse_chr6.simMouse.chr6 482568 1 + 636262 C +s Anc1.Anc1refChr6 132774 1 + 197743 C +s mr.mrrefChr3 36778 1 + 181027 C +s mr.mrrefChr3 36020 1 + 181027 C +s simHuman_chr6.simHuman.chr6 464987 1 + 601863 C +s simMouse_chr6.simMouse.chr6 481754 1 + 636262 C +s simRat_chr6.simRat.chr6 490072 1 + 647215 C +s simRat_chr6.simRat.chr6 490832 1 + 647215 C + +a +s simMouse_chr6.simMouse.chr6 482569 2 + 636262 TC +s Anc0.Anc0refChr3 99572 1 + 222631 -C +s Anc1.Anc1refChr6 132775 2 + 197743 AC +s Anc2.Anc2refChr1 10963 1 + 142988 -C +s mr.mrrefChr3 36779 2 + 181027 TC +s mr.mrrefChr3 36021 2 + 181027 CA +s simCow_chr6.simCow.chr6 467700 1 + 602619 -C +s simDog_chr6.simDog.chr6 457646 1 + 593897 -C +s simHuman_chr6.simHuman.chr6 464988 2 + 601863 AC +s simMouse_chr6.simMouse.chr6 481764 2 + 636262 CA +s simRat_chr6.simRat.chr6 490073 2 + 647215 CA +s simRat_chr6.simRat.chr6 490833 2 + 647215 TC + +a +s simMouse_chr6.simMouse.chr6 482571 7 + 636262 TCATTGC +s Anc0.Anc0refChr3 99573 7 + 222631 TCAATGT +s Anc1.Anc1refChr6 132777 7 + 197743 TCAATGT +s Anc2.Anc2refChr1 10964 7 + 142988 TCAATGA +s mr.mrrefChr3 36781 7 + 181027 TCATTGT +s mr.mrrefChr3 36023 7 + 181027 TCAGTGG +s simCow_chr6.simCow.chr6 467701 6 + 602619 TCAATG- +s simDog_chr6.simDog.chr6 457647 7 + 593897 TCAATAA +s simHuman_chr6.simHuman.chr6 464990 7 + 601863 TCAATGT +s simMouse_chr6.simMouse.chr6 481767 7 + 636262 TCAGTGG +s simRat_chr6.simRat.chr6 490075 7 + 647215 TCAGTGG +s simRat_chr6.simRat.chr6 490835 7 + 647215 TCAGTGT + +a s simMouse_chr6.simMouse.chr6 482578 3 + 636262 ACC s Anc0.Anc0refChr3 99580 3 + 222631 ATC s Anc1.Anc1refChr6 132784 3 + 197743 ATC @@ -185120,6 +195955,20 @@ s simRat_chr6.simRat.chr6 490842 3 + 647215 GTC a +s simMouse_chr6.simMouse.chr6 482581 9 + 636262 ATGTACAAA +s Anc0.Anc0refChr3 99583 9 + 222631 GAGTGCAAA +s Anc1.Anc1refChr6 132787 9 + 197743 GAGTGCAAA +s Anc2.Anc2refChr1 10974 9 + 142988 AAGTGCAAG +s mr.mrrefChr3 36791 9 + 181027 GTGTACAAA +s mr.mrrefChr3 36030 9 + 181027 GTGCAAGAA +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 481774 9 + 636262 GTGCAAGAA +s simRat_chr6.simRat.chr6 490082 9 + 647215 GTGCAAGAA +s simRat_chr6.simRat.chr6 490845 9 + 647215 GTGCACAAG + +a s simMouse_chr6.simMouse.chr6 482590 3 + 636262 TGG s Anc0.Anc0refChr3 99592 3 + 222631 AAG s Anc1.Anc1refChr6 132796 3 + 197743 AAG @@ -185131,11 +195980,123 @@ s simRat_chr6.simRat.chr6 490854 3 + 647215 TGG a +s simMouse_chr6.simMouse.chr6 482593 1 + 636262 A +s Anc0.Anc0refChr3 99595 1 + 222631 A +s Anc1.Anc1refChr6 132799 1 + 197743 A +s Anc2.Anc2refChr1 10986 1 + 142988 A +s mr.mrrefChr3 36803 1 + 181027 A +s mr.mrrefChr3 36039 1 + 181027 G +s simCow_chr6.simCow.chr6 467721 1 + 602619 A +s simDog_chr6.simDog.chr6 457669 1 + 593897 A +s simHuman_chr6.simHuman.chr6 465012 1 + 601863 A +s simMouse_chr6.simMouse.chr6 481783 1 + 636262 G +s simRat_chr6.simRat.chr6 490091 1 + 647215 G +s simRat_chr6.simRat.chr6 490857 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 482594 18 + 636262 AACAATAGAGCCAATACT +s Anc0.Anc0refChr3 99596 18 + 222631 AACAATAAAGCAATTACT +s Anc1.Anc1refChr6 132800 18 + 197743 AACAATAAAGCAATTACT +s Anc2.Anc2refChr1 10987 18 + 142988 AACAATAAAGCACTTACT +s mr.mrrefChr3 36804 18 + 181027 AACAATAAAGCAAATATT +s mr.mrrefChr3 36040 18 + 181027 AACAACAAAGTAAGCACT +s simCow_chr6.simCow.chr6 467722 18 + 602619 AACAATAAAACACTTACT +s simDog_chr6.simDog.chr6 457670 18 + 593897 AGCGATAAAGCGCGGACT +s simHuman_chr6.simHuman.chr6 465013 18 + 601863 AACAATAAAGCAATTATT +s simMouse_chr6.simMouse.chr6 481785 18 + 636262 AACAACAAAGTAAGCACT +s simRat_chr6.simRat.chr6 490092 18 + 647215 AACAATGAAGTAAGCACT +s simRat_chr6.simRat.chr6 490858 18 + 647215 AGCATTAAAGCAAATATT + +a +s simMouse_chr6.simMouse.chr6 482612 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 36822 1 + 181027 T +s mr.mrrefChr3 36058 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 481803 1 + 636262 T +s simRat_chr6.simRat.chr6 490110 1 + 647215 T +s simRat_chr6.simRat.chr6 490876 1 + 647215 T + +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 482633 14 + 636262 CTCTCCGCAATACT +s Anc0.Anc0refChr3 99615 14 + 222631 CTCTCCATGACACT +s Anc1.Anc1refChr6 132819 14 + 197743 CTCTCCATGACACT +s Anc2.Anc2refChr1 11006 14 + 142988 CTGTCCATGACACT +s mr.mrrefChr3 36840 14 + 181027 CTCTCCGTAATACT +s mr.mrrefChr3 36059 14 + 181027 CTCTCCCAGATACT +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 481804 14 + 636262 CTCTCCCAGATACT +s simRat_chr6.simRat.chr6 490111 14 + 647215 CTCTCCCAGACCTC +s simRat_chr6.simRat.chr6 490894 14 + 647215 CTCACTGTAATACT + +a +s simMouse_chr6.simMouse.chr6 482647 1 + 636262 C +s Anc0.Anc0refChr3 99629 1 + 222631 C +s Anc1.Anc1refChr6 132833 1 + 197743 C +s Anc2.Anc2refChr1 11020 1 + 142988 C +s mr.mrrefChr3 36854 1 + 181027 C +s mr.mrrefChr3 36074 1 + 181027 C +s simCow_chr6.simCow.chr6 467755 1 + 602619 C +s simDog_chr6.simDog.chr6 457703 1 + 593897 C +s simHuman_chr6.simHuman.chr6 465049 1 + 601863 C +s simMouse_chr6.simMouse.chr6 481819 1 + 636262 C +s simRat_chr6.simRat.chr6 490126 1 + 647215 C +s simRat_chr6.simRat.chr6 490908 1 + 647215 C + +a +s simMouse_chr6.simMouse.chr6 482648 25 + 636262 TTCTAAGTTTTTTAGCTGCTGACGT +s Anc0.Anc0refChr3 99630 20 + 222631 TA-----CAATCCAGCCGCTAACAT +s Anc1.Anc1refChr6 132834 25 + 197743 TACCAAGCAATCCAGCCGCTAACAT +s Anc2.Anc2refChr1 11021 20 + 142988 TA-----TGACCCAGACGCTAACAT +s mr.mrrefChr3 36855 25 + 181027 TACTAAGTTTTCTAGCTGCTGACGT +s mr.mrrefChr3 36075 25 + 181027 TTACAATCAATCCAGCTGCTAACAT +s simCow_chr6.simCow.chr6 467756 20 + 602619 TA-----TGAAGCAGTTGCTAACAC +s simDog_chr6.simDog.chr6 457704 20 + 593897 TA-----TGACCCAGACGCTAATGT +s simHuman_chr6.simHuman.chr6 465050 20 + 601863 TAC-----AATCCAGCCACTAACAT +s simMouse_chr6.simMouse.chr6 481821 25 + 636262 TTACAATCAATCCAGCTGCTAACAT +s simRat_chr6.simRat.chr6 490127 25 + 647215 TCACAATCAATTTAGCTGCTAACAT +s simRat_chr6.simRat.chr6 490909 23 + 647215 TACTAACTCTTCTAGCTTCTGAC-- + +a +s simMouse_chr6.simMouse.chr6 482673 2 + 636262 GT +s Anc0.Anc0refChr3 99650 2 + 222631 GT +s Anc1.Anc1refChr6 132859 2 + 197743 GT +s Anc2.Anc2refChr1 11041 2 + 142988 GT +s mr.mrrefChr3 36880 2 + 181027 GT +s mr.mrrefChr3 36100 2 + 181027 TC +s simCow_chr6.simCow.chr6 467776 2 + 602619 AT +s simDog_chr6.simDog.chr6 457724 2 + 593897 GT +s simHuman_chr6.simHuman.chr6 465070 2 + 601863 GT +s simMouse_chr6.simMouse.chr6 481848 2 + 636262 TC +s simRat_chr6.simRat.chr6 490152 2 + 647215 TG +s simRat_chr6.simRat.chr6 490932 1 + 647215 -T + +a +s simMouse_chr6.simMouse.chr6 482675 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 36882 1 + 181027 T +s mr.mrrefChr3 36102 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 481850 1 + 636262 T +s simRat_chr6.simRat.chr6 490154 1 + 647215 T +s simRat_chr6.simRat.chr6 490933 1 + 647215 T + +a s simMouse_chr6.simMouse.chr6 482676 1 + 636262 G s Anc0.Anc0refChr3 99654 1 + 222631 G s Anc1.Anc1refChr6 132863 1 + 197743 G @@ -185147,11 +196108,75 @@ s simRat_chr6.simRat.chr6 490934 1 + 647215 G a +s simMouse_chr6.simMouse.chr6 482677 26 + 636262 TTACAAAGTTTTCAAGTTGAGATACA +s Anc0.Anc0refChr3 99655 26 + 222631 TAATGAAGTTCTTAGGAGGGTAAACA +s Anc1.Anc1refChr6 132864 26 + 197743 TAATGAAGTTCTTAGGAGGGTAAACA +s Anc2.Anc2refChr1 11046 26 + 142988 TAATGAAGTTCTTATGAGGGTATACA +s mr.mrrefChr3 36884 26 + 181027 TTATGAGGTTTTCAAGTTGATAAACA +s mr.mrrefChr3 36103 26 + 181027 TAATGAAGTTGTGAGGATGTTAGATG +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 481851 26 + 636262 TAATGAAGTTGTGAGGATGTTAGATG +s simRat_chr6.simRat.chr6 490155 26 + 647215 TAACGAAGTTTTGAGGATCTTAGATG +s simRat_chr6.simRat.chr6 490935 26 + 647215 TTATGAGGTTTTCAAGTAGATAAAAA + +a +s simMouse_chr6.simMouse.chr6 482703 16 + 636262 TCCTGGGGCTACATGC +s Anc0.Anc0refChr3 99681 16 + 222631 TCATGGAGTCACATGC +s Anc1.Anc1refChr6 132890 16 + 197743 TCATGGAGTCACATGC +s Anc2.Anc2refChr1 11072 16 + 142988 TCATGGAGTCACATGC +s mr.mrrefChr3 36910 16 + 181027 TCCTGGGGCTACATGC +s mr.mrrefChr3 36135 16 + 181027 TCACGGTGTTACATAC +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 481883 16 + 636262 TCACGGTGTTACATAC +s simRat_chr6.simRat.chr6 490187 16 + 647215 TCACAATGTTACACAC +s simRat_chr6.simRat.chr6 490961 16 + 647215 TCCTGGGGCTACATGC + +a +s simMouse_chr6.simMouse.chr6 482719 5 + 636262 TGTAC +s Anc0.Anc0refChr3 99697 5 + 222631 TGCAT +s Anc1.Anc1refChr6 132906 5 + 197743 TGCAT +s Anc2.Anc2refChr1 11090 5 + 142988 TGCAT +s mr.mrrefChr3 36926 5 + 181027 TGTAC +s mr.mrrefChr3 36151 5 + 181027 TGCAC +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 481899 5 + 636262 TGCAC +s simRat_chr6.simRat.chr6 490203 5 + 647215 TGCAC +s simRat_chr6.simRat.chr6 490977 5 + 647215 TGTAC + +a +s simMouse_chr6.simMouse.chr6 482724 4 + 636262 TTGA +s Anc1.Anc1refChr6 132930 4 + 197743 TTGA +s mr.mrrefChr3 36931 4 + 181027 TTGA +s mr.mrrefChr3 36241 4 + 181027 TTGA +s simMouse_chr6.simMouse.chr6 481989 4 + 636262 TTGA +s simRat_chr6.simRat.chr6 490295 4 + 647215 TTGA +s simRat_chr6.simRat.chr6 490982 4 + 647215 TTGA + +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 482731 43 + 636262 TGGTGTGGTGGGGACTGTAGGAGTACTACTGATTAGCTGGCAC +s Anc0.Anc0refChr3 99720 1 + 222631 ------------------------------------------C +s Anc1.Anc1refChr6 132934 43 + 197743 TGATGTAGTGGGTATTGTTGCAGGACTACTGATTAGTTGGCAC +s Anc2.Anc2refChr1 11113 1 + 142988 ------------------------------------------T +s mr.mrrefChr3 36938 43 + 181027 TGGTGTGGTGGGGACTGTAGGAGTACTACTGATTAGCTGGCAC +s mr.mrrefChr3 36245 43 + 181027 TGATTCAGTGGGTTTCAATACATGATTCCTGAATAGTTGGCAC +s simCow_chr6.simCow.chr6 467839 1 + 602619 ------------------------------------------T +s simDog_chr6.simDog.chr6 457789 1 + 593897 ------------------------------------------T +s simMouse_chr6.simMouse.chr6 481993 43 + 636262 TGATTCAGTGGGTTTCAATACATGATTCCTGAATAGTTGGCAC +s simRat_chr6.simRat.chr6 490299 43 + 647215 TAATTCAGTCGGTTTTAATACAAGATGCCTGGGTAGTTTGCAC +s simRat_chr6.simRat.chr6 490989 43 + 647215 TGGTGTGGTGGGGACTGTAGGAGTAATATTGATTACCTGGCAC + +a s simMouse_chr6.simMouse.chr6 482774 55 + 636262 TTAACCCAAGTGTCCAACTGTAAATTCAGCATGGTTTTGGGGATCTGAGTCTGAA s Anc0.Anc0refChr3 99721 5 + 222631 --------------------------------------------------CTGGA s Anc1.Anc1refChr6 132977 5 + 197743 --------------------------------------------------CTGGA @@ -185240,6 +196265,32 @@ s simRat_chr6.simRat.chr6 491168 26 + 647215 GTATGAGGAGTCCCCTTTGTTCAGAG a +s simMouse_chr6.simMouse.chr6 482906 13 + 636262 ATGATGTAGCATA +s Anc0.Anc0refChr3 99815 11 + 222631 --CACGTTGAATA +s Anc1.Anc1refChr6 133072 13 + 197743 ATCACGTTGAATA +s Anc2.Anc2refChr1 11210 11 + 142988 --CACATTGAATA +s mr.mrrefChr3 37130 13 + 181027 ATGATGTAGAATA +s mr.mrrefChr3 36288 13 + 181027 ACACTGCTGAATA +s simDog_chr6.simDog.chr6 457895 11 + 593897 --CACATTGAATA +s simHuman_chr6.simHuman.chr6 465235 13 + 601863 ATCACTTTGAATA +s simMouse_chr6.simMouse.chr6 482036 13 + 636262 ACACTGCTGAATA +s simRat_chr6.simRat.chr6 490342 13 + 647215 CCACTGCCGAATA +s simRat_chr6.simRat.chr6 491194 13 + 647215 CTAATGTAGAATA + +a +s simMouse_chr6.simMouse.chr6 482919 1 + 636262 G +s Anc0.Anc0refChr3 99826 1 + 222631 G +s Anc1.Anc1refChr6 133085 1 + 197743 G +s Anc2.Anc2refChr1 11221 1 + 142988 G +s mr.mrrefChr3 37143 1 + 181027 G +s mr.mrrefChr3 36301 1 + 181027 A +s simDog_chr6.simDog.chr6 457906 1 + 593897 G +s simHuman_chr6.simHuman.chr6 465248 1 + 601863 T +s simMouse_chr6.simMouse.chr6 482049 1 + 636262 A +s simRat_chr6.simRat.chr6 490356 1 + 647215 A +s simRat_chr6.simRat.chr6 491207 1 + 647215 G + +a s simMouse_chr6.simMouse.chr6 482920 1 + 636262 C s Anc0.Anc0refChr3 99827 1 + 222631 A s Anc1.Anc1refChr6 133086 1 + 197743 A @@ -185250,7 +196301,32 @@ s simRat_chr6.simRat.chr6 491208 1 + 647215 C a -s simMouse_chr6.simMouse.chr6 482946 2 + 636262 TT +s simMouse_chr6.simMouse.chr6 482921 22 + 636262 TAATGACACTGTAATAAGTCAA +s Anc0.Anc0refChr3 99828 22 + 222631 TAACCGCACTTTAATAGGCCAA +s Anc1.Anc1refChr6 133087 22 + 197743 TAACCGCACTTTAATAGGCCAA +s Anc2.Anc2refChr1 11223 22 + 142988 TATCCGCACTTTAACAGGCCAA +s mr.mrrefChr3 37145 22 + 181027 TAATGACACTGTAATAAGTCAA +s mr.mrrefChr3 36302 22 + 181027 TAAGCGTGCTTTAATACACCAA +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 482050 22 + 636262 TAAGCGTGCTTTAATACACCAA +s simRat_chr6.simRat.chr6 490357 22 + 647215 TAAGCTCACTTTTAGAGACCAA +s simRat_chr6.simRat.chr6 491209 22 + 647215 TAATGACCCTGTAATAAGTGAA + +a +s simMouse_chr6.simMouse.chr6 482943 42 + 636262 TGTTTATTATCCTCAACTATGTCTATTAGAATTGGACATGGT +s Anc0.Anc0refChr3 99850 40 + 222631 TGC--ATTATCATCAACCATCTTTATTGGAATTGGACATGGC +s Anc1.Anc1refChr6 133109 40 + 197743 TGC--ATTATCATCAACCATCTTTATTGGAATTGGACATGGC +s Anc2.Anc2refChr1 11245 40 + 142988 TGC--ATTATCAACAACCATCTCTATTGGAATTGAACATCAC +s mr.mrrefChr3 37167 40 + 181027 TGC--ATTATCATCAACTATGTTTATTAGAATTGGACATGGT +s mr.mrrefChr3 36326 40 + 181027 TGC--ATTACCAGCAAGCATTATTTTTGGAGCTGGTCATGCC +s simCow_chr6.simCow.chr6 467953 40 + 602619 TGT--ATTATCAACAACAATCTCTAATGGAATTGAACATCAT +s simDog_chr6.simDog.chr6 457930 40 + 593897 TGC--ATTATCGACGATCATCTCTATTGGAATTGAACAACAC +s simHuman_chr6.simHuman.chr6 465272 39 + 601863 TGC--ATTATCATCAGCCAC-TTTATTGGAATTGGATATAGC +s simMouse_chr6.simMouse.chr6 482074 40 + 636262 TGC--ATTACCAGCAAGCATTATTTTTGGAGCTGGTCATGCC +s simRat_chr6.simRat.chr6 490381 40 + 647215 TGC--ATTACTAGTGAGCATTATTATTGAAGCTGGACATGCC +s simRat_chr6.simRat.chr6 491231 39 + 647215 CAC--ATTATCATCAACTATGTTTATTAGAACTCAACATG-T a s simMouse_chr6.simMouse.chr6 482985 1 + 636262 G @@ -185258,6 +196334,43 @@ s simRat_chr6.simRat.chr6 491270 1 + 647215 G a +s simMouse_chr6.simMouse.chr6 482986 1 + 636262 T +s Anc0.Anc0refChr3 99890 1 + 222631 A +s Anc1.Anc1refChr6 133149 1 + 197743 A +s Anc2.Anc2refChr1 11285 1 + 142988 A +s mr.mrrefChr3 37208 1 + 181027 T +s mr.mrrefChr3 36366 1 + 181027 T +s simCow_chr6.simCow.chr6 467993 1 + 602619 A +s simDog_chr6.simDog.chr6 457970 1 + 593897 A +s simHuman_chr6.simHuman.chr6 465311 1 + 601863 A +s simMouse_chr6.simMouse.chr6 482114 1 + 636262 T +s simRat_chr6.simRat.chr6 490421 1 + 647215 T +s simRat_chr6.simRat.chr6 491271 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 482987 21 + 636262 AACTCATATGCCATTGGGATA +s Anc0.Anc0refChr3 99891 2 + 222631 GA------------------- +s Anc1.Anc1refChr6 133150 21 + 197743 GACTCCCATGCCATTGAAGTA +s Anc2.Anc2refChr1 11286 2 + 142988 GG------------------- +s mr.mrrefChr3 37209 21 + 181027 AACTCATATGCCATTGGGATA +s mr.mrrefChr3 36367 21 + 181027 GACTACCCCACTACTGAAGTC +s simCow_chr6.simCow.chr6 467994 2 + 602619 AG------------------- +s simDog_chr6.simDog.chr6 457971 2 + 593897 GG------------------- +s simHuman_chr6.simHuman.chr6 465312 2 + 601863 GA------------------- +s simMouse_chr6.simMouse.chr6 482134 21 + 636262 GACTACCCCACTACTGAAGTC +s simRat_chr6.simRat.chr6 490422 21 + 647215 ATCTACTCCATAATTGAAGTC +s simRat_chr6.simRat.chr6 491272 21 + 647215 AACTCCTCTGCCATCGGCATT + +a +s simMouse_chr6.simMouse.chr6 483008 22 + 636262 GCTACCATGCCCTTACTTGAAT +s Anc1.Anc1refChr6 133171 22 + 197743 GCTACTATGGCCTTACTTGCAC +s mr.mrrefChr3 37230 22 + 181027 GCTACCATGCCCTTACTTGAAT +s mr.mrrefChr3 36388 22 + 181027 GCTCCTAGGGCATTACCTGCAC +s simMouse_chr6.simMouse.chr6 482155 22 + 636262 GCTCCTAGGGCATTACCTGCAC +s simRat_chr6.simRat.chr6 490443 22 + 647215 ACTACCAAGGTGTTACCTGCAC +s simRat_chr6.simRat.chr6 491299 22 + 647215 GCTACCACTCCAATACTTGAAT + +a s simMouse_chr6.simMouse.chr6 483030 13 + 636262 AAAACAATGTACT s Anc0.Anc0refChr3 99893 11 + 222631 --AACAATGTACT s Anc1.Anc1refChr6 133193 11 + 197743 --AACAATGTACT @@ -185269,6 +196382,76 @@ s simRat_chr6.simRat.chr6 491321 13 + 647215 AAAACAATGTACT a +s simMouse_chr6.simMouse.chr6 483043 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 37265 1 + 181027 C +s mr.mrrefChr3 36410 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 482177 1 + 636262 C +s simRat_chr6.simRat.chr6 490465 1 + 647215 C +s simRat_chr6.simRat.chr6 491334 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 483044 10 + 636262 AAATGTATAT +s Anc0.Anc0refChr3 99905 10 + 222631 AAATATATAT +s Anc1.Anc1refChr6 133205 10 + 197743 AAATATATAT +s Anc2.Anc2refChr1 11300 10 + 142988 TAATATTTAT +s mr.mrrefChr3 37266 10 + 181027 AAATGTATAT +s mr.mrrefChr3 36411 10 + 181027 AACTAGCTAC +s simCow_chr6.simCow.chr6 468008 9 + 602619 TAATATG-AT +s simDog_chr6.simDog.chr6 457985 10 + 593897 TAATGTTTAT +s simHuman_chr6.simHuman.chr6 465327 10 + 601863 AAATATATAT +s simMouse_chr6.simMouse.chr6 482178 10 + 636262 AACTAGCTAC +s simRat_chr6.simRat.chr6 490466 10 + 647215 AACTAGCTAT +s simRat_chr6.simRat.chr6 491335 10 + 647215 AAAGGTATAC + +a +s simMouse_chr6.simMouse.chr6 483054 11 + 636262 TGTACATACGC +s Anc0.Anc0refChr3 99915 11 + 222631 TGTATATACTC +s Anc1.Anc1refChr6 133215 11 + 197743 TGTATATACTC +s Anc2.Anc2refChr1 11310 11 + 142988 TATATATATTC +s mr.mrrefChr3 37276 11 + 181027 TGTATATACTC +s mr.mrrefChr3 36421 11 + 181027 TGTGCACCATA +s simCow_chr6.simCow.chr6 468017 11 + 602619 TCTATATATCC +s simDog_chr6.simDog.chr6 457995 11 + 593897 TATATATATTC +s simHuman_chr6.simHuman.chr6 465337 11 + 601863 ATTATATACTC +s simMouse_chr6.simMouse.chr6 482194 11 + 636262 TGTGCACCATA +s simRat_chr6.simRat.chr6 490476 11 + 647215 TGTGGCCCGTA +s simRat_chr6.simRat.chr6 491345 11 + 647215 TGTATGTACTC + +a +s simMouse_chr6.simMouse.chr6 483065 5 + 636262 CCAGT +s Anc0.Anc0refChr3 99926 5 + 222631 CCATT +s Anc1.Anc1refChr6 133226 5 + 197743 CCATT +s Anc2.Anc2refChr1 11321 5 + 142988 CTATT +s mr.mrrefChr3 37287 5 + 181027 CCATT +s mr.mrrefChr3 36432 5 + 181027 CCTGT +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 482205 5 + 636262 CCTGT +s simRat_chr6.simRat.chr6 490487 5 + 647215 CTTGT +s simRat_chr6.simRat.chr6 491391 5 + 647215 CCATT + +a +s simMouse_chr6.simMouse.chr6 483070 3 + 636262 GTT +s Anc0.Anc0refChr3 99931 3 + 222631 GTT +s Anc1.Anc1refChr6 133231 3 + 197743 GTT +s Anc2.Anc2refChr1 11326 3 + 142988 GTC +s mr.mrrefChr3 37292 3 + 181027 GTT +s mr.mrrefChr3 36437 3 + 181027 ATT +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 482210 3 + 636262 ATT +s simRat_chr6.simRat.chr6 490493 3 + 647215 ATT +s simRat_chr6.simRat.chr6 491396 3 + 647215 GTC + +a s simMouse_chr6.simMouse.chr6 483073 3 + 636262 ATG s Anc0.Anc0refChr3 99934 3 + 222631 ATT s Anc1.Anc1refChr6 133234 3 + 197743 ATT @@ -185280,20 +196463,73 @@ 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 +s simMouse_chr6.simMouse.chr6 483076 32 + 636262 TCAGTGCTGAGCCAAAATGTTGAACTGTTATT +s Anc0.Anc0refChr3 99937 30 + 222631 TCAGTGTTGAGCCAATGT-T-GAAGTATAATT +s Anc1.Anc1refChr6 133237 31 + 197743 TCAGTGTTGAGCCAATGTGT-GAAGTATAATT +s Anc2.Anc2refChr1 11332 30 + 142988 TCAGTGTTGGGCCAGTGT-C-GAAGTATAATT +s mr.mrrefChr3 37298 31 + 181027 TCAGTGCTGAGCCAAAATGT-GAACTGTTATT +s mr.mrrefChr3 36440 29 + 181027 CCATTGGTAAGCCCA--TGT-GAAAAAATATT +s simCow_chr6.simCow.chr6 468039 30 + 602619 CCAGTGCTGGGCCGATGT-T-GAAGTGTAATT +s simDog_chr6.simDog.chr6 458017 30 + 593897 TCAGTGTTGGGCTAGTGC-C-AAAGTATAACT +s simHuman_chr6.simHuman.chr6 465359 31 + 601863 TGAGTGTTAAGCCACTGTGG-GAAGTATAATT +s simMouse_chr6.simMouse.chr6 482213 29 + 636262 CCATTGGTAAGCCCA--TGT-GAAAAAATATT +s simRat_chr6.simRat.chr6 490496 29 + 647215 CCACTGTTAAGCCAA--TGT-GAAAAAATAAA +s simRat_chr6.simRat.chr6 491402 12 + 647215 TCAGTGCTGAGC-------------------- + +a +s simMouse_chr6.simMouse.chr6 483108 8 + 636262 ATAGCCAA +s Anc0.Anc0refChr3 99967 3 + 222631 ATA----- +s Anc1.Anc1refChr6 133268 3 + 197743 ATA----- +s Anc2.Anc2refChr1 11362 3 + 142988 TAA----- +s mr.mrrefChr3 37329 3 + 181027 ATA----- +s mr.mrrefChr3 36470 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 482243 3 + 636262 ATA----- +s simRat_chr6.simRat.chr6 490526 3 + 647215 ATA----- + +a +s simMouse_chr6.simMouse.chr6 483116 30 + 636262 ATTTGTAAGTAGATTGACCACAGTCATACC +s Anc0.Anc0refChr3 99970 30 + 222631 ATTCATGAATAGATGGGCCACAATCATGCA +s Anc1.Anc1refChr6 133271 30 + 197743 ATTCATGAATAGATGGGCCACAATCATGCA +s Anc2.Anc2refChr1 11365 30 + 142988 ATTCAGGAATAGATGGGCCACAATCATGCA +s mr.mrrefChr3 37332 30 + 181027 ATTTGTAAGTAGATTGACCACAGTCATACA +s mr.mrrefChr3 36478 30 + 181027 ATTCTTGGATTAGCAGACCACAATCCTGCA +s simCow_chr6.simCow.chr6 468077 30 + 602619 GTTCATGAATAGATGGGCCACAATCATGCA +s simDog_chr6.simDog.chr6 458050 30 + 593897 ATCCAGGAATGGATGGGCCACAATCATGTG +s simHuman_chr6.simHuman.chr6 465393 30 + 601863 ATTCACGAATAGATGGGCCACAATTTTACA +s simMouse_chr6.simMouse.chr6 482251 30 + 636262 ATTCTTGGATTAGCAGACCACAATCCTGCA +s simRat_chr6.simRat.chr6 490534 30 + 647215 ATTCTGGGATCACCAGACCACAATCTTGCA +s simRat_chr6.simRat.chr6 491414 27 + 647215 --TTGTA-GTAGATAAACCACAGTCATACA + +a +s simMouse_chr6.simMouse.chr6 483146 3 + 636262 TCA +s Anc0.Anc0refChr3 100000 3 + 222631 CCA +s Anc1.Anc1refChr6 133301 3 + 197743 CCA +s Anc2.Anc2refChr1 11395 3 + 142988 CCA +s mr.mrrefChr3 37362 3 + 181027 TCA +s mr.mrrefChr3 36508 3 + 181027 CCA +s simCow_chr6.simCow.chr6 468107 3 + 602619 CCA +s simDog_chr6.simDog.chr6 458080 3 + 593897 CCA +s simHuman_chr6.simHuman.chr6 465423 3 + 601863 CCA +s simMouse_chr6.simMouse.chr6 482298 3 + 636262 CCA +s simRat_chr6.simRat.chr6 490564 3 + 647215 CCA +s simRat_chr6.simRat.chr6 491441 3 + 647215 TCG + +a +s simMouse_chr6.simMouse.chr6 483149 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 37365 1 + 181027 T +s mr.mrrefChr3 36514 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 482304 1 + 636262 T +s simRat_chr6.simRat.chr6 490570 1 + 647215 C +s simRat_chr6.simRat.chr6 491444 1 + 647215 T a s simMouse_chr6.simMouse.chr6 483150 19 + 636262 TAAGAAACAAGATATATAG @@ -187844,6 +199080,67 @@ s simRat_chr6.simRat.chr6 497846 4 + 647215 ACCT a +s simMouse_chr6.simMouse.chr6 489949 25 + 636262 AAGTACTTATATAACCACACTCCCC +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 336944 25 + 636262 AAGTACTTATATAACCGCACTCCCC +s simRat_chr6.simRat.chr6 328069 25 + 647215 AAGTCCTTATCTAACCATACTCCAA + +a +s simMouse_chr6.simMouse.chr6 489974 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 336969 36 + 636262 AGACTTACATTTAGGACATAGTTATTAAGCTTATAG +s simRat_chr6.simRat.chr6 328094 33 + 647215 AGACTTACATTTAGGACATAGTTA---GGCTCATAT + +a +s simMouse_chr6.simMouse.chr6 490010 25 + 636262 CTTTTCCAATAACTCCCTCCTTATG +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 337005 25 + 636262 CTTTACCAATAACTCCCTCCTAATG +s simRat_chr6.simRat.chr6 328127 25 + 647215 ACTTACCCATGAGTCCCACCTAATG + +a +s simMouse_chr6.simMouse.chr6 490035 23 + 636262 AGATGTATGACCTCAATGGCTTG +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 337030 23 + 636262 AGATGTATGACCTCACTGGCTTG +s simRat_chr6.simRat.chr6 328152 23 + 647215 AGATGTATGAACTCAATCGCTTA + +a +s simMouse_chr6.simMouse.chr6 490058 7 + 636262 TATTTAT +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 337053 7 + 636262 TATTTAC +s simRat_chr6.simRat.chr6 328175 7 + 647215 TATTTAC + +a s simMouse_chr6.simMouse.chr6 490065 17 + 636262 TACAGCACACCAGGGAA s Anc0.Anc0refChr3 105996 17 + 222631 TACAGAGCAGCAAGGAA s Anc1.Anc1refChr6 139635 17 + 197743 TACAGAGCAGCAAGGAA @@ -188399,6 +199696,40 @@ s simRat_chr6.simRat.chr6 499312 5 + 647215 CAGCC a +s simMouse_chr6.simMouse.chr6 491178 4 + 636262 ACCA +s Anc0.Anc0refChr3 107396 4 + 222631 ACCA +s Anc1.Anc1refChr6 141067 4 + 197743 ACCA +s Anc2.Anc2refChr1 19272 4 + 142988 GCCC +s Anc2.Anc2refChr2 22804 4 - 27695 CCTG +s mr.mrrefChr0 40394 4 - 130230 ACCA +s mr.mrrefChr3 45364 4 + 181027 ACCA +s simCow_chr6.simCow.chr6 475764 4 + 602619 GCCC +s simDog_chr6.simDog.chr6 493223 4 - 593897 CCTG +s simDog_chr6.simDog.chr6 466198 4 + 593897 GTCC +s simHuman_chr6.simHuman.chr6 512266 4 - 601863 ACCA +s simHuman_chr6.simHuman.chr6 472921 4 + 601863 ACCA +s simMouse_chr6.simMouse.chr6 541568 4 - 636262 ACCA +s simRat_chr6.simRat.chr6 560388 4 - 647215 ACCA +s simRat_chr6.simRat.chr6 499317 4 + 647215 ACCA + +a +s simMouse_chr6.simMouse.chr6 491182 8 + 636262 ACTGGAAA +s Anc0.Anc0refChr3 107400 8 + 222631 ATTGGAAA +s Anc1.Anc1refChr6 141071 8 + 197743 ATTGGAAA +s Anc2.Anc2refChr1 19276 8 + 142988 ATTGGAAA +s Anc2.Anc2refChr2 22808 8 - 27695 ATTAGAAA +s mr.mrrefChr0 40398 8 - 130230 ATTGGAAA +s mr.mrrefChr3 45368 8 + 181027 ACTGGAAA +s simCow_chr6.simCow.chr6 475780 8 + 602619 GTTGGAAA +s simDog_chr6.simDog.chr6 493227 8 - 593897 ATTAGAAA +s simDog_chr6.simDog.chr6 466202 8 + 593897 ATTGGGAA +s simHuman_chr6.simHuman.chr6 512270 8 - 601863 ATTGGAAA +s simHuman_chr6.simHuman.chr6 472925 8 + 601863 ATTGGAAA +s simMouse_chr6.simMouse.chr6 541572 8 - 636262 ATTGGAAA +s simRat_chr6.simRat.chr6 560392 8 - 647215 TTTGGGAA +s simRat_chr6.simRat.chr6 499321 8 + 647215 ACTGGTAA + +a s simMouse_chr6.simMouse.chr6 491190 1 + 636262 A s Anc0.Anc0refChr3 107408 1 + 222631 A s Anc1.Anc1refChr6 141079 1 + 197743 A @@ -188410,23 +199741,162 @@ 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 +s simMouse_chr6.simMouse.chr6 491191 8 + 636262 GATGGAAG +s Anc0.Anc0refChr3 107409 8 + 222631 GATGGAAG +s Anc1.Anc1refChr6 141080 8 + 197743 GATGGAAG +s Anc2.Anc2refChr1 19285 8 + 142988 GATGGGAG +s Anc2.Anc2refChr2 22816 8 - 27695 GACAGAAA +s mr.mrrefChr0 40406 8 - 130230 TATGGCAG +s mr.mrrefChr3 45377 8 + 181027 GATGGAAG +s simCow_chr6.simCow.chr6 475789 8 + 602619 GATGGGAG +s simDog_chr6.simDog.chr6 493235 8 - 593897 GACAGAAA +s simDog_chr6.simDog.chr6 466211 8 + 593897 GATGGGAG +s simHuman_chr6.simHuman.chr6 512278 7 - 601863 GATGGAA- +s simHuman_chr6.simHuman.chr6 472934 7 + 601863 GATGGAA- +s simMouse_chr6.simMouse.chr6 541580 8 - 636262 TATGGCAG +s simRat_chr6.simRat.chr6 560400 8 - 647215 TATGGAGA +s simRat_chr6.simRat.chr6 499330 8 + 647215 GATGGAAG + +a +s simMouse_chr6.simMouse.chr6 491199 5 + 636262 AATGA +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 45385 5 + 181027 AACGA +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 499338 5 + 647215 GACGA + +a +s simMouse_chr6.simMouse.chr6 491204 2 + 636262 CA +s Anc0.Anc0refChr3 107419 2 + 222631 CA +s Anc1.Anc1refChr6 141091 2 + 197743 CA +s Anc2.Anc2refChr1 19295 2 + 142988 CA +s Anc2.Anc2refChr2 22826 2 - 27695 CT +s mr.mrrefChr0 40414 2 - 130230 TA +s mr.mrrefChr3 45390 2 + 181027 CA +s simCow_chr6.simCow.chr6 475799 2 + 602619 CA +s simDog_chr6.simDog.chr6 493245 2 - 593897 CT +s simDog_chr6.simDog.chr6 466221 2 + 593897 CA +s simHuman_chr6.simHuman.chr6 512288 2 - 601863 CA +s simHuman_chr6.simHuman.chr6 472944 2 + 601863 CA +s simMouse_chr6.simMouse.chr6 541588 2 - 636262 TA +s simRat_chr6.simRat.chr6 560408 2 - 647215 TT +s simRat_chr6.simRat.chr6 499343 2 + 647215 CA + +a +s simMouse_chr6.simMouse.chr6 491206 11 + 636262 GATAACAATGT +s Anc0.Anc0refChr3 107421 11 + 222631 GATAATAATGT +s Anc1.Anc1refChr6 141093 11 + 197743 GATAATAATGT +s Anc2.Anc2refChr1 19297 11 + 142988 GATAATAATGT +s Anc2.Anc2refChr2 22828 11 - 27695 AAAAATAATGC +s mr.mrrefChr0 40416 11 - 130230 GGTTGTTATAT +s mr.mrrefChr3 45392 11 + 181027 GATAATAATGT +s simCow_chr6.simCow.chr6 475801 11 + 602619 GATAATAATAT +s simDog_chr6.simDog.chr6 493247 11 - 593897 AAAAATAATGC +s simDog_chr6.simDog.chr6 466223 11 + 593897 GATAATAATGT +s simHuman_chr6.simHuman.chr6 512290 11 - 601863 GATAGTAATGT +s simHuman_chr6.simHuman.chr6 472946 11 + 601863 GATAATAATGT +s simMouse_chr6.simMouse.chr6 541592 11 - 636262 GGTTGTTATAT +s simRat_chr6.simRat.chr6 560410 11 - 647215 GTTTGTCATGT +s simRat_chr6.simRat.chr6 499345 11 + 647215 GACAATAACGT + +a +s simMouse_chr6.simMouse.chr6 491217 6 + 636262 TATCTC +s Anc0.Anc0refChr3 107432 6 + 222631 TATCTC +s Anc1.Anc1refChr6 141104 6 + 197743 TATCTC +s Anc2.Anc2refChr1 19308 6 + 142988 TATCTC +s mr.mrrefChr0 40427 6 - 130230 CAGCTC +s mr.mrrefChr3 45403 6 + 181027 TATCTC +s simCow_chr6.simCow.chr6 475812 6 + 602619 TATCTC +s simDog_chr6.simDog.chr6 466234 6 + 593897 TATCTC +s simHuman_chr6.simHuman.chr6 512301 6 - 601863 CATCTC +s simHuman_chr6.simHuman.chr6 472957 6 + 601863 TGTCTC +s simMouse_chr6.simMouse.chr6 541603 6 - 636262 CAGCTC +s simRat_chr6.simRat.chr6 560421 6 - 647215 AATCTC +s simRat_chr6.simRat.chr6 499356 6 + 647215 TATCTC + +a +s simMouse_chr6.simMouse.chr6 491223 10 + 636262 AGGCCAGCAA +s Anc0.Anc0refChr3 107438 10 + 222631 AGGGCAGCAA +s Anc1.Anc1refChr6 141110 10 + 197743 AGGGCAGCAA +s Anc2.Anc2refChr1 19314 10 + 142988 AGGGCAGCAA +s mr.mrrefChr0 40433 10 - 130230 AGCAAAGTGT +s mr.mrrefChr3 45409 10 + 181027 AGGCCAGCAA +s simCow_chr6.simCow.chr6 507266 10 - 602619 AAGACTATAC +s simCow_chr6.simCow.chr6 475818 10 + 602619 AGGGCAACCA +s simDog_chr6.simDog.chr6 466240 10 + 593897 AGGGCAGCAA +s simHuman_chr6.simHuman.chr6 512307 10 - 601863 AGGGAAGCAA +s simHuman_chr6.simHuman.chr6 472963 10 + 601863 AGGACAGCAA +s simMouse_chr6.simMouse.chr6 541609 10 - 636262 AGCAAAGTGT +s simRat_chr6.simRat.chr6 560427 10 - 647215 AGCAAAGCAT +s simRat_chr6.simRat.chr6 499362 6 + 647215 AGGCCA---- + +a +s simMouse_chr6.simMouse.chr6 491233 14 + 636262 CCACTAATAGATTG +s Anc0.Anc0refChr3 107448 14 + 222631 CCACTAATAGATTG +s Anc1.Anc1refChr6 141120 14 + 197743 CCACTAATAGATTG +s Anc2.Anc2refChr1 19324 14 + 142988 CCACTAATAGATTG +s mr.mrrefChr0 40443 14 - 130230 CCACTGATAGCTTG +s mr.mrrefChr3 45419 14 + 181027 CCACTAATAGATTG +s simCow_chr6.simCow.chr6 475828 14 + 602619 CCACTAATAGATTG +s simDog_chr6.simDog.chr6 466250 14 + 593897 CCACTAATAGATTG +s simHuman_chr6.simHuman.chr6 512317 14 - 601863 CCACTAATCCCTTG +s simHuman_chr6.simHuman.chr6 472973 14 + 601863 CCACTAATAGATTG +s simMouse_chr6.simMouse.chr6 541619 14 - 636262 CCACTGATAGCTTG +s simRat_chr6.simRat.chr6 560437 14 - 647215 CTACTGATAGCTCG +s simRat_chr6.simRat.chr6 499368 12 + 647215 --ACTAATAGATTG + +a +s simMouse_chr6.simMouse.chr6 491247 32 + 636262 GGATCAAATCAAGGAGGAGGGATTAAAATGGC +s Anc0.Anc0refChr3 107462 32 + 222631 GGATCAAATCAGGGAGGAGGGATTAAAATGGC +s Anc1.Anc1refChr6 141134 32 + 197743 GGATCAAATCAGGGAGGAGGGATTAAAATGGC +s Anc2.Anc2refChr1 19338 32 + 142988 GGATCAAATCAGGGAGGAGGGATTAAAATGGC +s mr.mrrefChr0 40457 32 - 130230 GGGCCAAAGGAGGGAGGAGCGGTCATAATAGC +s mr.mrrefChr3 45433 32 + 181027 GGATCAAATCAAGGAGGAGGGATTAAAATGGC +s simCow_chr6.simCow.chr6 507276 32 - 602619 AGGCCAAAGTAGGGGGGAAGGATTAAACCGGT +s simCow_chr6.simCow.chr6 475842 32 + 602619 GGATCAAATTAGGGAGGAGGGACTAAAATGGC +s simDog_chr6.simDog.chr6 466264 32 + 593897 GGATCAAATCAGGGAGGAGGGTCTAAAATGGC +s simHuman_chr6.simHuman.chr6 512331 32 - 601863 AGGCCAAAGCAGGGAGGAGGGATAAAAATAGC +s simHuman_chr6.simHuman.chr6 472987 32 + 601863 GGATCAAATCAGGGAGGAGGGATTAAAATGGC +s simMouse_chr6.simMouse.chr6 541633 32 - 636262 GGGCCAAAGGAGGGAGGAGCGGTCATAATAGC +s simRat_chr6.simRat.chr6 560451 32 - 647215 GGGCCAAATGAGGGAGGAGTGGTGATAATGGC +s simRat_chr6.simRat.chr6 499380 32 + 647215 GGATCAAATCAAGGAGGAGGGATTAAAATGGC + +a +s simMouse_chr6.simMouse.chr6 491279 4 + 636262 AAAA +s Anc0.Anc0refChr3 107494 4 + 222631 AAAA +s Anc1.Anc1refChr6 141166 4 + 197743 AAAA +s Anc2.Anc2refChr1 19370 4 + 142988 AAAA +s mr.mrrefChr0 40489 4 - 130230 CAAA +s mr.mrrefChr3 45465 4 + 181027 AAAA +s simCow_chr6.simCow.chr6 475874 4 + 602619 AAAA +s simDog_chr6.simDog.chr6 466296 4 + 593897 AAAA +s simHuman_chr6.simHuman.chr6 512363 4 - 601863 ACAA +s simHuman_chr6.simHuman.chr6 473019 4 + 601863 AAAA +s simMouse_chr6.simMouse.chr6 541665 4 - 636262 CAAA +s simRat_chr6.simRat.chr6 560483 4 - 647215 CAAA +s simRat_chr6.simRat.chr6 499412 4 + 647215 GAAA + +a +s simMouse_chr6.simMouse.chr6 491283 4 + 636262 GAGT +s Anc0.Anc0refChr3 107498 4 + 222631 GAGT +s Anc1.Anc1refChr6 141170 4 + 197743 GAGT +s Anc2.Anc2refChr1 19374 4 + 142988 GAGT +s mr.mrrefChr0 40493 4 - 130230 GGGT +s mr.mrrefChr3 45469 4 + 181027 GAGT +s simCow_chr6.simCow.chr6 507308 4 - 602619 GAGT +s simCow_chr6.simCow.chr6 475878 4 + 602619 AAGT +s simDog_chr6.simDog.chr6 466300 4 + 593897 GAGT +s simHuman_chr6.simHuman.chr6 512367 4 - 601863 GGGC +s simHuman_chr6.simHuman.chr6 473023 4 + 601863 GAGT +s simMouse_chr6.simMouse.chr6 541669 4 - 636262 GGGT +s simRat_chr6.simRat.chr6 560487 4 - 647215 GGGT +s simRat_chr6.simRat.chr6 499416 4 + 647215 GAGT a s simMouse_chr6.simMouse.chr6 491287 1 + 636262 G @@ -188442,6 +199912,22 @@ s simRat_chr6.simRat.chr6 499420 1 + 647215 G a +s simMouse_chr6.simMouse.chr6 491288 18 + 636262 AGTGGGCAGGTTGGGCCT +s Anc0.Anc0refChr3 107503 18 + 222631 AGTGGGCGGGTCAGGCAT +s Anc1.Anc1refChr6 141175 18 + 197743 AGTGGGCGGGTCAGGCAT +s Anc2.Anc2refChr1 19379 18 + 142988 AGTGGGCGGGTCAGGTAT +s mr.mrrefChr0 40497 18 - 130230 AGTTGGCATGTCAGGCCT +s mr.mrrefChr3 45474 18 + 181027 AGTGGGCAGGTTGGGCCT +s simCow_chr6.simCow.chr6 507313 18 - 602619 AGTAGGCGGATAAGATAT +s simCow_chr6.simCow.chr6 475883 18 + 602619 AGTGGGTGGGTCAGGAAT +s simDog_chr6.simDog.chr6 466305 18 + 593897 AATGGGCAGGTCAGGTTT +s simHuman_chr6.simHuman.chr6 512372 18 - 601863 AGTGGGTGGGTCAAACAT +s simHuman_chr6.simHuman.chr6 473028 18 + 601863 AGTGGGCGGGTTAGGCAT +s simMouse_chr6.simMouse.chr6 541673 18 - 636262 AGTTGGCATGTCAGGCCT +s simRat_chr6.simRat.chr6 560491 18 - 647215 AGTGGGCATGTCAGACCA +s simRat_chr6.simRat.chr6 499421 18 + 647215 AGTGGGCAGGTTGGGCCT + +a s simMouse_chr6.simMouse.chr6 491306 1 + 636262 G s Anc0.Anc0refChr3 107521 1 + 222631 G s Anc1.Anc1refChr6 141193 1 + 197743 G @@ -188455,6 +199941,54 @@ s simRat_chr6.simRat.chr6 499439 1 + 647215 G a +s simMouse_chr6.simMouse.chr6 491307 13 + 636262 TTGACCATGTACT +s Anc0.Anc0refChr3 107522 13 + 222631 TCAACCATATGCT +s Anc1.Anc1refChr6 141194 13 + 197743 TCAACCATATGCT +s Anc2.Anc2refChr1 19398 13 + 142988 TCAACCATATGCT +s mr.mrrefChr0 40515 13 - 130230 TCAACCACATTCT +s mr.mrrefChr3 45493 13 + 181027 TTGACCATGTACT +s simCow_chr6.simCow.chr6 507332 13 - 602619 TCAACCACAGGCT +s simCow_chr6.simCow.chr6 475902 13 + 602619 GCTATCATATGCT +s simDog_chr6.simDog.chr6 466324 13 + 593897 CAGACCACATGCT +s simHuman_chr6.simHuman.chr6 512391 13 - 601863 TCAGCCATGTGCT +s simHuman_chr6.simHuman.chr6 473047 13 + 601863 ACAACTGTATGCT +s simMouse_chr6.simMouse.chr6 541691 13 - 636262 TCAACCACATTCT +s simRat_chr6.simRat.chr6 560509 13 - 647215 TCAACCACATCCT +s simRat_chr6.simRat.chr6 499440 13 + 647215 TTGATCATCTACT + +a +s simMouse_chr6.simMouse.chr6 491320 5 + 636262 CCAAA +s Anc0.Anc0refChr3 107537 5 + 222631 TCAAG +s Anc1.Anc1refChr6 141209 5 + 197743 TCAAG +s Anc2.Anc2refChr1 19413 5 + 142988 TCAAG +s mr.mrrefChr0 40530 5 - 130230 TTGAT +s mr.mrrefChr3 45506 5 + 181027 CCAAA +s simCow_chr6.simCow.chr6 507347 5 - 602619 TCGAA +s simCow_chr6.simCow.chr6 475915 2 + 602619 ---AG +s simDog_chr6.simDog.chr6 466339 5 + 593897 TCAAG +s simHuman_chr6.simHuman.chr6 512406 5 - 601863 TCAAG +s simHuman_chr6.simHuman.chr6 473062 5 + 601863 CCAAG +s simMouse_chr6.simMouse.chr6 541706 5 - 636262 TTGAT +s simRat_chr6.simRat.chr6 560524 5 - 647215 TCAAT +s simRat_chr6.simRat.chr6 499453 5 + 647215 CCAAA + +a +s simMouse_chr6.simMouse.chr6 491325 5 + 636262 GTTAT +s Anc0.Anc0refChr3 107542 5 + 222631 GCTAT +s Anc1.Anc1refChr6 141214 5 + 197743 GCTAT +s Anc2.Anc2refChr1 19418 5 + 142988 GCGAT +s mr.mrrefChr0 40535 5 - 130230 TCTAT +s mr.mrrefChr3 45511 5 + 181027 GTTAT +s simCow_chr6.simCow.chr6 507352 5 - 602619 GCTAT +s simCow_chr6.simCow.chr6 475917 5 + 602619 GTGAT +s simDog_chr6.simDog.chr6 466344 4 + 593897 GC-AT +s simHuman_chr6.simHuman.chr6 512411 5 - 601863 ACTAT +s simHuman_chr6.simHuman.chr6 473075 5 + 601863 GTTAG +s simMouse_chr6.simMouse.chr6 541711 5 - 636262 TCTAT +s simRat_chr6.simRat.chr6 560529 5 - 647215 TCTAC +s simRat_chr6.simRat.chr6 499458 5 + 647215 GTTAT + +a s simMouse_chr6.simMouse.chr6 491330 5 + 636262 CCATG s Anc0.Anc0refChr3 107547 5 + 222631 CCACA s Anc1.Anc1refChr6 141219 5 + 197743 CCACA @@ -188468,6 +200002,22 @@ s simRat_chr6.simRat.chr6 499463 5 + 647215 CCATG a +s simMouse_chr6.simMouse.chr6 491335 10 + 636262 TGTTAGGGTG +s Anc0.Anc0refChr3 107552 10 + 222631 TGATAGGATG +s Anc1.Anc1refChr6 141224 10 + 197743 TGATAGGATG +s Anc2.Anc2refChr1 19428 10 + 142988 TGATAGGATG +s mr.mrrefChr0 40540 10 - 130230 TGCTATGATA +s mr.mrrefChr3 45521 10 + 181027 TGTTAGGGTG +s simCow_chr6.simCow.chr6 507362 10 - 602619 TTATAAGATG +s simCow_chr6.simCow.chr6 475927 10 + 602619 TGACAAGATG +s simDog_chr6.simDog.chr6 466353 10 + 593897 TGATAGGATA +s simHuman_chr6.simHuman.chr6 512421 10 - 601863 TGATAGGAGG +s simHuman_chr6.simHuman.chr6 473085 10 + 601863 TGATAGGATG +s simMouse_chr6.simMouse.chr6 541716 10 - 636262 TGCTATGATA +s simRat_chr6.simRat.chr6 560534 10 - 647215 TCCTATGATA +s simRat_chr6.simRat.chr6 499468 10 + 647215 TGTTAGCGTG + +a s simMouse_chr6.simMouse.chr6 491345 1 + 636262 C s Anc0.Anc0refChr3 107562 1 + 222631 C s Anc1.Anc1refChr6 141234 1 + 197743 C @@ -188481,6 +200031,148 @@ s simRat_chr6.simRat.chr6 499478 1 + 647215 C a +s simMouse_chr6.simMouse.chr6 491346 9 + 636262 TTTTGATAC +s Anc0.Anc0refChr3 107563 9 + 222631 TTTAGGTAC +s Anc1.Anc1refChr6 141235 9 + 197743 TTTAGGTAC +s Anc2.Anc2refChr1 19439 9 + 142988 TTTAGGTAC +s mr.mrrefChr0 40550 9 - 130230 TTTAGGTGC +s mr.mrrefChr3 45532 9 + 181027 TTTTGATAC +s simCow_chr6.simCow.chr6 507373 9 - 602619 TCTAGGTAC +s simCow_chr6.simCow.chr6 475938 9 + 602619 TTCAGATAC +s simDog_chr6.simDog.chr6 466364 9 + 593897 TTTAAGTAC +s simHuman_chr6.simHuman.chr6 512432 9 - 601863 TTTAGGTAC +s simHuman_chr6.simHuman.chr6 473096 9 + 601863 TTTAGATAC +s simMouse_chr6.simMouse.chr6 541726 9 - 636262 TTTAGGTGC +s simRat_chr6.simRat.chr6 560550 9 - 647215 TTTAGGTGC +s simRat_chr6.simRat.chr6 499479 9 + 647215 ATTTGATAC + +a +s simMouse_chr6.simMouse.chr6 491355 24 + 636262 CTTCATGTTTCTATGCTAGAATCA +s Anc0.Anc0refChr3 107581 24 + 222631 CTTGGTGTTTCTACACTTGTATCT +s Anc1.Anc1refChr6 141253 24 + 197743 CTTGGTGTTTCTACACTTGTATCT +s Anc2.Anc2refChr1 19457 24 + 142988 CTTGGTGTTTCTGCACTTGTATCT +s mr.mrrefChr0 40568 24 - 130230 GATGGTACTTCTATACTCGCATCT +s mr.mrrefChr3 45541 24 + 181027 CTTGGTGTTTCTATACTTGAATCA +s simCow_chr6.simCow.chr6 507391 24 - 602619 CTTGGTATTTCTCCACTTGCATCT +s simCow_chr6.simCow.chr6 475956 24 + 602619 CTTGATGTTTCTGCCCTTGTGCTT +s simDog_chr6.simDog.chr6 466382 24 + 593897 CTTGGTGTTTCTGCAATTGTATCT +s simHuman_chr6.simHuman.chr6 512450 24 - 601863 CTAGGTATTTCTACACCTGCATCT +s simHuman_chr6.simHuman.chr6 473114 24 + 601863 TGTGGTGTTTCTAGATGTGTATCT +s simMouse_chr6.simMouse.chr6 541744 24 - 636262 GATGGTACTTCTATACTCGCATCT +s simRat_chr6.simRat.chr6 560568 24 - 647215 GATGGTGCTTATAAACTTACATCT +s simRat_chr6.simRat.chr6 499488 24 + 647215 CTTGGTGTTTCCATACTTCAATCA + +a +s simMouse_chr6.simMouse.chr6 491379 1 + 636262 C +s Anc0.Anc0refChr3 107605 1 + 222631 C +s Anc1.Anc1refChr6 141277 1 + 197743 C +s Anc2.Anc2refChr1 19481 1 + 142988 C +s mr.mrrefChr0 40592 1 - 130230 C +s mr.mrrefChr3 45565 1 + 181027 C +s simCow_chr6.simCow.chr6 507415 1 - 602619 T +s simCow_chr6.simCow.chr6 475983 1 + 602619 C +s simDog_chr6.simDog.chr6 466406 1 + 593897 C +s simHuman_chr6.simHuman.chr6 512474 1 - 601863 C +s simHuman_chr6.simHuman.chr6 473138 1 + 601863 T +s simMouse_chr6.simMouse.chr6 541768 1 - 636262 C +s simRat_chr6.simRat.chr6 560592 1 - 647215 C +s simRat_chr6.simRat.chr6 499512 1 + 647215 C + +a +s simMouse_chr6.simMouse.chr6 491380 16 + 636262 AGGATAAGCATTCACT +s Anc0.Anc0refChr3 107606 16 + 222631 AGGACATGCATTCACT +s Anc1.Anc1refChr6 141278 16 + 197743 AGGACATGCATTCACT +s Anc2.Anc2refChr1 19482 16 + 142988 AGGACATGCCTTCACT +s mr.mrrefChr0 40593 16 - 130230 AGGACATGCTTTTGCT +s mr.mrrefChr3 45566 16 + 181027 AGGATAAGCATTCACT +s simCow_chr6.simCow.chr6 475984 16 + 602619 AGGACATGTCTCCACT +s simDog_chr6.simDog.chr6 466407 16 + 593897 AGGACATGCCTTCACT +s simHuman_chr6.simHuman.chr6 512475 16 - 601863 AGGACAGGCTTTCACT +s simHuman_chr6.simHuman.chr6 473139 16 + 601863 AGGACAGGCATTCACT +s simMouse_chr6.simMouse.chr6 541769 16 - 636262 AGGACATGCTTTTGCT +s simRat_chr6.simRat.chr6 560593 16 - 647215 AGGAAATGCTTTTCCT +s simRat_chr6.simRat.chr6 499513 16 + 647215 TGAATGAGCATTCAAT + +a +s simMouse_chr6.simMouse.chr6 491396 6 + 636262 ATACTA +s Anc0.Anc0refChr3 107623 6 + 222631 AGACTA +s Anc1.Anc1refChr6 141295 6 + 197743 AGACTA +s Anc2.Anc2refChr1 19499 6 + 142988 AGAATA +s mr.mrrefChr0 40610 6 - 130230 AGACTA +s mr.mrrefChr3 45582 6 + 181027 AGACTA +s simCow_chr6.simCow.chr6 476001 6 + 602619 TGACTA +s simDog_chr6.simDog.chr6 466424 6 + 593897 AGAATA +s simHuman_chr6.simHuman.chr6 512492 6 - 601863 AGACTA +s simHuman_chr6.simHuman.chr6 473156 6 + 601863 AGAATA +s simMouse_chr6.simMouse.chr6 541786 6 - 636262 AGACTA +s simRat_chr6.simRat.chr6 560610 6 - 647215 AGACTA +s simRat_chr6.simRat.chr6 499529 6 + 647215 GGACTG + +a +s simMouse_chr6.simMouse.chr6 491402 14 + 636262 GTACCAGCTGTTGT +s Anc0.Anc0refChr3 107629 14 + 222631 GCACCAGCTGTCAT +s Anc1.Anc1refChr6 141301 14 + 197743 GCACCAGCTGTCAT +s Anc2.Anc2refChr1 19505 14 + 142988 GCACCAGCTGTCAT +s mr.mrrefChr0 40616 14 - 130230 GTTTCAGCTGTCAT +s mr.mrrefChr3 45588 14 + 181027 GTACCAGCTGTCAT +s simCow_chr6.simCow.chr6 507416 14 - 602619 GCCCCAGCTGTCAT +s simCow_chr6.simCow.chr6 476007 14 + 602619 GCACCAGTTGTCCC +s simDog_chr6.simDog.chr6 466430 14 + 593897 GCACCAGCTGTCAC +s simHuman_chr6.simHuman.chr6 512498 14 - 601863 GCACCAGATGTCAT +s simHuman_chr6.simHuman.chr6 473162 14 + 601863 TCACCAGCTGACAT +s simMouse_chr6.simMouse.chr6 541792 14 - 636262 GTTTCAGCTGTCAT +s simRat_chr6.simRat.chr6 560616 14 - 647215 GCGCCAGCTGTCCT +s simRat_chr6.simRat.chr6 499535 14 + 647215 GTACCGGCTGTCAG + +a +s simMouse_chr6.simMouse.chr6 491416 6 + 636262 AATGTA +s Anc0.Anc0refChr3 107645 6 + 222631 ATTGCA +s Anc1.Anc1refChr6 141317 6 + 197743 ATTGCA +s Anc2.Anc2refChr1 19521 6 + 142988 ATTGCA +s mr.mrrefChr0 40632 6 - 130230 GATGCA +s mr.mrrefChr3 45602 6 + 181027 AATGTA +s simCow_chr6.simCow.chr6 507432 6 - 602619 ATTACA +s simCow_chr6.simCow.chr6 476023 6 + 602619 ATTACA +s simDog_chr6.simDog.chr6 466446 6 + 593897 ATTGCA +s simHuman_chr6.simHuman.chr6 512514 6 - 601863 ATTGCA +s simHuman_chr6.simHuman.chr6 473178 6 + 601863 ACTGCA +s simMouse_chr6.simMouse.chr6 541808 6 - 636262 GATGCA +s simRat_chr6.simRat.chr6 560632 6 - 647215 AATGCA +s simRat_chr6.simRat.chr6 499549 6 + 647215 AGTGTA + +a +s simMouse_chr6.simMouse.chr6 491422 4 + 636262 GACG +s Anc0.Anc0refChr3 107651 4 + 222631 GATG +s Anc1.Anc1refChr6 141323 4 + 197743 GATG +s Anc2.Anc2refChr1 19527 4 + 142988 GATC +s mr.mrrefChr0 40638 4 - 130230 GATG +s mr.mrrefChr3 45608 4 + 181027 AACG +s simCow_chr6.simCow.chr6 507445 4 - 602619 GATG +s simCow_chr6.simCow.chr6 476029 4 + 602619 GACC +s simDog_chr6.simDog.chr6 466452 4 + 593897 GATC +s simHuman_chr6.simHuman.chr6 512520 4 - 601863 TATG +s simHuman_chr6.simHuman.chr6 473184 4 + 601863 AACC +s simMouse_chr6.simMouse.chr6 541814 4 - 636262 GATG +s simRat_chr6.simRat.chr6 560638 4 - 647215 GATG +s simRat_chr6.simRat.chr6 499555 4 + 647215 AACC + +a +s simMouse_chr6.simMouse.chr6 491426 14 + 636262 TTCTATATCTTTAC +s Anc0.Anc0refChr3 107656 14 + 222631 GTGCATACATTTAT +s Anc1.Anc1refChr6 141328 14 + 197743 GTGCATACATTTAT +s Anc2.Anc2refChr1 19532 14 + 142988 GTGCATACATTTAT +s mr.mrrefChr0 40643 14 - 130230 CTACTTATATTTAT +s mr.mrrefChr3 45612 14 + 181027 GTCTATATCTTTAC +s simCow_chr6.simCow.chr6 507450 14 - 602619 GAGCACTCATCTAT +s simCow_chr6.simCow.chr6 476034 14 + 602619 GTGCATACATTTAT +s simDog_chr6.simDog.chr6 466457 14 + 593897 GTGCACACATCTCT +s simHuman_chr6.simHuman.chr6 512525 14 - 601863 ATGCTTACATTTAT +s simHuman_chr6.simHuman.chr6 473189 14 + 601863 GTGCATACATTTAT +s simMouse_chr6.simMouse.chr6 541819 14 - 636262 CTACTTATATTTAT +s simRat_chr6.simRat.chr6 560643 14 - 647215 GTACTTACATGTAT +s simRat_chr6.simRat.chr6 499559 14 + 647215 GTCTATATCTTTAC + +a s simMouse_chr6.simMouse.chr6 491440 2 + 636262 TG s Anc0.Anc0refChr3 107670 2 + 222631 AG s Anc1.Anc1refChr6 141342 2 + 197743 AG @@ -188492,6 +200184,299 @@ s simRat_chr6.simRat.chr6 499573 2 + 647215 TG a +s simMouse_chr6.simMouse.chr6 491442 12 + 636262 CCGACAAGGGAT +s Anc0.Anc0refChr3 107672 12 + 222631 ATGACAAGGAAT +s Anc1.Anc1refChr6 141344 12 + 197743 ATGACAAGGAAT +s Anc2.Anc2refChr1 19548 12 + 142988 ATGACAAGGAAT +s Anc2.Anc2refChr2 22841 12 - 27695 ATGACAAGCAGT +s mr.mrrefChr0 40657 12 - 130230 ATGCCAGATGGT +s mr.mrrefChr3 45628 12 + 181027 CCGACAAGGAAT +s simCow_chr6.simCow.chr6 507464 12 - 602619 ATGTTAAGCTGT +s simCow_chr6.simCow.chr6 476050 12 + 602619 GCAGTAAGGACT +s simDog_chr6.simDog.chr6 493364 12 - 593897 AGGACAACCAGT +s simDog_chr6.simDog.chr6 466473 12 + 593897 ATGACCAGGAAT +s simHuman_chr6.simHuman.chr6 512539 12 - 601863 ATGACAAGCAGT +s simHuman_chr6.simHuman.chr6 473205 11 + 601863 CTGACAAAGAA- +s simMouse_chr6.simMouse.chr6 541833 12 - 636262 ATGCCAGATGGT +s simRat_chr6.simRat.chr6 560657 12 - 647215 ATGCCAGGTAGT +s simRat_chr6.simRat.chr6 499575 12 + 647215 CCGACAAGGAAT + +a +s simMouse_chr6.simMouse.chr6 491454 5 + 636262 GATGA +s Anc0.Anc0refChr3 107684 5 + 222631 GGTGA +s Anc1.Anc1refChr6 141356 5 + 197743 GGTGA +s Anc2.Anc2refChr1 19560 5 + 142988 GGTGA +s Anc2.Anc2refChr2 22853 5 - 27695 GGTGA +s mr.mrrefChr0 40669 5 - 130230 GGTGT +s mr.mrrefChr3 45640 5 + 181027 GGTGA +s simCow_chr6.simCow.chr6 507476 5 - 602619 GGTGA +s simCow_chr6.simCow.chr6 476063 5 + 602619 GGAGA +s simDog_chr6.simDog.chr6 493376 5 - 593897 GGTGA +s simDog_chr6.simDog.chr6 466485 5 + 593897 GGTGA +s simHuman_chr6.simHuman.chr6 512551 5 - 601863 GGTGA +s simHuman_chr6.simHuman.chr6 473216 3 + 601863 --TGA +s simMouse_chr6.simMouse.chr6 541845 5 - 636262 GGTGT +s simRat_chr6.simRat.chr6 560669 5 - 647215 GGTGT +s simRat_chr6.simRat.chr6 499587 5 + 647215 AGTGA + +a +s simMouse_chr6.simMouse.chr6 491459 2 + 636262 CA +s Anc0.Anc0refChr3 107689 2 + 222631 GA +s Anc1.Anc1refChr6 141361 2 + 197743 GA +s Anc2.Anc2refChr1 19565 2 + 142988 GA +s Anc2.Anc2refChr2 22858 2 - 27695 GA +s mr.mrrefChr0 40674 2 - 130230 GA +s mr.mrrefChr3 45645 2 + 181027 GA +s simCow_chr6.simCow.chr6 476068 2 + 602619 GA +s simDog_chr6.simDog.chr6 493381 2 - 593897 GA +s simDog_chr6.simDog.chr6 466490 2 + 593897 GA +s simHuman_chr6.simHuman.chr6 512556 2 - 601863 GA +s simHuman_chr6.simHuman.chr6 473219 2 + 601863 GA +s simMouse_chr6.simMouse.chr6 541850 2 - 636262 GA +s simRat_chr6.simRat.chr6 560674 2 - 647215 GA +s simRat_chr6.simRat.chr6 499592 2 + 647215 GA + +a +s simMouse_chr6.simMouse.chr6 491461 9 + 636262 ACCAGTTCA +s Anc0.Anc0refChr3 107691 9 + 222631 AAGAGTTCA +s Anc1.Anc1refChr6 141363 9 + 197743 AAGAGTTCA +s Anc2.Anc2refChr1 19567 9 + 142988 GAGAGTCCA +s Anc2.Anc2refChr2 22860 9 - 27695 ATCAGTTCA +s mr.mrrefChr0 40676 9 - 130230 AATAGTTCA +s mr.mrrefChr3 45647 9 + 181027 ACCAGTTCA +s simCow_chr6.simCow.chr6 507481 9 - 602619 AGCAGTCTA +s simCow_chr6.simCow.chr6 476070 9 + 602619 GATAGTCCA +s simDog_chr6.simDog.chr6 493383 9 - 593897 ATCAGGTCA +s simDog_chr6.simDog.chr6 466492 9 + 593897 AAGAGTCCG +s simHuman_chr6.simHuman.chr6 512558 9 - 601863 AACAGTTCA +s simHuman_chr6.simHuman.chr6 473221 9 + 601863 GAGAGTTCA +s simMouse_chr6.simMouse.chr6 541852 9 - 636262 AATAGTTCA +s simRat_chr6.simRat.chr6 560676 9 - 647215 AACAGTTCA +s simRat_chr6.simRat.chr6 499594 9 + 647215 ACCAGTTCA + +a +s simMouse_chr6.simMouse.chr6 491470 5 + 636262 ACATG +s Anc0.Anc0refChr3 107700 5 + 222631 ACATG +s Anc1.Anc1refChr6 141372 5 + 197743 ACATG +s Anc2.Anc2refChr1 19576 5 + 142988 AGATG +s Anc2.Anc2refChr2 22869 5 - 27695 ACATG +s mr.mrrefChr0 40685 5 - 130230 ACATG +s mr.mrrefChr3 45656 5 + 181027 ACATG +s simCow_chr6.simCow.chr6 507490 5 - 602619 ACATG +s simCow_chr6.simCow.chr6 476085 5 + 602619 AGGTG +s simDog_chr6.simDog.chr6 493392 5 - 593897 GCATA +s simDog_chr6.simDog.chr6 466501 5 + 593897 AGATA +s simHuman_chr6.simHuman.chr6 512567 5 - 601863 ACATG +s simHuman_chr6.simHuman.chr6 473230 5 + 601863 ACATG +s simMouse_chr6.simMouse.chr6 541861 5 - 636262 ACATG +s simRat_chr6.simRat.chr6 560685 5 - 647215 ACCTG +s simRat_chr6.simRat.chr6 499603 5 + 647215 ACATG + +a +s simMouse_chr6.simMouse.chr6 491475 2 + 636262 TC +s Anc0.Anc0refChr3 107705 2 + 222631 TG +s Anc1.Anc1refChr6 141377 2 + 197743 TG +s Anc2.Anc2refChr1 19581 2 + 142988 TG +s Anc2.Anc2refChr2 22874 2 - 27695 TG +s mr.mrrefChr0 40690 2 - 130230 GG +s mr.mrrefChr3 45661 2 + 181027 TC +s simCow_chr6.simCow.chr6 507495 2 - 602619 TG +s simCow_chr6.simCow.chr6 476090 2 + 602619 AG +s simDog_chr6.simDog.chr6 493397 2 - 593897 AG +s simDog_chr6.simDog.chr6 466510 2 + 593897 TG +s simHuman_chr6.simHuman.chr6 512572 2 - 601863 TG +s simHuman_chr6.simHuman.chr6 473235 2 + 601863 CG +s simMouse_chr6.simMouse.chr6 541866 2 - 636262 GG +s simRat_chr6.simRat.chr6 560690 2 - 647215 GG +s simRat_chr6.simRat.chr6 499608 2 + 647215 TC + +a +s simMouse_chr6.simMouse.chr6 491477 2 + 636262 TA +s Anc0.Anc0refChr3 107707 2 + 222631 TA +s Anc1.Anc1refChr6 141379 2 + 197743 TA +s Anc2.Anc2refChr1 19583 2 + 142988 TA +s Anc2.Anc2refChr2 22876 2 - 27695 TA +s mr.mrrefChr0 40692 2 - 130230 CA +s mr.mrrefChr3 45663 2 + 181027 TA +s simCow_chr6.simCow.chr6 507500 2 - 602619 TG +s simCow_chr6.simCow.chr6 476092 2 + 602619 TA +s simDog_chr6.simDog.chr6 493399 2 - 593897 AA +s simDog_chr6.simDog.chr6 466512 2 + 593897 CA +s simHuman_chr6.simHuman.chr6 512574 2 - 601863 TA +s simHuman_chr6.simHuman.chr6 473237 1 + 601863 T- +s simMouse_chr6.simMouse.chr6 541868 2 - 636262 CA +s simRat_chr6.simRat.chr6 560692 2 - 647215 CA +s simRat_chr6.simRat.chr6 499610 2 + 647215 TA + +a +s simMouse_chr6.simMouse.chr6 491479 5 + 636262 GTTTT +s Anc0.Anc0refChr3 107797 5 + 222631 ATCTG +s Anc1.Anc1refChr6 141469 5 + 197743 ATCTG +s Anc2.Anc2refChr1 19670 5 + 142988 ATCTG +s Anc2.Anc2refChr2 22966 5 - 27695 ATCTA +s mr.mrrefChr0 40768 5 - 130230 AGTGA +s mr.mrrefChr3 45665 5 + 181027 GTTTA +s simCow_chr6.simCow.chr6 507596 5 - 602619 ATCTA +s simCow_chr6.simCow.chr6 476178 5 + 602619 ACCTG +s simDog_chr6.simDog.chr6 493489 5 - 593897 ATCCA +s simDog_chr6.simDog.chr6 466599 5 + 593897 ATCTG +s simHuman_chr6.simHuman.chr6 512665 5 - 601863 ATCTG +s simHuman_chr6.simHuman.chr6 473323 5 + 601863 ATCTG +s simMouse_chr6.simMouse.chr6 541944 5 - 636262 AGTGA +s simRat_chr6.simRat.chr6 560768 5 - 647215 GGTGA +s simRat_chr6.simRat.chr6 499612 5 + 647215 GTTCA + +a +s simMouse_chr6.simMouse.chr6 491484 11 + 636262 CCATCAAAACT +s Anc0.Anc0refChr3 107802 11 + 222631 CAAACAACCCT +s Anc1.Anc1refChr6 141474 11 + 197743 CAAACAACACT +s Anc2.Anc2refChr1 19675 11 + 142988 TAAACAACCCT +s Anc2.Anc2refChr2 22971 11 - 27695 CAAACAACCCT +s mr.mrrefChr0 40813 11 - 130230 AGATTAATGTA +s mr.mrrefChr3 45670 11 + 181027 CAATTGAAACT +s simCow_chr6.simCow.chr6 507601 11 - 602619 CAAGCAACCCT +s simCow_chr6.simCow.chr6 476183 11 + 602619 TAAACCACCCT +s simDog_chr6.simDog.chr6 493494 11 - 593897 CGAACAACCCT +s simDog_chr6.simDog.chr6 466604 10 + 593897 TAAACAACCC- +s simHuman_chr6.simHuman.chr6 512670 11 - 601863 CAAACAACACT +s simHuman_chr6.simHuman.chr6 473328 6 + 601863 CAAACA----- +s simMouse_chr6.simMouse.chr6 541989 11 - 636262 AGATTAATGTA +s simRat_chr6.simRat.chr6 560814 11 - 647215 GGAGTAATGTG +s simRat_chr6.simRat.chr6 499617 11 + 647215 CAGTTGAAACT + +a +s simMouse_chr6.simMouse.chr6 491495 1 + 636262 A +s Anc0.Anc0refChr3 107813 1 + 222631 A +s Anc1.Anc1refChr6 141485 1 + 197743 A +s Anc2.Anc2refChr1 19686 1 + 142988 G +s Anc2.Anc2refChr2 22982 1 - 27695 A +s mr.mrrefChr0 40824 1 - 130230 A +s mr.mrrefChr3 45681 1 + 181027 A +s simCow_chr6.simCow.chr6 507612 1 - 602619 A +s simCow_chr6.simCow.chr6 476194 1 + 602619 G +s simDog_chr6.simDog.chr6 493505 1 - 593897 A +s simDog_chr6.simDog.chr6 466614 1 + 593897 G +s simHuman_chr6.simHuman.chr6 512683 1 - 601863 A +s simHuman_chr6.simHuman.chr6 473334 1 + 601863 A +s simMouse_chr6.simMouse.chr6 542000 1 - 636262 A +s simRat_chr6.simRat.chr6 560825 1 - 647215 A +s simRat_chr6.simRat.chr6 499628 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 491496 5 + 636262 CCCTG +s Anc0.Anc0refChr3 107814 3 + 222631 CAC-- +s Anc1.Anc1refChr6 141486 5 + 197743 CCCTA +s Anc2.Anc2refChr1 19687 3 + 142988 CAT-- +s Anc2.Anc2refChr2 22983 3 - 27695 CAC-- +s mr.mrrefChr0 40825 5 - 130230 CCTTT +s mr.mrrefChr3 45682 5 + 181027 CCCTA +s simCow_chr6.simCow.chr6 476195 3 + 602619 TGC-- +s simDog_chr6.simDog.chr6 493506 3 - 593897 CAC-- +s simDog_chr6.simDog.chr6 466615 3 + 593897 CAT-- +s simHuman_chr6.simHuman.chr6 512684 5 - 601863 CATCT +s simHuman_chr6.simHuman.chr6 473335 5 + 601863 CTCTA +s simMouse_chr6.simMouse.chr6 542001 5 - 636262 CCTTC +s simRat_chr6.simRat.chr6 560826 5 - 647215 TCTTT +s simRat_chr6.simRat.chr6 499629 5 + 647215 CCGCA + +a +s simMouse_chr6.simMouse.chr6 491501 13 + 636262 CACATGACCTAAA +s Anc0.Anc0refChr3 107817 13 + 222631 CACATGAACTCAT +s Anc1.Anc1refChr6 141491 13 + 197743 CACATGAACTCAT +s Anc2.Anc2refChr1 19690 10 + 142988 ---ATGAACTCAT +s Anc2.Anc2refChr2 22986 13 - 27695 CACATGAACTCAT +s mr.mrrefChr0 40830 13 - 130230 CACATGAACTCAT +s mr.mrrefChr3 45687 13 + 181027 CACATGACCTCAA +s simCow_chr6.simCow.chr6 507613 13 - 602619 CACATGAACTCAT +s simCow_chr6.simCow.chr6 476198 10 + 602619 ---ATGAACTCAG +s simDog_chr6.simDog.chr6 466618 10 + 593897 ---ATGAACTCAT +s simHuman_chr6.simHuman.chr6 512689 13 - 601863 CACATCATCTCAT +s simHuman_chr6.simHuman.chr6 473340 13 + 601863 CAAATGAACTCAT +s simMouse_chr6.simMouse.chr6 542006 13 - 636262 CACATGAACTCAT +s simRat_chr6.simRat.chr6 560831 13 - 647215 TACATGAACTCAT +s simRat_chr6.simRat.chr6 499634 13 + 647215 CCCATGACCTCAA + +a +s simMouse_chr6.simMouse.chr6 491514 1 + 636262 T +s Anc0.Anc0refChr3 107830 1 + 222631 T +s Anc1.Anc1refChr6 141504 1 + 197743 T +s Anc2.Anc2refChr1 19700 1 + 142988 C +s mr.mrrefChr0 40843 1 - 130230 G +s mr.mrrefChr3 45700 1 + 181027 T +s simCow_chr6.simCow.chr6 476208 1 + 602619 C +s simDog_chr6.simDog.chr6 466628 1 + 593897 C +s simHuman_chr6.simHuman.chr6 512702 1 - 601863 T +s simHuman_chr6.simHuman.chr6 473353 1 + 601863 A +s simMouse_chr6.simMouse.chr6 542019 1 - 636262 G +s simRat_chr6.simRat.chr6 560844 1 - 647215 G +s simRat_chr6.simRat.chr6 499647 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 491515 1 + 636262 G +s Anc0.Anc0refChr3 107831 1 + 222631 G +s Anc1.Anc1refChr6 141505 1 + 197743 G +s Anc2.Anc2refChr1 19701 1 + 142988 A +s Anc2.Anc2refChr2 22999 1 - 27695 G +s mr.mrrefChr0 40844 1 - 130230 G +s mr.mrrefChr3 45701 1 + 181027 G +s simCow_chr6.simCow.chr6 507627 1 - 602619 G +s simCow_chr6.simCow.chr6 476209 1 + 602619 A +s simDog_chr6.simDog.chr6 466629 1 + 593897 A +s simHuman_chr6.simHuman.chr6 512703 1 - 601863 G +s simHuman_chr6.simHuman.chr6 473354 1 + 601863 G +s simMouse_chr6.simMouse.chr6 542020 1 - 636262 G +s simRat_chr6.simRat.chr6 560845 1 - 647215 G +s simRat_chr6.simRat.chr6 499648 1 + 647215 G + +a +s simMouse_chr6.simMouse.chr6 491516 2 + 636262 GT +s Anc0.Anc0refChr3 107832 2 + 222631 GC +s Anc1.Anc1refChr6 141506 2 + 197743 GC +s Anc2.Anc2refChr1 19702 2 + 142988 GC +s Anc2.Anc2refChr2 23000 2 - 27695 GT +s mr.mrrefChr0 40845 2 - 130230 GC +s mr.mrrefChr3 45702 2 + 181027 GC +s simCow_chr6.simCow.chr6 507628 2 - 602619 GT +s simCow_chr6.simCow.chr6 476210 2 + 602619 GC +s simDog_chr6.simDog.chr6 466630 1 + 593897 G- +s simHuman_chr6.simHuman.chr6 473355 2 + 601863 GC +s simMouse_chr6.simMouse.chr6 542021 2 - 636262 GC +s simRat_chr6.simRat.chr6 560846 2 - 647215 GC +s simRat_chr6.simRat.chr6 499649 2 + 647215 GC + +a +s simMouse_chr6.simMouse.chr6 491518 9 + 636262 CCATCTGGC +s Anc0.Anc0refChr3 107834 9 + 222631 CCATCTGGA +s Anc1.Anc1refChr6 141508 9 + 197743 CCATCTGGA +s Anc2.Anc2refChr1 19704 9 + 142988 CCATCTGGA +s Anc2.Anc2refChr2 23002 9 - 27695 CCATCCGGA +s mr.mrrefChr0 40847 9 - 130230 CAATCTGGA +s mr.mrrefChr3 45704 9 + 181027 CCATCTGGC +s simCow_chr6.simCow.chr6 507630 9 - 602619 CCATCCGGA +s simCow_chr6.simCow.chr6 476212 9 + 602619 CCATCTGGA +s simHuman_chr6.simHuman.chr6 512704 9 - 601863 TCATTCAGC +s simHuman_chr6.simHuman.chr6 473357 9 + 601863 CCTTCTGAA +s simMouse_chr6.simMouse.chr6 542023 9 - 636262 CAATCTGGA +s simRat_chr6.simRat.chr6 560848 9 - 647215 CAATCTGGA +s simRat_chr6.simRat.chr6 499651 9 + 647215 CCATCAGGC + +a +s simMouse_chr6.simMouse.chr6 491527 2 + 636262 CC +s Anc0.Anc0refChr3 107843 2 + 222631 CC +s Anc1.Anc1refChr6 141517 2 + 197743 CC +s Anc2.Anc2refChr1 19713 2 + 142988 CC +s Anc2.Anc2refChr2 23011 2 - 27695 CC +s mr.mrrefChr0 40856 2 - 130230 TC +s mr.mrrefChr3 45713 2 + 181027 CC +s simCow_chr6.simCow.chr6 507639 2 - 602619 CC +s simCow_chr6.simCow.chr6 476221 2 + 602619 CC +s simHuman_chr6.simHuman.chr6 512714 2 - 601863 CC +s simHuman_chr6.simHuman.chr6 473366 2 + 601863 CC +s simMouse_chr6.simMouse.chr6 542032 2 - 636262 TC +s simRat_chr6.simRat.chr6 560857 2 - 647215 TC +s simRat_chr6.simRat.chr6 499660 2 + 647215 CC + +a s simMouse_chr6.simMouse.chr6 491529 1 + 636262 C s Anc0.Anc0refChr3 107845 1 + 222631 C s Anc1.Anc1refChr6 141519 1 + 197743 C @@ -188505,11 +200490,135 @@ s simRat_chr6.simRat.chr6 499662 1 + 647215 C a +s simMouse_chr6.simMouse.chr6 491530 8 + 636262 ACTAGGTG +s Anc0.Anc0refChr3 107846 8 + 222631 ACTGAGAG +s Anc1.Anc1refChr6 141520 8 + 197743 ACTGAGAG +s Anc2.Anc2refChr1 19716 8 + 142988 AACTAGTG +s Anc2.Anc2refChr2 23014 8 - 27695 GCTAAGAG +s mr.mrrefChr0 40858 8 - 130230 ACTGTGAG +s mr.mrrefChr3 45716 8 + 181027 ACTAGGTG +s simCow_chr6.simCow.chr6 507642 8 - 602619 GCTAAAAG +s simCow_chr6.simCow.chr6 476224 8 + 602619 AACTAGTG +s simDog_chr6.simDog.chr6 493509 5 - 593897 ---AAGAG +s simDog_chr6.simDog.chr6 466631 1 + 593897 -------G +s simHuman_chr6.simHuman.chr6 512717 8 - 601863 ACTAAGAG +s simHuman_chr6.simHuman.chr6 473369 8 + 601863 AGTGAGAG +s simMouse_chr6.simMouse.chr6 542034 8 - 636262 ACTGTGAG +s simRat_chr6.simRat.chr6 560859 8 - 647215 GCTGTGAG +s simRat_chr6.simRat.chr6 499663 8 + 647215 ACTAGGTG + +a +s simMouse_chr6.simMouse.chr6 491538 10 + 636262 ATCAGAAGTG +s Anc0.Anc0refChr3 107856 10 + 222631 ATAAGGAAAA +s Anc1.Anc1refChr6 141530 10 + 197743 ATAAGGAAAA +s Anc2.Anc2refChr1 19726 9 + 142988 ATAAGAA-AA +s Anc2.Anc2refChr2 23024 10 - 27695 ATAAGGACAA +s mr.mrrefChr0 40868 10 - 130230 ATAAGCAAAA +s mr.mrrefChr3 45724 10 + 181027 ATCAGAAGTA +s simCow_chr6.simCow.chr6 507652 10 - 602619 AAAAGGGAAA +s simCow_chr6.simCow.chr6 476234 9 + 602619 ATAATAA-AA +s simDog_chr6.simDog.chr6 493517 10 - 593897 ATGGGCACAA +s simDog_chr6.simDog.chr6 466634 9 + 593897 ATAAGAA-AA +s simHuman_chr6.simHuman.chr6 512727 10 - 601863 ATAAGGAGGA +s simHuman_chr6.simHuman.chr6 473379 9 + 601863 AT-ATGAAAA +s simMouse_chr6.simMouse.chr6 542044 10 - 636262 TTAAGCAAAA +s simRat_chr6.simRat.chr6 560869 10 - 647215 ACGAGCAAAA +s simRat_chr6.simRat.chr6 499671 10 + 647215 ATCAGAAGCA + +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 491550 7 + 636262 TAGGGGC +s Anc0.Anc0refChr3 107866 7 + 222631 TAGGGAA +s Anc1.Anc1refChr6 141540 7 + 197743 TAGGGAA +s Anc2.Anc2refChr1 19735 7 + 142988 TAGGGAA +s Anc2.Anc2refChr2 23034 7 - 27695 TAGGGGA +s mr.mrrefChr0 40878 7 - 130230 TAGGGAA +s mr.mrrefChr3 45736 7 + 181027 TAGGGGC +s simCow_chr6.simCow.chr6 507662 7 - 602619 TAGGGGA +s simCow_chr6.simCow.chr6 476243 7 + 602619 TAGTGAA +s simDog_chr6.simDog.chr6 493527 7 - 593897 TGTGGGA +s simDog_chr6.simDog.chr6 466643 7 + 593897 TAGGGAA +s simHuman_chr6.simHuman.chr6 512737 7 - 601863 TAGGGAA +s simHuman_chr6.simHuman.chr6 473388 7 + 601863 CAGGGGT +s simMouse_chr6.simMouse.chr6 542054 7 - 636262 TAAGGAA +s simRat_chr6.simRat.chr6 560879 7 - 647215 TAGGGAA +s simRat_chr6.simRat.chr6 499683 7 + 647215 TAGGGGC + +a +s simMouse_chr6.simMouse.chr6 491557 3 + 636262 CTT +s Anc0.Anc0refChr3 107873 3 + 222631 CTT +s Anc1.Anc1refChr6 141547 3 + 197743 CTT +s Anc2.Anc2refChr1 19742 3 + 142988 CTT +s Anc2.Anc2refChr2 23041 3 - 27695 TTA +s mr.mrrefChr0 40885 3 - 130230 CCT +s mr.mrrefChr3 45743 3 + 181027 CTT +s simCow_chr6.simCow.chr6 507669 3 - 602619 TTA +s simCow_chr6.simCow.chr6 476250 3 + 602619 CCC +s simDog_chr6.simDog.chr6 466650 3 + 593897 CTT +s simHuman_chr6.simHuman.chr6 512744 3 - 601863 CCT +s simHuman_chr6.simHuman.chr6 473395 3 + 601863 CTT +s simMouse_chr6.simMouse.chr6 542061 3 - 636262 TCT +s simRat_chr6.simRat.chr6 560886 3 - 647215 CCT +s simRat_chr6.simRat.chr6 499690 3 + 647215 CTT + +a +s simMouse_chr6.simMouse.chr6 491560 4 + 636262 TGTC +s Anc0.Anc0refChr3 107876 4 + 222631 TGTC +s Anc1.Anc1refChr6 141550 4 + 197743 TGTC +s Anc2.Anc2refChr1 19745 4 + 142988 TGTC +s Anc2.Anc2refChr2 23044 4 - 27695 TGTC +s mr.mrrefChr0 40888 4 - 130230 TGGC +s mr.mrrefChr3 45746 4 + 181027 TGTC +s simCow_chr6.simCow.chr6 507672 4 - 602619 TGTC +s simCow_chr6.simCow.chr6 476253 4 + 602619 TGCC +s simDog_chr6.simDog.chr6 493534 4 - 593897 TGTC +s simDog_chr6.simDog.chr6 466653 4 + 593897 TGTC +s simHuman_chr6.simHuman.chr6 512747 4 - 601863 TGTG +s simHuman_chr6.simHuman.chr6 473398 4 + 601863 TGTC +s simMouse_chr6.simMouse.chr6 542064 4 - 636262 TGGC +s simRat_chr6.simRat.chr6 560889 4 - 647215 CGGC +s simRat_chr6.simRat.chr6 499693 4 + 647215 TGTC + +a +s simMouse_chr6.simMouse.chr6 491564 1 + 636262 T +s Anc0.Anc0refChr3 107880 1 + 222631 T +s Anc1.Anc1refChr6 141554 1 + 197743 T +s Anc2.Anc2refChr1 19749 1 + 142988 T +s Anc2.Anc2refChr2 23048 1 - 27695 T +s mr.mrrefChr0 40892 1 - 130230 T +s mr.mrrefChr3 45750 1 + 181027 T +s simCow_chr6.simCow.chr6 476257 1 + 602619 T +s simDog_chr6.simDog.chr6 493538 1 - 593897 T +s simDog_chr6.simDog.chr6 466657 1 + 593897 T +s simHuman_chr6.simHuman.chr6 512751 1 - 601863 T +s simHuman_chr6.simHuman.chr6 473402 1 + 601863 T +s simMouse_chr6.simMouse.chr6 542068 1 - 636262 T +s simRat_chr6.simRat.chr6 560893 1 - 647215 C +s simRat_chr6.simRat.chr6 499697 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 491565 9 + 636262 TGCAAACAA +s Anc0.Anc0refChr3 107881 9 + 222631 TGTAAACAA +s Anc1.Anc1refChr6 141555 9 + 197743 TGTAAACAA +s Anc2.Anc2refChr1 19750 9 + 142988 TTTAAACAA +s Anc2.Anc2refChr2 23049 9 - 27695 TGTTAACAT +s mr.mrrefChr0 40893 9 - 130230 TGTAAGTAA +s mr.mrrefChr3 45751 9 + 181027 TGTAAACAA +s simCow_chr6.simCow.chr6 507676 9 - 602619 TGTGAACAT +s simCow_chr6.simCow.chr6 476258 9 + 602619 TACAAACAA +s simDog_chr6.simDog.chr6 493539 9 - 593897 TGTTAACGT +s simDog_chr6.simDog.chr6 466658 4 + 593897 TTTA----- +s simHuman_chr6.simHuman.chr6 512752 9 - 601863 TGTAAACAA +s simHuman_chr6.simHuman.chr6 473403 9 + 601863 TGTATACAA +s simMouse_chr6.simMouse.chr6 542069 9 - 636262 TGTAAGTAA +s simRat_chr6.simRat.chr6 560894 9 - 647215 TGTAAGTAA +s simRat_chr6.simRat.chr6 499698 9 + 647215 TGTAATCAA + +a s simMouse_chr6.simMouse.chr6 491574 6 + 636262 ATTGCT s Anc0.Anc0refChr3 107890 6 + 222631 ATGGCT s Anc1.Anc1refChr6 141564 6 + 197743 ATAGCT @@ -188524,17 +200633,104 @@ 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 +s simMouse_chr6.simMouse.chr6 491580 1 + 636262 A +s Anc0.Anc0refChr3 107896 1 + 222631 G +s Anc1.Anc1refChr6 141570 1 + 197743 G +s Anc2.Anc2refChr1 19765 1 + 142988 A +s Anc2.Anc2refChr2 23064 1 - 27695 G +s mr.mrrefChr0 40902 1 - 130230 G +s mr.mrrefChr3 45766 1 + 181027 A +s simCow_chr6.simCow.chr6 507691 1 - 602619 A +s simCow_chr6.simCow.chr6 476273 1 + 602619 A +s simDog_chr6.simDog.chr6 493554 1 - 593897 G +s simHuman_chr6.simHuman.chr6 512768 1 - 601863 G +s simHuman_chr6.simHuman.chr6 473418 1 + 601863 G +s simMouse_chr6.simMouse.chr6 542078 1 - 636262 G +s simRat_chr6.simRat.chr6 560903 1 - 647215 G +s simRat_chr6.simRat.chr6 499713 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 491581 7 + 636262 GAGTTAA +s Anc0.Anc0refChr3 107898 7 + 222631 AAGTTAA +s Anc1.Anc1refChr6 141572 7 + 197743 GAGTTAA +s Anc2.Anc2refChr1 19767 7 + 142988 AAATTAA +s Anc2.Anc2refChr2 23066 7 - 27695 AAGTTAA +s mr.mrrefChr0 40904 7 - 130230 GAGTTAA +s mr.mrrefChr3 45768 7 + 181027 GAGTTAA +s simCow_chr6.simCow.chr6 507693 7 - 602619 AAGATAA +s simCow_chr6.simCow.chr6 476275 7 + 602619 AAATTAA +s simDog_chr6.simDog.chr6 493556 7 - 593897 AGGTTAA +s simHuman_chr6.simHuman.chr6 512770 7 - 601863 AAGTTAA +s simHuman_chr6.simHuman.chr6 473420 7 + 601863 GAGCTAA +s simMouse_chr6.simMouse.chr6 542080 7 - 636262 GAGTTAA +s simRat_chr6.simRat.chr6 560905 7 - 647215 GAGTCGA +s simRat_chr6.simRat.chr6 499715 7 + 647215 GAGTTAA + +a +s simMouse_chr6.simMouse.chr6 491588 6 + 636262 AGTAAT +s Anc0.Anc0refChr3 107905 6 + 222631 GCAAAT +s Anc1.Anc1refChr6 141579 6 + 197743 GCAAAT +s Anc2.Anc2refChr1 19774 6 + 142988 GCAAAT +s Anc2.Anc2refChr2 23073 6 - 27695 GCAAAT +s mr.mrrefChr0 40911 4 - 130230 GC--AT +s mr.mrrefChr3 45775 6 + 181027 AGTAAT +s simCow_chr6.simCow.chr6 507700 6 - 602619 GCAAAT +s simCow_chr6.simCow.chr6 476283 6 + 602619 GCAAAT +s simDog_chr6.simDog.chr6 493563 6 - 593897 GCAGAT +s simHuman_chr6.simHuman.chr6 512777 6 - 601863 GCAAAT +s simHuman_chr6.simHuman.chr6 473427 6 + 601863 GCAAAT +s simMouse_chr6.simMouse.chr6 542087 4 - 636262 GC--AT +s simRat_chr6.simRat.chr6 560912 4 - 647215 GC--AT +s simRat_chr6.simRat.chr6 499722 2 + 647215 TG---- + +a +s simMouse_chr6.simMouse.chr6 491594 7 + 636262 GTAATAA +s Anc0.Anc0refChr3 107911 7 + 222631 GTTATAA +s Anc1.Anc1refChr6 141585 7 + 197743 GTTATAA +s Anc2.Anc2refChr1 19780 7 + 142988 GTTATAA +s Anc2.Anc2refChr2 23079 7 - 27695 GTCATAA +s mr.mrrefChr0 40915 7 - 130230 GTCATAG +s mr.mrrefChr3 45781 7 + 181027 GTAATAA +s simCow_chr6.simCow.chr6 476289 7 + 602619 GTTATAA +s simDog_chr6.simDog.chr6 493569 7 - 593897 GTCATAA +s simHuman_chr6.simHuman.chr6 512783 7 - 601863 GTTATAA +s simHuman_chr6.simHuman.chr6 473433 7 + 601863 GTTATAA +s simMouse_chr6.simMouse.chr6 542091 7 - 636262 GTCATAG +s simRat_chr6.simRat.chr6 560916 7 - 647215 GTCATAG +s simRat_chr6.simRat.chr6 499724 5 + 647215 --AATAA + +a +s simMouse_chr6.simMouse.chr6 491601 3 + 636262 GAC +s Anc0.Anc0refChr3 107918 3 + 222631 GAC +s Anc1.Anc1refChr6 141592 3 + 197743 GAC +s Anc2.Anc2refChr1 19787 3 + 142988 TGC +s Anc2.Anc2refChr2 23086 3 - 27695 GAG +s mr.mrrefChr0 40922 3 - 130230 TAT +s mr.mrrefChr3 45788 3 + 181027 GAC +s simCow_chr6.simCow.chr6 476296 3 + 602619 TGC +s simDog_chr6.simDog.chr6 493576 3 - 593897 GAG +s simHuman_chr6.simHuman.chr6 512797 3 - 601863 GAC +s simHuman_chr6.simHuman.chr6 473440 3 + 601863 GAC +s simMouse_chr6.simMouse.chr6 542098 3 - 636262 TAT +s simRat_chr6.simRat.chr6 560923 3 - 647215 TAC +s simRat_chr6.simRat.chr6 499729 3 + 647215 GAC + +a +s simMouse_chr6.simMouse.chr6 491604 2 + 636262 AT +s Anc0.Anc0refChr3 107921 2 + 222631 AT +s Anc1.Anc1refChr6 141595 2 + 197743 AT +s Anc2.Anc2refChr1 19790 2 + 142988 AT +s Anc2.Anc2refChr2 23089 2 - 27695 AT +s mr.mrrefChr0 40925 2 - 130230 AT +s mr.mrrefChr3 45791 2 + 181027 AT +s simCow_chr6.simCow.chr6 507706 2 - 602619 AC +s simCow_chr6.simCow.chr6 476299 2 + 602619 AT +s simDog_chr6.simDog.chr6 493579 2 - 593897 AT +s simHuman_chr6.simHuman.chr6 512800 2 - 601863 AT +s simHuman_chr6.simHuman.chr6 473443 2 + 601863 AT +s simMouse_chr6.simMouse.chr6 542101 2 - 636262 AT +s simRat_chr6.simRat.chr6 560926 2 - 647215 AA +s simRat_chr6.simRat.chr6 499732 2 + 647215 AT a s simMouse_chr6.simMouse.chr6 491606 27 + 636262 GTCAACCTGCTTGGTGTCTAGTGAAAC @@ -189021,14 +201217,37 @@ 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 +s simMouse_chr6.simMouse.chr6 492845 9 + 636262 TATTAGATG +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 70543 9 + 636262 TAATCCTTG + +a +s simMouse_chr6.simMouse.chr6 492854 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 70552 78 + 636262 AGATGGAAAAGTGGCCTTAAGGTCCCGATCTGCATTTATGACACCTTAGTTTAATGTTAAAGGCCTCTAGCCAGTTCT + +a +s simMouse_chr6.simMouse.chr6 492932 4 + 636262 AGTC +s Anc0.Anc0refChr3 109234 4 + 222631 AGAC +s Anc1.Anc1refChr6 142974 4 + 197743 AGAC +s Anc2.Anc2refChr1 21175 4 + 142988 AGAC +s mr.mrrefChr3 47200 4 + 181027 AGTC +s simCow_chr6.simCow.chr6 477530 4 + 602619 GGAC +s simDog_chr6.simDog.chr6 467942 4 + 593897 AGAC +s simHuman_chr6.simHuman.chr6 474853 4 + 601863 AGAC +s simMouse_chr6.simMouse.chr6 70630 1 + 636262 A--- a s simMouse_chr6.simMouse.chr6 492936 60 + 636262 TTGATTTGATTGCCGAAGGATTTTTGATGTGGTCCCTAAAAGGTCTGATGAAAGTATAAT @@ -189911,11 +202130,109 @@ s simRat_chr6.simRat.chr6 503339 126 + 647215 TTTTAGTCCCATGCGTGGCCACTATTGTATGGTATAGATCTGATAGGTGTAGCGCGAGCTGGCACAGGGAAGACATTGTGCTATGTAATGCCCGGTCTCATTCACCTGGTGCTCCAGCCCAGGTCA a +s simMouse_chr6.simMouse.chr6 495631 4 + 636262 CCTT +s Anc0.Anc0refChr3 111827 4 + 222631 TCTT +s Anc1.Anc1refChr6 145626 4 + 197743 TCTT +s Anc2.Anc2refChr1 23904 4 + 142988 GCTT +s mr.mrrefChr3 49543 4 + 181027 CCTT +s mr.mrrefChr3 180926 4 - 181027 TTGT +s simCow_chr6.simCow.chr6 480231 4 + 602619 CCTC +s simDog_chr6.simDog.chr6 470568 4 + 593897 GCTT +s simHuman_chr6.simHuman.chr6 477524 4 + 601863 TCTT +s simMouse_chr6.simMouse.chr6 194482 4 - 636262 CTGT +s simRat_chr6.simRat.chr6 193352 4 - 647215 TTGT +s simRat_chr6.simRat.chr6 503465 4 + 647215 CCTT + +a +s simMouse_chr6.simMouse.chr6 495635 1 + 636262 A +s Anc0.Anc0refChr3 111833 1 + 222631 A +s Anc1.Anc1refChr6 145632 1 + 197743 A +s Anc2.Anc2refChr1 23912 1 + 142988 A +s mr.mrrefChr3 49547 1 + 181027 A +s mr.mrrefChr3 180930 1 - 181027 A +s simCow_chr6.simCow.chr6 480239 1 + 602619 A +s simDog_chr6.simDog.chr6 470576 1 + 593897 A +s simHuman_chr6.simHuman.chr6 477530 1 + 601863 A +s simMouse_chr6.simMouse.chr6 194486 1 - 636262 A +s simRat_chr6.simRat.chr6 193356 1 - 647215 A +s simRat_chr6.simRat.chr6 503469 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 495636 14 + 636262 TGTATTATTCCTGT +s Anc0.Anc0refChr3 111834 14 + 222631 TTTGTTATTCCTTT +s Anc1.Anc1refChr6 145633 14 + 197743 TTTGTTATTCCTTT +s Anc2.Anc2refChr1 23913 14 + 142988 TTTGTTCGTCCTTT +s mr.mrrefChr3 49548 14 + 181027 TGTATTATTCCTGT +s mr.mrrefChr3 180931 14 - 181027 TGTATGATTCCCAT +s simCow_chr6.simCow.chr6 480344 14 + 602619 TGTATTGGTCCATT +s simDog_chr6.simDog.chr6 470577 14 + 593897 TTTGTTCGTTATTT +s simHuman_chr6.simHuman.chr6 477531 14 + 601863 TTTGTAATTCCTTT +s simMouse_chr6.simMouse.chr6 194487 14 - 636262 TGTATGATTCCCAT +s simRat_chr6.simRat.chr6 193357 14 - 647215 TGTATGACTCCCAT +s simRat_chr6.simRat.chr6 503470 14 + 647215 TGTACGATTACTGT + +a +s simMouse_chr6.simMouse.chr6 495650 35 + 636262 TCTGATCTCCTGGATGCCGCTGAAGCTCGAATGAG +s Anc0.Anc0refChr3 111848 35 + 222631 TCTGATTTCTTGGATGCTCTTAAAGCTCCAACCAG +s Anc1.Anc1refChr6 145647 35 + 197743 TCTGATTTCTTGGATGCTCTTAAAGCTCCAACCAG +s Anc2.Anc2refChr1 23927 35 + 142988 TCTGATTTCTTGGCAACTCTTAAAGCTCCAACCAG +s mr.mrrefChr3 49562 35 + 181027 TCTGATCTCCTGGATGCCGCTGAAGCTCGAATGAG +s mr.mrrefChr3 180945 35 - 181027 TCTGATTTCTTTTACGCCACTAGAGCTCCAATCAG +s simCow_chr6.simCow.chr6 480358 35 + 602619 TCTGATTTCTTGATCACTCTTAAAGATTCAACCAG +s simDog_chr6.simDog.chr6 470591 35 + 593897 TCTGACTTCTTGGCAAACCTCAAAGCTCCAACCAG +s simHuman_chr6.simHuman.chr6 477545 35 + 601863 TCCAATTTCTTGGATGCTCTTGGAGCTCTAACCAG +s simMouse_chr6.simMouse.chr6 194501 35 - 636262 TCTGATTTCTTTTACGCCACTAGAGCTCCAATCAG +s simRat_chr6.simRat.chr6 193371 35 - 647215 TCTGGTTTCCTGGATGCCACTAAAGCTCCAACCAG +s simRat_chr6.simRat.chr6 507967 35 + 647215 tcgggtatcctgggtgccgctgaagctccattgag + +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 495686 3 + 636262 TTT +s Anc0.Anc0refChr3 111883 3 + 222631 TTT +s Anc1.Anc1refChr6 145682 3 + 197743 TTT +s Anc2.Anc2refChr1 23962 3 + 142988 TCT +s mr.mrrefChr3 49598 3 + 181027 TTt +s mr.mrrefChr3 180980 3 - 181027 CTT +s simCow_chr6.simCow.chr6 480393 3 + 602619 TCT +s simDog_chr6.simDog.chr6 470626 3 + 593897 TCT +s simHuman_chr6.simHuman.chr6 477580 3 + 601863 TTG +s simMouse_chr6.simMouse.chr6 194536 3 - 636262 CTT +s simRat_chr6.simRat.chr6 193406 3 - 647215 TTT +s simRat_chr6.simRat.chr6 508003 3 + 647215 ttt + +a +s simMouse_chr6.simMouse.chr6 495689 28 + 636262 ACCTACTTCAACAGTATCAATAAAAAAA +s Anc0.Anc0refChr3 111886 28 + 222631 ACTTTTGTCAACAGGATAAACAAAAAAA +s Anc1.Anc1refChr6 145685 28 + 197743 ACTTTTGTCAACAGGATAAACAAAAAAA +s Anc2.Anc2refChr1 23965 28 + 142988 ACTTTTGTCAACATGATAAACAAAATAA +s mr.mrrefChr3 49601 28 + 181027 ACCTTCTTCAACAGGATCAACAAAAAAA +s mr.mrrefChr3 180983 28 - 181027 AATTTTTTCACCAGGATAGACACAAAAA +s simCow_chr6.simCow.chr6 480396 28 + 602619 TCTTTGGTCAACAGGATACACAAAACAT +s simDog_chr6.simDog.chr6 470631 28 + 593897 ACTTTTGCCACCATGATAAACAAAATTA +s simHuman_chr6.simHuman.chr6 477583 28 + 601863 ACGTTTGTCAACAAGATAAACAAAAGAA +s simMouse_chr6.simMouse.chr6 194539 28 - 636262 AATTTTTTCACCAGGATAGACACAAAAA +s simRat_chr6.simRat.chr6 193409 28 - 647215 AATTTTTTAAACAGGATAAACAAAAAAA +s simRat_chr6.simRat.chr6 508006 28 + 647215 cccttcttcaacaggattaacaaaaaaa + +a +s simMouse_chr6.simMouse.chr6 495717 14 + 636262 CTTTGTAAGGGCAG +s Anc0.Anc0refChr3 111915 14 + 222631 CTGTATAGAGACAA +s Anc1.Anc1refChr6 145714 14 + 197743 CTGTATAGAGACAA +s Anc2.Anc2refChr1 23994 14 + 142988 CTGTATAGAAAAAA +s mr.mrrefChr3 49629 14 + 181027 CTTTATAAGGGCAG +s mr.mrrefChr3 181012 14 - 181027 CTGTATAAGGACAG +s simCow_chr6.simCow.chr6 480425 14 + 602619 CTGCATAGAAAAAA +s simDog_chr6.simDog.chr6 470660 14 + 593897 CTGTAAGGAAAAAG +s simHuman_chr6.simHuman.chr6 477612 14 + 601863 CTGTATAGAGATAA +s simMouse_chr6.simMouse.chr6 194568 14 - 636262 CTGTATAAGGACAG +s simRat_chr6.simRat.chr6 193438 14 - 647215 CTGTATAGGGACAG +s simRat_chr6.simRat.chr6 508034 14 + 647215 ccttataagggcgG + +a s simMouse_chr6.simMouse.chr6 495731 1 + 636262 C s Anc0.Anc0refChr3 111929 1 + 222631 C s Anc1.Anc1refChr6 145728 1 + 197743 C @@ -189927,16 +202244,30 @@ 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 +s simMouse_chr6.simMouse.chr6 495732 3 + 636262 TGA +s Anc0.Anc0refChr3 111930 3 + 222631 TGG +s Anc1.Anc1refChr6 145729 3 + 197743 TGG +s Anc2.Anc2refChr1 24009 3 + 142988 TGG +s mr.mrrefChr3 49644 3 + 181027 TGG +s simCow_chr6.simCow.chr6 480443 3 + 602619 TGG +s simDog_chr6.simDog.chr6 470675 3 + 593897 TGG +s simHuman_chr6.simHuman.chr6 477627 3 + 601863 TGG +s simMouse_chr6.simMouse.chr6 194583 3 - 636262 TGG +s simRat_chr6.simRat.chr6 193453 3 - 647215 CAA +s simRat_chr6.simRat.chr6 508049 3 + 647215 TGG + +a +s simMouse_chr6.simMouse.chr6 495735 13 + 636262 ATAATTTGCCTCC +s Anc0.Anc0refChr3 111934 13 + 222631 GTAAATTGGTCCA +s Anc1.Anc1refChr6 145733 13 + 197743 GTAAATTGGTCCA +s Anc2.Anc2refChr1 24013 13 + 142988 ATAAATTGGTCCA +s mr.mrrefChr3 49648 13 + 181027 GTAATTTGCTTCA +s simCow_chr6.simCow.chr6 480447 13 + 602619 ATAAGTTGGTTCA +s simDog_chr6.simDog.chr6 470679 13 + 593897 AGGAATTGGTCCA +s simHuman_chr6.simHuman.chr6 477631 13 + 601863 GTAACTTTGTCCA +s simMouse_chr6.simMouse.chr6 194587 1 - 636262 G------------ +s simRat_chr6.simRat.chr6 193457 13 - 647215 GTGGTTTGGTTCA +s simRat_chr6.simRat.chr6 508053 13 + 647215 GTTATTTGCTTCA a s simMouse_chr6.simMouse.chr6 495748 27 + 636262 CTGCAGATTCTTATGATGCTTACAATA @@ -190022,16 +202353,30 @@ 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 +s simMouse_chr6.simMouse.chr6 495900 5 + 636262 TTAAG +s Anc0.Anc0refChr3 112111 5 + 222631 TCAAG +s Anc1.Anc1refChr6 145910 5 + 197743 TCAAG +s Anc2.Anc2refChr1 24190 5 + 142988 TCAAG +s mr.mrrefChr3 49816 5 + 181027 TTAAG +s simCow_chr6.simCow.chr6 480601 5 + 602619 TTGCG +s simDog_chr6.simDog.chr6 470874 5 + 593897 TCAAG +s simHuman_chr6.simHuman.chr6 477808 5 + 601863 TCAAG +s simMouse_chr6.simMouse.chr6 194588 1 - 636262 ----G +s simRat_chr6.simRat.chr6 193627 5 - 647215 CCAAG +s simRat_chr6.simRat.chr6 508210 5 + 647215 TTAAG + +a +s simMouse_chr6.simMouse.chr6 495905 28 + 636262 ATTTGGTAGAGTGGACTATCTACATTTT +s Anc0.Anc0refChr3 112116 28 + 222631 GTTGGCTAGAGTAAACTTTCCACATCTT +s Anc1.Anc1refChr6 145915 28 + 197743 GTTGGCTAGAGTAAACTTTCCACATCTT +s Anc2.Anc2refChr1 24195 28 + 142988 GTTAGCTAGAGTAAACTTTCCTTATCTT +s mr.mrrefChr3 49821 28 + 181027 ATTGGCTAGAGTGAACTGTCCACATCTC +s simCow_chr6.simCow.chr6 480606 28 + 602619 GTTTGCTAGAGTAAACTTTCATGGTCCT +s simDog_chr6.simDog.chr6 470885 28 + 593897 GCTAGCTAGGGTAAACTTTCCTTATCTT +s simHuman_chr6.simHuman.chr6 477813 28 + 601863 GTTGGCTAGAGTAAACTTTCCACATCTT +s simMouse_chr6.simMouse.chr6 194589 28 - 636262 AATGGCTAGTGTGAACTGTTCATGACTC +s simRat_chr6.simRat.chr6 193632 28 - 647215 AATGGCTAGTGTGAACTGTCCACATCTC +s simRat_chr6.simRat.chr6 508215 28 + 647215 ATGTGGTAGAGTGAGCTGTCCACATTTA a s simMouse_chr6.simMouse.chr6 495933 1 + 636262 G @@ -190045,7 +202390,143 @@ s simRat_chr6.simRat.chr6 508243 1 + 647215 G a -s simMouse_chr6.simMouse.chr6 495940 1 + 636262 A +s simMouse_chr6.simMouse.chr6 495934 12 + 636262 AGAAGTATATAA +s Anc0.Anc0refChr3 112145 10 + 222631 -GGTAT-TATAA +s Anc1.Anc1refChr6 145944 11 + 197743 AGGTAT-TATAA +s Anc2.Anc2refChr1 24224 10 + 142988 -GGTAT-TATAA +s mr.mrrefChr3 49850 11 + 181027 AGACGT-TATAA +s simCow_chr6.simCow.chr6 480635 10 + 602619 -GGTAT-TATAA +s simDog_chr6.simDog.chr6 470914 10 + 593897 -TGTAT-TAGGA +s simHuman_chr6.simHuman.chr6 477842 11 + 601863 AGGGAT-TATAG +s simMouse_chr6.simMouse.chr6 194617 11 - 636262 AAACAT-TATAA +s simRat_chr6.simRat.chr6 193660 11 - 647215 AAACGT-CAAAA +s simRat_chr6.simRat.chr6 508244 11 + 647215 AGTGGT-ATTAG + +a +s simMouse_chr6.simMouse.chr6 495946 3 + 636262 TTG +s Anc0.Anc0refChr3 112155 3 + 222631 CTG +s Anc1.Anc1refChr6 145955 3 + 197743 CTG +s Anc2.Anc2refChr1 24234 3 + 142988 CTG +s mr.mrrefChr3 49861 3 + 181027 CTG +s simCow_chr6.simCow.chr6 480645 3 + 602619 CTG +s simDog_chr6.simDog.chr6 470924 3 + 593897 CTG +s simHuman_chr6.simHuman.chr6 477853 3 + 601863 CTG +s simMouse_chr6.simMouse.chr6 194628 3 - 636262 CTG +s simRat_chr6.simRat.chr6 193671 3 - 647215 CGG +s simRat_chr6.simRat.chr6 508305 3 + 647215 TTG + +a +s simMouse_chr6.simMouse.chr6 495949 17 + 636262 TTAAAAGAAGAAAAGCG +s Anc0.Anc0refChr3 112161 17 + 222631 TTGAAAAAGGAAAAGCC +s Anc1.Anc1refChr6 145961 17 + 197743 TTGAAAAAGGAAAAGCC +s Anc2.Anc2refChr1 24240 17 + 142988 TTGAAAAAGGAAAAGCC +s mr.mrrefChr3 49867 17 + 181027 TTAAAAAAGGAAAAGCT +s simCow_chr6.simCow.chr6 480651 17 + 602619 CTAAAAAAAGATAAGCC +s simDog_chr6.simDog.chr6 470930 17 + 593897 TTGAAAAAGGAAAAGCC +s simHuman_chr6.simHuman.chr6 477859 17 + 601863 TTGAGAAAGGAAAAGCC +s simMouse_chr6.simMouse.chr6 194634 17 - 636262 TTAGAAAAGGACAAGTT +s simRat_chr6.simRat.chr6 193677 17 - 647215 TTAGACAAAGAAAAGTT +s simRat_chr6.simRat.chr6 508311 17 + 647215 TGAAATGAGGAAAAGCC + +a +s simMouse_chr6.simMouse.chr6 495966 18 + 636262 ATACAATAAGTGGAAACA +s Anc0.Anc0refChr3 112178 18 + 222631 ATATAATAAGTCAAATCA +s Anc1.Anc1refChr6 145978 18 + 197743 ATATAATAAGTCAAATCA +s Anc2.Anc2refChr1 24257 18 + 142988 ATATAATAAGTCAAATCA +s mr.mrrefChr3 49884 18 + 181027 ATACAGTAAGTGAAATCA +s simCow_chr6.simCow.chr6 480668 14 + 602619 ATACTTTGAGCCAA---- +s simDog_chr6.simDog.chr6 470947 18 + 593897 ATATAATAAGTCAAATCA +s simHuman_chr6.simHuman.chr6 477877 18 + 601863 AAATCATAAGTCAAATCT +s simMouse_chr6.simMouse.chr6 194651 18 - 636262 GTATAGTAAGTTATATCA +s simRat_chr6.simRat.chr6 193694 18 - 647215 GTAAAGTAAGTCATATCA +s simRat_chr6.simRat.chr6 508328 18 + 647215 ATACAGCAAGTGAAAACA + +a +s simMouse_chr6.simMouse.chr6 495984 1 + 636262 G +s Anc0.Anc0refChr3 112196 1 + 222631 G +s Anc1.Anc1refChr6 145996 1 + 197743 G +s Anc2.Anc2refChr1 24275 1 + 142988 G +s mr.mrrefChr3 49902 1 + 181027 G +s simDog_chr6.simDog.chr6 470968 1 + 593897 G +s simHuman_chr6.simHuman.chr6 477895 1 + 601863 G +s simMouse_chr6.simMouse.chr6 194669 1 - 636262 G +s simRat_chr6.simRat.chr6 193712 1 - 647215 G +s simRat_chr6.simRat.chr6 508346 1 + 647215 G + +a +s simMouse_chr6.simMouse.chr6 495985 10 + 636262 TGAGGAAATT +s Anc0.Anc0refChr3 112197 10 + 222631 TTAGGATATT +s Anc1.Anc1refChr6 145997 10 + 197743 TTAGGATATT +s Anc2.Anc2refChr1 24276 10 + 142988 TTATGATATT +s mr.mrrefChr3 49903 10 + 181027 TGAGGATATT +s simCow_chr6.simCow.chr6 480682 10 + 602619 TTACGATATT +s simDog_chr6.simDog.chr6 470969 10 + 593897 TTGTGATATT +s simHuman_chr6.simHuman.chr6 477896 10 + 601863 TTAGGATAAT +s simMouse_chr6.simMouse.chr6 194679 10 - 636262 TGAGGATATT +s simRat_chr6.simRat.chr6 193713 10 - 647215 TGAGGACATT +s simRat_chr6.simRat.chr6 508347 10 + 647215 TGAGGATATT + +a +s simMouse_chr6.simMouse.chr6 495995 15 + 636262 CCAATTCTTGAGGCT +s Anc0.Anc0refChr3 112207 15 + 222631 CCAACTGTTAAGGCT +s Anc1.Anc1refChr6 146007 15 + 197743 CCAACTGTTAAGGCT +s Anc2.Anc2refChr1 24286 15 + 142988 CCAACTGTTAAGGCT +s mr.mrrefChr3 49913 15 + 181027 CCAATTGTTAAGGCT +s simCow_chr6.simCow.chr6 480693 15 + 602619 CCAGCCATCAAGGCG +s simDog_chr6.simDog.chr6 470979 15 + 593897 CGAATTGATAAGGTT +s simHuman_chr6.simHuman.chr6 477906 15 + 601863 CCAACTGTTAAGGCT +s simMouse_chr6.simMouse.chr6 194689 15 - 636262 TCAATAGTTAATTCT +s simRat_chr6.simRat.chr6 193723 15 - 647215 CCTACAGTGAATGCT +s simRat_chr6.simRat.chr6 508357 15 + 647215 CCAATTCTTGAGGTA + +a +s simMouse_chr6.simMouse.chr6 496010 16 + 636262 CTGCCAGGTTCTATGG +s Anc0.Anc0refChr3 112222 16 + 222631 CTGCCATGTTCTACAT +s Anc1.Anc1refChr6 146022 16 + 197743 CTGCCATGTTCTACAT +s Anc2.Anc2refChr1 24301 16 + 142988 GTGCTATGTTCTACAT +s mr.mrrefChr3 49928 16 + 181027 CTGCCAGGTTCTACAT +s simCow_chr6.simCow.chr6 480711 16 + 602619 GTTCTATGTTCTACAT +s simDog_chr6.simDog.chr6 470994 10 + 593897 GTGCTACGTT------ +s simHuman_chr6.simHuman.chr6 477921 16 + 601863 CTGCCATGTTCCAGAT +s simMouse_chr6.simMouse.chr6 194704 16 - 636262 CTACCAGGTTCTGCAT +s simRat_chr6.simRat.chr6 193738 16 - 647215 CTGCCAGGTTATGCAT +s simRat_chr6.simRat.chr6 508372 16 + 647215 CTGCCAGGTTCTATAT + +a +s simMouse_chr6.simMouse.chr6 496026 11 + 636262 CTATACAAATT +s Anc0.Anc0refChr3 112246 8 + 222631 ATATAT---TA +s Anc1.Anc1refChr6 146046 11 + 197743 ATATATAAATA +s Anc2.Anc2refChr1 24325 8 + 142988 ATATGT---TA +s mr.mrrefChr3 49952 11 + 181027 CTATATAAATT +s simCow_chr6.simCow.chr6 480735 8 + 602619 ATATGT---TA +s simHuman_chr6.simHuman.chr6 477945 11 + 601863 TTATATAAATA +s simMouse_chr6.simMouse.chr6 194728 11 - 636262 ATATATAAATT +s simRat_chr6.simRat.chr6 193762 11 - 647215 CTATATGAATT +s simRat_chr6.simRat.chr6 508396 11 + 647215 TTATACAAAAT + +a +s simMouse_chr6.simMouse.chr6 496037 2 + 636262 CA +s Anc0.Anc0refChr3 112254 2 + 222631 CA +s Anc1.Anc1refChr6 146057 2 + 197743 CA +s Anc2.Anc2refChr1 24333 2 + 142988 CA +s mr.mrrefChr3 49963 2 + 181027 CA +s simCow_chr6.simCow.chr6 480743 2 + 602619 CA +s simHuman_chr6.simHuman.chr6 477956 2 + 601863 CA +s simMouse_chr6.simMouse.chr6 194746 2 - 636262 CG +s simRat_chr6.simRat.chr6 193773 2 - 647215 TA +s simRat_chr6.simRat.chr6 508407 2 + 647215 CA + +a +s simMouse_chr6.simMouse.chr6 496039 4 + 636262 GCCG +s Anc0.Anc0refChr3 112259 4 + 222631 GCTA +s Anc1.Anc1refChr6 146062 4 + 197743 GCTA +s Anc2.Anc2refChr1 24338 4 + 142988 ACAA +s mr.mrrefChr3 49965 4 + 181027 GTTG +s simCow_chr6.simCow.chr6 480748 4 + 602619 ACAA +s simHuman_chr6.simHuman.chr6 477961 4 + 601863 GCTC +s simMouse_chr6.simMouse.chr6 194748 4 - 636262 GTTG +s simRat_chr6.simRat.chr6 193775 4 - 647215 GTTG +s simRat_chr6.simRat.chr6 508409 4 + 647215 TTTG a s simMouse_chr6.simMouse.chr6 496043 1 + 636262 C @@ -190058,15 +202539,158 @@ 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 +s simMouse_chr6.simMouse.chr6 496044 6 + 636262 CCATGT +s Anc0.Anc0refChr3 112264 6 + 222631 TCATGG +s Anc1.Anc1refChr6 146067 6 + 197743 TCATGG +s Anc2.Anc2refChr1 24343 6 + 142988 TCATAG +s mr.mrrefChr3 49970 6 + 181027 CCATGT +s simCow_chr6.simCow.chr6 480753 6 + 602619 TCATAG +s simHuman_chr6.simHuman.chr6 477966 6 + 601863 ACATGG +s simMouse_chr6.simMouse.chr6 194752 6 - 636262 CCATGT +s simRat_chr6.simRat.chr6 193779 6 - 647215 CCATGT +s simRat_chr6.simRat.chr6 508414 6 + 647215 CCATGT + +a +s simMouse_chr6.simMouse.chr6 496050 2 + 636262 AT +s Anc0.Anc0refChr3 112270 2 + 222631 AT +s Anc1.Anc1refChr6 146073 2 + 197743 AT +s Anc2.Anc2refChr1 24349 2 + 142988 AC +s mr.mrrefChr3 49976 2 + 181027 AT +s simCow_chr6.simCow.chr6 480774 2 + 602619 AC +s simHuman_chr6.simHuman.chr6 477972 2 + 601863 AT +s simMouse_chr6.simMouse.chr6 194758 2 - 636262 AT +s simRat_chr6.simRat.chr6 193785 2 - 647215 AT +s simRat_chr6.simRat.chr6 508420 2 + 647215 AT + +a +s simMouse_chr6.simMouse.chr6 496052 7 + 636262 GAAGAGA +s Anc0.Anc0refChr3 112273 7 + 222631 AATCATA +s Anc1.Anc1refChr6 146076 7 + 197743 AATCATA +s Anc2.Anc2refChr1 24352 7 + 142988 ATTCATA +s mr.mrrefChr3 49978 7 + 181027 AATCAGA +s simCow_chr6.simCow.chr6 480777 7 + 602619 ATTCATA +s simHuman_chr6.simHuman.chr6 477975 7 + 601863 AATCAAG +s simMouse_chr6.simMouse.chr6 194760 7 - 636262 AATCAAA +s simRat_chr6.simRat.chr6 193787 7 - 647215 AATCAAA +s simRat_chr6.simRat.chr6 508422 7 + 647215 TATCAGA + +a +s simMouse_chr6.simMouse.chr6 496059 2 + 636262 GT +s Anc0.Anc0refChr3 112280 2 + 222631 AT +s Anc1.Anc1refChr6 146083 2 + 197743 AT +s Anc2.Anc2refChr1 24359 2 + 142988 GT +s mr.mrrefChr3 49985 2 + 181027 AT +s simCow_chr6.simCow.chr6 480784 2 + 602619 GT +s simHuman_chr6.simHuman.chr6 477982 2 + 601863 AG +s simMouse_chr6.simMouse.chr6 194767 2 - 636262 AT +s simRat_chr6.simRat.chr6 508429 2 + 647215 AT + +a +s simMouse_chr6.simMouse.chr6 496061 14 + 636262 TTCTTAGTTATGCA +s Anc0.Anc0refChr3 112282 14 + 222631 CTATCTAATAAGCA +s Anc1.Anc1refChr6 146085 14 + 197743 CTATCTAATAAGCA +s Anc2.Anc2refChr1 24361 14 + 142988 CTATCTAATAAGCC +s mr.mrrefChr3 49987 14 + 181027 CTCTTAGTTATGCA +s simCow_chr6.simCow.chr6 480786 14 + 602619 CTATCTAATAAGCC +s simHuman_chr6.simHuman.chr6 477984 14 + 601863 CTATCCAATAAGCA +s simMouse_chr6.simMouse.chr6 194769 14 - 636262 CTACTAATTAGGCA +s simRat_chr6.simRat.chr6 193794 14 - 647215 CTGTTAGTTAAGCA +s simRat_chr6.simRat.chr6 508431 14 + 647215 CTCTTAGTTATGCA + +a +s simMouse_chr6.simMouse.chr6 496075 42 + 636262 GTAGATAGCTCAATCATCAGCAGTTTTATTGCAGCACACAAC +s Anc0.Anc0refChr3 112296 41 + 222631 CAAGAGAGGTGGATCATCAGCAATTTTATTGCATCTCACAA- +s Anc1.Anc1refChr6 146099 42 + 197743 CAAGAGAGGTGGATCATCAGCAATTTTATTGCATCTCACAAC +s Anc2.Anc2refChr1 24375 41 + 142988 CAAAACAGGGGGATTATCAGTAATTTTATTACATCTCACAA- +s mr.mrrefChr3 50001 42 + 181027 GAAGAGAGGTGGATCATCAGCAGTTTTTTTGCAGCATACAAC +s simCow_chr6.simCow.chr6 480800 41 + 602619 CAAAACAGGGGGATTATCAGTAATTTTATTACATCTCACAA- +s simHuman_chr6.simHuman.chr6 477998 42 + 601863 CCAGCGAGGTGGATCATCAGCAATTTTATTGCATCTCACAAC +s simMouse_chr6.simMouse.chr6 194783 38 - 636262 GAAGAGAGGTGGGCCATCAGCAATTTTTTTGCAACATA---- +s simRat_chr6.simRat.chr6 193808 42 - 647215 GAAGAGAGGTAGGCCATCAGCAGTTTTTTTGCAACATGTGAC +s simRat_chr6.simRat.chr6 508451 42 + 647215 GTAGATAGCTTGATCATTGGCAGTTTTGTTGCAGTATACAAC + +a +s simMouse_chr6.simMouse.chr6 496117 22 + 636262 ATCTATCAAAGGGTATCCTCTT +s Anc0.Anc0refChr3 112396 17 + 222631 ACCTATCAAAGGGCA-----TC +s Anc1.Anc1refChr6 146202 17 + 197743 ACCTATCAAAGGGCA-----TC +s Anc2.Anc2refChr1 24475 17 + 142988 ACCTACCAAAGATCA-----TC +s mr.mrrefChr3 50092 22 + 181027 ATCTATCAAAGGGTATCCTCTC +s simCow_chr6.simCow.chr6 480909 17 + 602619 ACCTACCAAAGATCA-----TC +s simHuman_chr6.simHuman.chr6 478101 17 + 601863 ACCTATCAAAGGGCA-----TA +s simMouse_chr6.simMouse.chr6 194866 22 - 636262 GTCTATCAAAGGGTATCCTCTC +s simRat_chr6.simRat.chr6 193898 22 - 647215 ATCTATCAAAGGGTATCCTCTC +s simRat_chr6.simRat.chr6 508542 21 + 647215 -TGTATCAAAGGGTATCCTCTT + +a +s simMouse_chr6.simMouse.chr6 496139 26 + 636262 CTTGCCTAGAGATTAGCACTAGTGGC +s Anc0.Anc0refChr3 112413 26 + 222631 CTTGCCTAGACCTTAACACTAGTGGC +s Anc1.Anc1refChr6 146219 26 + 197743 CTTGCCTAGACCTTAACACTAGTGGC +s Anc2.Anc2refChr1 24492 26 + 142988 CTTGCGTAGACCTTAACACTGGTGGC +s mr.mrrefChr3 50114 26 + 181027 CTTGCCTAGATATTAACACTAGTGGC +s simCow_chr6.simCow.chr6 480928 26 + 602619 CTTGCGTAGACCTTAACACTGGTGGC +s simHuman_chr6.simHuman.chr6 478118 26 + 601863 ATTGCCTAGACCTTAACACCAATGAC +s simMouse_chr6.simMouse.chr6 194888 26 - 636262 CTTGCCTAGGTATTAACACTAGTGGC +s simRat_chr6.simRat.chr6 193920 26 - 647215 CTTGCCCAGATATTAACACTAGTGGC +s simRat_chr6.simRat.chr6 508563 26 + 647215 TTTGCCTAGACATTAGCGCCAGTGGC + +a +s simMouse_chr6.simMouse.chr6 496165 9 + 636262 ATGATTATG +s Anc0.Anc0refChr3 112439 9 + 222631 ATGATCATG +s Anc1.Anc1refChr6 146245 9 + 197743 ATGATCATG +s Anc2.Anc2refChr1 24518 9 + 142988 ATGATCATG +s mr.mrrefChr3 50140 9 + 181027 ATGATCATG +s simCow_chr6.simCow.chr6 480954 9 + 602619 ATGATCATG +s simHuman_chr6.simHuman.chr6 478144 9 + 601863 GTGATTGTG +s simMouse_chr6.simMouse.chr6 194914 9 - 636262 ACAATCATA +s simRat_chr6.simRat.chr6 508589 9 + 647215 ATCATCATG + +a +s simMouse_chr6.simMouse.chr6 496174 16 + 636262 ACTTGCTATGCATACT +s Anc0.Anc0refChr3 112448 16 + 222631 GCTTGCCACACTTACC +s Anc1.Anc1refChr6 146254 16 + 197743 GCTTGCCACACTTACC +s Anc2.Anc2refChr1 24527 16 + 142988 GCTTGCCACACTTATC +s mr.mrrefChr3 50149 16 + 181027 ACTTGCAACACATACT +s simCow_chr6.simCow.chr6 480963 16 + 602619 GCTTGCCACACTTATC +s simHuman_chr6.simHuman.chr6 478153 16 + 601863 CCTTGCCACACCTACC +s simMouse_chr6.simMouse.chr6 194923 16 - 636262 ATTTGCAACACCTATT +s simRat_chr6.simRat.chr6 196843 16 - 647215 ACTTGCAACACATATT +s simRat_chr6.simRat.chr6 508598 13 + 647215 A--TGCTATGC-TACT + +a +s simMouse_chr6.simMouse.chr6 496190 3 + 636262 TTC +s Anc0.Anc0refChr3 112464 3 + 222631 TTC +s Anc1.Anc1refChr6 146270 3 + 197743 TTC +s Anc2.Anc2refChr1 24543 3 + 142988 TTA +s mr.mrrefChr3 50165 3 + 181027 TTC +s simCow_chr6.simCow.chr6 480979 3 + 602619 TTA +s simHuman_chr6.simHuman.chr6 478169 3 + 601863 TTC +s simMouse_chr6.simMouse.chr6 194939 3 - 636262 CTC +s simRat_chr6.simRat.chr6 196862 3 - 647215 CTC +s simRat_chr6.simRat.chr6 508611 3 + 647215 TTC + +a +s simMouse_chr6.simMouse.chr6 496193 2 + 636262 GT +s Anc0.Anc0refChr3 112485 2 + 222631 GT +s Anc1.Anc1refChr6 146291 2 + 197743 GT +s Anc2.Anc2refChr1 24564 2 + 142988 AT +s mr.mrrefChr3 50186 2 + 181027 GT +s simCow_chr6.simCow.chr6 481000 2 + 602619 AT +s simHuman_chr6.simHuman.chr6 478190 2 + 601863 GT +s simMouse_chr6.simMouse.chr6 194960 2 - 636262 GA +s simRat_chr6.simRat.chr6 196883 2 - 647215 GT +s simRat_chr6.simRat.chr6 508614 2 + 647215 AT + +a +s simMouse_chr6.simMouse.chr6 496195 5 + 636262 GGGTA +s Anc0.Anc0refChr3 112499 5 + 222631 GGTTT +s Anc1.Anc1refChr6 146305 5 + 197743 GGTTT +s Anc2.Anc2refChr1 24578 5 + 142988 AGTTA +s mr.mrrefChr3 50200 5 + 181027 GGGTT +s simCow_chr6.simCow.chr6 481014 5 + 602619 AGTTA +s simHuman_chr6.simHuman.chr6 478204 5 + 601863 GGTTT +s simMouse_chr6.simMouse.chr6 194974 5 - 636262 GACTT +s simRat_chr6.simRat.chr6 196897 5 - 647215 GACTT +s simRat_chr6.simRat.chr6 508628 5 + 647215 GGGTA a s simMouse_chr6.simMouse.chr6 496200 1 + 636262 A @@ -190079,6 +202703,32 @@ s simRat_chr6.simRat.chr6 508633 1 + 647215 A a +s simMouse_chr6.simMouse.chr6 496201 34 + 636262 TCATTTTTAAATTCCTGATTTCCTTTACATTCAG +s Anc0.Anc0refChr3 112505 34 + 222631 TTATCTCTGAATACCTGGTTTTCTTTACATTCAG +s Anc1.Anc1refChr6 146311 34 + 197743 TTATCTCTGAATACCTGGTTTTCTTTACATTCAG +s Anc2.Anc2refChr1 24584 34 + 142988 TTAACTCTGAGTACCCAGTTTTCCTTACATTCCA +s mr.mrrefChr3 50206 34 + 181027 TCATCTTTGAATTCCTGATTTCCTTTACATTCAG +s simCow_chr6.simCow.chr6 481020 34 + 602619 TTAACTCTGAGTACCCAGTTTTCCTTACATTCCA +s simDog_chr6.simDog.chr6 471004 4 + 593897 ------------------------------TCCA +s simHuman_chr6.simHuman.chr6 478210 34 + 601863 GTATCTCTGAACACCTGGTTTACTTTACATTCAG +s simMouse_chr6.simMouse.chr6 194979 34 - 636262 TCATCCTTGTATTCCCAATTGCCTTTACACTTAG +s simRat_chr6.simRat.chr6 196902 34 - 647215 TCATCTTTGAATTCCCAATTGCCTTTACACTCAG +s simRat_chr6.simRat.chr6 508634 34 + 647215 TCGTTTCTGAATTCCTGAGTTCCTTTGCATTCAG + +a +s simMouse_chr6.simMouse.chr6 496235 11 + 636262 CTTGTAGAACT +s Anc0.Anc0refChr3 112539 11 + 222631 CATCTAGAACT +s Anc1.Anc1refChr6 146345 11 + 197743 CATCTAGAACT +s Anc2.Anc2refChr1 24618 11 + 142988 CATCTAGAACT +s mr.mrrefChr3 50240 11 + 181027 CTTCTAGAACT +s simCow_chr6.simCow.chr6 481055 11 + 602619 CATCTTGAACT +s simDog_chr6.simDog.chr6 471008 11 + 593897 CATCTAGATCT +s simHuman_chr6.simHuman.chr6 478244 11 + 601863 CATCTGGAACT +s simMouse_chr6.simMouse.chr6 195013 11 - 636262 CTTCTAGAACT +s simRat_chr6.simRat.chr6 196936 11 - 647215 CTTCTAGGACT +s simRat_chr6.simRat.chr6 508668 11 + 647215 CTTGTAGAACT + +a s simMouse_chr6.simMouse.chr6 496246 13 + 636262 GTTACAGGTGTGC s Anc0.Anc0refChr3 112550 13 + 222631 TCTGCAGGTGTGT s Anc1.Anc1refChr6 146356 13 + 197743 TCTGCAGGTGTGT @@ -190089,18 +202739,82 @@ 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 +s simMouse_chr6.simMouse.chr6 496259 20 + 636262 TATCTCAGTAAGTGAAGGCA +s Anc0.Anc0refChr3 112563 17 + 222631 TCCCT---TAATTGGAGGCA +s Anc1.Anc1refChr6 146369 17 + 197743 TCCCT---TAATTGGAGGCA +s Anc2.Anc2refChr1 24647 17 + 142988 CCCCC---TAATTAGAGGCA +s mr.mrrefChr3 50264 20 + 181027 TACCTTAGTAAGTGGAGGCA +s simCow_chr6.simCow.chr6 481084 17 + 602619 CTCCC---TAATTCGAGGCA +s simDog_chr6.simDog.chr6 471037 17 + 593897 CCCCC---TAATCAGAGGCA +s simHuman_chr6.simHuman.chr6 478255 17 + 601863 TCCCT---TAGTTGGAGGCA +s simMouse_chr6.simMouse.chr6 195024 20 - 636262 AACTCTGGTGTGTTGTCCCA +s simRat_chr6.simRat.chr6 196947 20 - 647215 AACTATGGTATGTTGGGTCA +s simRat_chr6.simRat.chr6 508692 20 + 647215 TATCTCAGTAATCGAAGACA + +a +s simMouse_chr6.simMouse.chr6 496279 10 + 636262 TATTCCCAAT +s Anc0.Anc0refChr3 112580 10 + 222631 TGTTCCCAAT +s Anc1.Anc1refChr6 146386 10 + 197743 TGTTCCCAAT +s Anc2.Anc2refChr1 24664 10 + 142988 TGTTCCCAAT +s mr.mrrefChr3 50290 10 + 181027 TATTCCCAAG +s simCow_chr6.simCow.chr6 481101 10 + 602619 TGTTCCCAGT +s simDog_chr6.simDog.chr6 471054 10 + 593897 TGTTCCCAAT +s simHuman_chr6.simHuman.chr6 478272 10 + 601863 TGTTCCTAAT +s simMouse_chr6.simMouse.chr6 195057 10 - 636262 CATTCCCAAG +s simRat_chr6.simRat.chr6 196973 10 - 647215 TATTCCCAAG +s simRat_chr6.simRat.chr6 508712 10 + 647215 TATTCCCAAC + +a +s simMouse_chr6.simMouse.chr6 496289 9 + 636262 ATAAGCCCA +s Anc0.Anc0refChr3 112590 9 + 222631 ATAAGGCCA +s Anc1.Anc1refChr6 146396 9 + 197743 ATAAGGCCA +s Anc2.Anc2refChr1 24674 9 + 142988 ATAAGGCCA +s mr.mrrefChr3 50300 9 + 181027 ATAAGGCCA +s simCow_chr6.simCow.chr6 481111 4 + 602619 ACCA----- +s simDog_chr6.simDog.chr6 471064 9 + 593897 ATAAGGCCA +s simHuman_chr6.simHuman.chr6 478282 9 + 601863 ATAAGGCCA +s simMouse_chr6.simMouse.chr6 195068 8 - 636262 ATAAGGCC- +s simRat_chr6.simRat.chr6 196983 9 - 647215 ATAAGGCCG +s simRat_chr6.simRat.chr6 508722 9 + 647215 ATAAGCCCA + +a +s simMouse_chr6.simMouse.chr6 496298 5 + 636262 CATAA +s Anc0.Anc0refChr3 112602 5 + 222631 CCTAA +s Anc1.Anc1refChr6 146408 5 + 197743 CCTAA +s Anc2.Anc2refChr1 24686 5 + 142988 CCTAA +s mr.mrrefChr3 50312 5 + 181027 CTTAA +s simCow_chr6.simCow.chr6 481116 5 + 602619 ACTAA +s simDog_chr6.simDog.chr6 471076 5 + 593897 CCTAA +s simHuman_chr6.simHuman.chr6 478294 5 + 601863 CCTTG +s simMouse_chr6.simMouse.chr6 195079 5 - 636262 CTCCA +s simRat_chr6.simRat.chr6 196995 5 - 647215 CTCAA +s simRat_chr6.simRat.chr6 508731 5 + 647215 CCTGG + +a +s simMouse_chr6.simMouse.chr6 496303 35 + 636262 CACACTTGGCACTTTTGACAACTTCAATTCAAAAG +s Anc0.Anc0refChr3 112607 35 + 222631 CACATTTTGCCCACCTTACACCTTAAATTTACACA +s Anc1.Anc1refChr6 146413 35 + 197743 CACATTTTGCCCACCTTACACCTTAAATTTACACA +s Anc2.Anc2refChr1 24691 35 + 142988 CACATTTTGCCCACCTTACACCTTAAACTTACACA +s mr.mrrefChr3 50318 35 + 181027 CATAGTTTGCACATTTTACAACTTCAATTTACAGG +s simCow_chr6.simCow.chr6 481121 35 + 602619 CAGATTTTGCCCACCTTACACCTTAATCTTACAAG +s simDog_chr6.simDog.chr6 471081 35 + 593897 CACATTTTGCACACCTTACACCTTAAACTCACACA +s simHuman_chr6.simHuman.chr6 478299 35 + 601863 CACATTTTGCCCACCTTGCACCTCAAATTTACATA +s simMouse_chr6.simMouse.chr6 195085 35 - 636262 CATAGATTGAACATTTTACCATATCAACTTCCAGG +s simRat_chr6.simRat.chr6 197001 35 - 647215 CATAGATTGAACATTTTACTATATCAACTTACAGG +s simRat_chr6.simRat.chr6 508736 35 + 647215 TAGACTTTGCACATCTGACAACTTCAATTCACAGG + +a +s simMouse_chr6.simMouse.chr6 496338 27 + 636262 TTCATTACCCCCCCCAGACCTGGAAGC +s Anc0.Anc0refChr3 112642 17 + 222631 TTCATTACTCC----AGTCAT------ +s Anc1.Anc1refChr6 146448 17 + 197743 TTCATTACTCC----AGTCAT------ +s Anc2.Anc2refChr1 24726 17 + 142988 TTCATTACTCC----AGTCAT------ +s mr.mrrefChr3 50353 23 + 181027 TTCATTACTCC----AGTCATGGAAGC +s simCow_chr6.simCow.chr6 481156 17 + 602619 TTCATTACTCG----AGTCAT------ +s simDog_chr6.simDog.chr6 471125 16 + 593897 CTCGTTGCTCC----AGTCA------- +s simHuman_chr6.simHuman.chr6 478334 17 + 601863 TTCATTACTGC----AGTCAT------ +s simMouse_chr6.simMouse.chr6 195120 23 - 636262 TTCATTACTCC----TATCATGGAAGC +s simRat_chr6.simRat.chr6 197036 23 - 647215 TTCATCACTCC----TGTCATGGAAGT +s simRat_chr6.simRat.chr6 508771 23 + 647215 TTCATTACCCC----AGTGATAGAAGC a s simMouse_chr6.simMouse.chr6 496365 1 + 636262 C @@ -190108,31 +202822,42 @@ s simRat_chr6.simRat.chr6 508794 1 + 647215 C a +s simMouse_chr6.simMouse.chr6 496366 7 + 636262 AATTGAA +s mr.mrrefChr3 50377 7 + 181027 AATAGAA +s simMouse_chr6.simMouse.chr6 195143 7 - 636262 AATAGAA +s simRat_chr6.simRat.chr6 197059 7 - 647215 AATAGAA +s simRat_chr6.simRat.chr6 508795 7 + 647215 AATAGCA + +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 +s simMouse_chr6.simMouse.chr6 496380 54 + 636262 CACAAGTCGTGACCCCAAGTCATTGAAGCCAACAGAGACACACGGAAACTTGGT +s Anc0.Anc0refChr3 112659 29 + 222631 -----------------------GGAAG-CAACAGAAACACACAGCAG-TTTGT +s Anc1.Anc1refChr6 146465 31 + 197743 -----------------------GGAAGCCAACAGAAACACACAGCAGCTTTGT +s Anc2.Anc2refChr1 24743 29 + 142988 -----------------------GGAAG-CAACAGAAACACTCAGCAG-TTTCT +s mr.mrrefChr3 50391 54 + 181027 CACAAGTCATGACCCCAAGCCATGGAAGCCAACAGAAACACATGGGAGCTTTGT +s simCow_chr6.simCow.chr6 481173 26 + 602619 -----------------------GGAAG-C---AGGAACACTCAGCAG-TTTCT +s simDog_chr6.simDog.chr6 471141 9 + 593897 ------------------------------AACAGAAAC--------------- +s simHuman_chr6.simHuman.chr6 478351 31 + 601863 -----------------------AGCAGCCAACAGAATCACACAACAGCTTTGT +s simMouse_chr6.simMouse.chr6 195150 53 - 636262 ACACAGCCATGGCCCCAATCTGTGGAAGTGAACAGAAACACATGGGAGATTTG- +s simRat_chr6.simRat.chr6 197066 54 - 647215 CACAAGTCATGGCCCCAAGCCATGGAAGTGAACAGAAACACATGGGAGATTTAT +s simRat_chr6.simRat.chr6 508809 54 + 647215 TACAAGTCATGACCCCAAGTCATTGAAGCCAACAGAAACGCATGGAAACTTGGT + +a +s simMouse_chr6.simMouse.chr6 496434 18 + 636262 TGGGAACTAAAGCTCTGT +s Anc0.Anc0refChr3 112688 18 + 222631 CACGTACTAATACTTTAT +s Anc1.Anc1refChr6 146496 18 + 197743 CACGTACTAATACTTTAT +s Anc2.Anc2refChr1 24772 18 + 142988 CACGTTCTAATACGTTAT +s mr.mrrefChr3 50445 18 + 181027 CAGGAACTAAAATTTTAT +s simCow_chr6.simCow.chr6 481199 18 + 602619 CACGTTCTAATACGTTAT +s simDog_chr6.simDog.chr6 471150 1 + 593897 -----------------T +s simHuman_chr6.simHuman.chr6 478383 18 + 601863 CAAGTACTCATACTTTAT +s simMouse_chr6.simMouse.chr6 195203 6 - 636262 ------------TATCTA +s simRat_chr6.simRat.chr6 197120 18 - 647215 CAAGAACCAAAATTCTAT +s simRat_chr6.simRat.chr6 508863 18 + 647215 CTGGAATTAAAATGTCAT a s simMouse_chr6.simMouse.chr6 496452 47 + 636262 ATAGCTTAAGCTTAAGGGGTCAAAGGAACAGACCTAGTACCTTAGTC @@ -190248,7 +202973,31 @@ s simRat_chr6.simRat.chr6 509337 3 + 647215 TAC a -s simMouse_chr6.simMouse.chr6 496704 10 + 636262 CCTTGCTTCA +s simMouse_chr6.simMouse.chr6 496692 11 + 636262 CTCCTTGCTTC +s Anc0.Anc0refChr3 112937 3 + 222631 --------TTC +s Anc1.Anc1refChr6 146750 11 + 197743 CTTCTTGCTTC +s Anc2.Anc2refChr1 25045 3 + 142988 --------TTC +s mr.mrrefChr3 50704 11 + 181027 CTCCTTGCTTC +s mr.mrrefChr5 294285 11 + 294540 CTTCTTGCCTT +s simCow_chr6.simCow.chr6 481464 3 + 602619 --------TTC +s simDog_chr6.simDog.chr6 471408 3 + 593897 --------TCC +s simMouse_chr6.simMouse.chr6 440798 11 + 636262 CTTCTTGCCTT +s simRat_chr6.simRat.chr6 449218 11 + 647215 CTTCTTATCTT +s simRat_chr6.simRat.chr6 509340 11 + 647215 CTCCTTACTTC + +a +s simMouse_chr6.simMouse.chr6 496703 17 + 636262 ACCTTGCTTCAGAAGGT +s Anc0.Anc0refChr3 112940 7 + 222631 A----------GGAGGT +s Anc1.Anc1refChr6 146761 7 + 197743 A----------GGAGGT +s Anc2.Anc2refChr1 25048 7 + 142988 A----------GGGGGT +s mr.mrrefChr3 50715 7 + 181027 A----------GAAGGT +s mr.mrrefChr5 294296 7 + 294540 A----------ACAGAC +s simCow_chr6.simCow.chr6 481467 7 + 602619 A----------AGGGGT +s simDog_chr6.simDog.chr6 471411 7 + 593897 A----------GAGGGC +s simMouse_chr6.simMouse.chr6 440809 7 + 636262 A----------ACAGAC +s simRat_chr6.simRat.chr6 449229 7 + 647215 A----------ACAGAC +s simRat_chr6.simRat.chr6 197396 7 - 647215 A----------GGAAGC +s simRat_chr6.simRat.chr6 509351 7 + 647215 A----------GAAGAT a s simMouse_chr6.simMouse.chr6 496720 3 + 636262 TTT @@ -190261,6 +203010,89 @@ s simRat_chr6.simRat.chr6 509358 3 + 647215 CTT a +s simMouse_chr6.simMouse.chr6 496723 10 + 636262 TAGTAGTCAT +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 440816 10 + 636262 TATCAAACAA +s simRat_chr6.simRat.chr6 449236 10 + 647215 TATCAAACAA +s simRat_chr6.simRat.chr6 509361 10 + 647215 TAGTAGGCTT + +a +s simMouse_chr6.simMouse.chr6 496733 10 + 636262 AGTTGTCTTG +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 440826 10 + 636262 ACTTAACCTG +s simRat_chr6.simRat.chr6 449310 10 + 647215 GCTTAACCTG +s simRat_chr6.simRat.chr6 509371 10 + 647215 AGTTGTCTTT + +a +s simMouse_chr6.simMouse.chr6 496743 10 + 636262 GCTATCCAGT +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 440838 10 + 636262 GGCATCCAAA +s simRat_chr6.simRat.chr6 449322 10 + 647215 GGCATGCAAC +s simRat_chr6.simRat.chr6 509381 10 + 647215 GCCATGCAAT + +a +s simMouse_chr6.simMouse.chr6 496753 14 + 636262 TTGGTACCTCTGGG +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 440848 14 + 636262 TCTTTAAATCTGGG +s simRat_chr6.simRat.chr6 449332 14 + 647215 TCTTTAAATCTGGG +s simRat_chr6.simRat.chr6 509391 14 + 647215 TTGTTACCTCTGGG + +a +s simMouse_chr6.simMouse.chr6 496767 22 + 636262 GCCGAGTGGTATTCACCAAATC +s Anc0.Anc0refChr3 112991 22 + 222631 ACTGAGTGATATTCACCAAAAC +s Anc1.Anc1refChr6 146817 22 + 197743 ACTGAGTGATATTCACCAAAAC +s Anc2.Anc2refChr1 25099 22 + 142988 ACTAAGTGTTATTCACCAAAAC +s mr.mrrefChr3 50769 22 + 181027 GCCGAGTGATATTCACCAAATC +s mr.mrrefChr5 294349 22 + 294540 ATTGAATGATATTCATTGAAAC +s simCow_chr6.simCow.chr6 481521 21 + 602619 -CCAGGTGGCATTCACCAAAAC +s simDog_chr6.simDog.chr6 471462 22 + 593897 AATAAGAATTATTCACCAAGAC +s simHuman_chr6.simHuman.chr6 478669 22 + 601863 GCTGAGTGATATCCGCCAAAAC +s simMouse_chr6.simMouse.chr6 440862 22 + 636262 ATTGAATGATATTCATTGAAAC +s simRat_chr6.simRat.chr6 449346 22 + 647215 GCTGAGTGGTTTTCATCAAAAC +s simRat_chr6.simRat.chr6 509405 21 + 647215 GCCAAGTGA-ATTCACCAAATC + +a +s simMouse_chr6.simMouse.chr6 496789 10 + 636262 TCATTTTTCA +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 440884 10 + 636262 TTGTCCTTCA +s simRat_chr6.simRat.chr6 449368 10 + 647215 TTGTCTTGCA +s simRat_chr6.simRat.chr6 509426 10 + 647215 TCATTTTTCA + +a s simMouse_chr6.simMouse.chr6 496799 1 + 636262 G s Anc0.Anc0refChr3 113023 1 + 222631 A s Anc1.Anc1refChr6 146849 1 + 197743 A @@ -190272,6 +203104,104 @@ s simRat_chr6.simRat.chr6 509436 1 + 647215 G a +s simMouse_chr6.simMouse.chr6 496800 52 + 636262 GGAGTTGTTGGCTCCTTCCTGCAACACTAGTCCATTTCAGGTGGGCTCTCAC +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 440894 52 + 636262 AGAGCCCTCATCTCACTCCAACACCGCTAGTGTCGTTTGGGTCAACTCTCAC +s simRat_chr6.simRat.chr6 449378 52 + 647215 AGAGCCAGTATCTGACTCCAACAGTGCTAGTATCATTTGGGTGGACTCTCAC +s simRat_chr6.simRat.chr6 509437 52 + 647215 GGAATTGCTATCTCACTCCTACAACGCTAGTCAGTTTCAGGTGGACTCTCAC + +a +s simMouse_chr6.simMouse.chr6 496852 3 + 636262 AAA +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 440946 3 + 636262 ATG +s simRat_chr6.simRat.chr6 449430 3 + 647215 ATG +s simRat_chr6.simRat.chr6 509489 3 + 647215 ATA + +a +s simMouse_chr6.simMouse.chr6 496855 16 + 636262 TTGAAGATCCAAAGCC +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 440949 16 + 636262 TTGAGGATCCAGAGCC +s simRat_chr6.simRat.chr6 449433 16 + 647215 TTGAAAATCCGAAGCC +s simRat_chr6.simRat.chr6 509492 16 + 647215 TTGAGGATCCAAAGCC + +a +s simMouse_chr6.simMouse.chr6 496871 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 440965 1 + 636262 A +s simRat_chr6.simRat.chr6 449449 1 + 647215 A +s simRat_chr6.simRat.chr6 509508 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 496872 12 + 636262 CCTGCTATGGAC +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 440966 12 + 636262 CCTGCTCAGAGC +s simRat_chr6.simRat.chr6 449450 12 + 647215 TCCGCTCTGGGC +s simRat_chr6.simRat.chr6 509509 12 + 647215 CCTGCTGTGGAC + +a +s simMouse_chr6.simMouse.chr6 496884 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 440979 2 + 636262 TT +s simRat_chr6.simRat.chr6 449463 2 + 647215 TT +s simRat_chr6.simRat.chr6 509521 2 + 647215 TT + +a +s simMouse_chr6.simMouse.chr6 496886 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 440981 5 + 636262 TCTGT +s simRat_chr6.simRat.chr6 449484 5 + 647215 TCTAT +s simRat_chr6.simRat.chr6 509523 5 + 647215 TCTGT + +a s simMouse_chr6.simMouse.chr6 496891 20 + 636262 TGAGGTCTGGCTCTTCGTAC s Anc0.Anc0refChr3 113155 20 + 222631 TGAGGTCTTGCTTTTCCTGT s Anc1.Anc1refChr6 146981 20 + 197743 TGAGGTCTTGCTTTTCCTGT @@ -190283,6 +203213,20 @@ s simRat_chr6.simRat.chr6 509528 20 + 647215 TGAGGTCTGGCCCTTTGTAC a +s simMouse_chr6.simMouse.chr6 496911 66 + 636262 TAGAGCATCTGTATACATTGTGGTGATAGTAACAAAGATGATCAGATACAAGATCTGAAGAATGGT +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 440986 66 + 636262 CAGTGCATTTGCATGTATGATGGTGACAGTAACAAAGAAAATCTGATACATGTGCTGAAGAATGGT +s simRat_chr6.simRat.chr6 449489 66 + 647215 CAGTGCATTTGCATATATTGTCCTAACAGAAACAAAGAGGATCAGATACAATTGCTGAAGAGTGGT +s simRat_chr6.simRat.chr6 509548 66 + 647215 TAAAGCATTTGTATATATTGTGGTGATAGTAACAAAGATGATCAGATACAAGATCTGAAGAATGGT + +a s simMouse_chr6.simMouse.chr6 496977 2 + 636262 GT s Anc0.Anc0refChr3 113241 2 + 222631 GT s Anc1.Anc1refChr6 147067 2 + 197743 GT @@ -190306,6 +203250,21 @@ s simRat_chr6.simRat.chr6 509616 1 + 647215 G a +s simMouse_chr6.simMouse.chr6 496980 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 441052 1 + 636262 G +s simRat_chr6.simRat.chr6 449555 1 + 647215 G +s simRat_chr6.simRat.chr6 449558 1 + 647215 G +s simRat_chr6.simRat.chr6 509617 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 @@ -191469,14 +204428,351 @@ 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 +s simMouse_chr6.simMouse.chr6 500909 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 499522 29 + 636262 ATGCAAAAATGGACATAGGGTTACAATGG +s simRat_chr6.simRat.chr6 512135 29 + 647215 ATGCACAAATAGACATGAGGTTACAATGA + +a +s simMouse_chr6.simMouse.chr6 500938 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 499551 11 + 636262 CACCAAATCAT +s simRat_chr6.simRat.chr6 512164 11 + 647215 CACCGAATCGT + +a +s simMouse_chr6.simMouse.chr6 500949 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 499562 41 + 636262 TTAATGTCTAACAATTAAATATGTCAGACTCTGTACCTATG +s simRat_chr6.simRat.chr6 512175 38 + 647215 TTAATGTCTAACTGTTAAATACATGAGACCCTGTACCT--- + +a +s simMouse_chr6.simMouse.chr6 500990 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 499603 37 + 636262 GTCACTCATAAGAAGAGAGCCAAGTGTAAATTTTGAA +s simRat_chr6.simRat.chr6 512213 35 + 647215 --CACTCATAAGAAGAGAGCCAAGTGTAAATTTTGAA + +a +s simMouse_chr6.simMouse.chr6 501027 172 + 636262 GGACGCTTTTTTGGCCACATACCCTGTGCCCTAGCACCTTACTGTACCAAATTTGTCTTTAAAAATGTGGTTATATTATTACTGGAATATCCTAGCTACGTGCTGACTTCTATTGTGCTTTAGTAAAGCTCTGGCTGCGGACACCTATCATGCTGAGTGGTTTAGTAAAGCT +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 499640 172 + 636262 GGACGCATTTTTGGCCACATACCCTGTGCCCTAGCACCTTACTGTACCAAATTTGTCTTTAAAAATGTGGCTATATTATTACTGGAATATCCTAGCTACGTGCTGACTTCTATTGTGCTTTAGTAAAGCTCTGGCTGCGGACACCTATCATGCTGAGTGGTTTAGTAAAGCT +s simRat_chr6.simRat.chr6 512281 163 + 647215 AGATGTATTTTTGATCAGATACAATGTGCCCTAGCACC---------CAGATGTGCCTTTAAAAATGTGGTTATATATTTACTGAACTGTTCTAGTTGGGTGCTGACATCTATCATAGTTTAGTAAAGCTCTGGCCACTGACACCTATCATGCTGAGTGGTTCAATAAAACT + +a +s simMouse_chr6.simMouse.chr6 501199 66 + 636262 TTTTGGAATAAATTTCATCATGTTTCCTGCTAAGTTCGCCCTATGTCCACATGTACTAGTACAAAA +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 499812 66 + 636262 TTTTGGAATAAATTTCATCATGTTACCTGCTAAGTTCGCCCTATGTCCACATGTACTAGTACAAAA +s simRat_chr6.simRat.chr6 512444 53 + 647215 TTT-GGAATAAATTTCATCATGTTTCCTGC------------ATGTCCACTTGTACTAGTCCATGA + +a +s simMouse_chr6.simMouse.chr6 501265 8 + 636262 ACAGACCT +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 499878 8 + 636262 ACAGACGT +s simRat_chr6.simRat.chr6 512497 8 + 647215 ACATACCT + +a +s simMouse_chr6.simMouse.chr6 501273 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 499886 7 + 636262 ATGAAAA +s simRat_chr6.simRat.chr6 512505 7 + 647215 TTGAAAA + +a +s simMouse_chr6.simMouse.chr6 501280 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 499893 33 + 636262 ATTGCAGACCATTCCAGTCAAGGAGAATCATTT +s simRat_chr6.simRat.chr6 512524 33 + 647215 GTTGCAGCCCACCCCAGCCAAGGAAAATCATTT + +a +s simMouse_chr6.simMouse.chr6 501313 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 499926 92 + 636262 TTAAAGGAGTTAAAAATATACTTTGGTATTATTAAGATGATATGAGCAATACTTACCCTAGGACCCTGTTTGTGTGATTAGAATCCCATACT +s simRat_chr6.simRat.chr6 512557 92 + 647215 TCAAAGGAGTCAAAAATATACTCTGGTATTATTGAGATGATATAAGAAATGCCCACCCTAGGACCCTGTTTGTGTGATCAGAATCCCATACT + +a +s simMouse_chr6.simMouse.chr6 501405 304 + 636262 TAAAAGGTCTACCATTTGCAGATTTAAGGTAAGTGCCTAAGTTGAGACAGTatggctgttaaaaattagtctcccagctatccaattacttgatgtttgagcaaaatcctttagtgggctatgagtttgaacttgaccctttaggcccagagttcattattcaataaatgatactgggggaaccgggttatctgtccatcaatagtttaaatttgatactttttcttaaacacccgatgtgttttatactaagattaagaccatatgcaagcggactaaagatgtaaattcttgttcctcaaag +s mr.mrrefChr3 53976 304 + 181027 TAAAAGGTCTACCATTTGCAGATTTAAGGTAAGTGCCTAAGTTGAGACAGTatggctgttaaaaattagtctcccagctatccaattacttgatgtttgagcaaaatccttcagtgggctatgagtttgaacttgaccctttaggcccagagttcattattcaataaatgatactggaggaaccgggttatctgtccatcaagagtttaaatttgatactttttcttaaacacccgatgtgttttatactaagattaagaccatatgcaagcggactaaagatgtaaattcttgttcctcaaag +s simMouse_chr6.simMouse.chr6 500018 304 + 636262 TAAAAGGTCTACCATTTGCAGATTTAAGGTAAGTGCCTAAGTTGAGACAGTatggctgttaaaaattagtctcccagctatccaattacttgatgtttgagcaaaatccttcagtgggctatgagtttgaacttgaccctttaggcccagagttcattattcaataaatgatactggaggaaccgggttatctgtccatcgagagtttaaatttgatactttttcttaaacacccgatgtgttttatactaagattaagaccatatgcaagcgcactaaagatgtaaattcttggtcctcaaag +s simRat_chr6.simRat.chr6 512650 300 + 647215 GAAGACATCGACCATTTGCGGAGTTAAGGAAAGTGCCTAAGTCGAGACAACATGGCTGTTGAAGTTCAGTCTcccaactattcaattacttgatgtttaaggaaaatccttcagtgggctatgagtttgaacgtgaccctt-gggcccaaagtgcattatccaataaatgatgctggtggaactgg-ttatctatccaccaacagtttaaatttgctccttt--cttatacaccctatatgttttataccgagattaagaccatgtgcaagtggactaaagatgcgaattcttgttcctcaaag + +a +s simMouse_chr6.simMouse.chr6 501709 7 + 636262 agtaaaa +s mr.mrrefChr3 54280 7 + 181027 agtaaaa +s simMouse_chr6.simMouse.chr6 500322 7 + 636262 agtaaaa +s simRat_chr6.simRat.chr6 512952 7 + 647215 agtaaaa + +a +s simMouse_chr6.simMouse.chr6 501716 19 + 636262 ggacagaagaattgtctat +s mr.mrrefChr3 54287 19 + 181027 ggacagaagaattgtctat +s simMouse_chr6.simMouse.chr6 500329 19 + 636262 ggacagaagaattgtctat +s simRat_chr6.simRat.chr6 512999 19 + 647215 ggacagaagaattgcctac + +a +s simMouse_chr6.simMouse.chr6 501735 26 + 636262 cctgaagctgtcaaaatcaatggcag +s mr.mrrefChr3 54306 26 + 181027 cctgaagctgtcaaaatcaatggcag +s simMouse_chr6.simMouse.chr6 500348 26 + 636262 cctgaagccgtcaaaatcaatggcag +s simRat_chr6.simRat.chr6 513020 26 + 647215 actgaagatgccaaagtcaaaggcag + +a +s simMouse_chr6.simMouse.chr6 501761 75 + 636262 ttaaacccacaatccacgagaatgtgaatgtacacatttaaagacgccatgtaggttacaagaagagaagtctTG +s mr.mrrefChr3 54332 75 + 181027 ttaaacccacaatccacaagaatgtgaatgtacacatttaaagacgccatgtaggttacaagaagagaagtctTG +s simMouse_chr6.simMouse.chr6 500374 75 + 636262 ttaaacccacaatccacaagaatgtgaatgtacacatttaaagacgccatgtaggttacaagaagagaagtctTG +s simRat_chr6.simRat.chr6 513047 75 + 647215 ttcaacccataatccacaagaatgtgaatgtacacaatcaaagaggccatgtgtattacaagaagagaagtctTG + +a +s simMouse_chr6.simMouse.chr6 501836 69 + 636262 AAAGCATATTGTAAGATAAGATGTGCCCAGTGCCCAATTATCTTTTGGGTTTTAATCACTGTGATGGAT +s Anc0.Anc0refChr3 115446 52 + 222631 ----------GTAACATGACATGTGCCCAGTG-------ATCTTTTAGATTTTTATCAGTCTACTAGAT +s Anc1.Anc1refChr6 149325 52 + 197743 ----------GTAACATGACATGTGCCCAGTG-------ATCTTTTAGATTTTTATCAGTCTACTAGAT +s Anc2.Anc2refChr1 27596 52 + 142988 ----------TTAACATGACATGTGCCCAGTG-------ATCTTTTAGATTTTTGTCAGTCTACTAGAT +s mr.mrrefChr3 54407 69 + 181027 AAAGCATATTGTAAGATAAGATGTGCCCAGTGCCCAATTATCTTTTGGGTTTTAATCACTGTGATGGAT +s simCow_chr6.simCow.chr6 484092 45 + 602619 -----------TAGCATGAGATGTGGCCAGTG-------ATCTTTTAG------CTCCGTCTACTTGAT +s simDog_chr6.simDog.chr6 474430 52 + 593897 ----------TTAACATGACATGTGCCCGGTC-------CTCTTTTACATTTTTGTCAGCCTACTAGGT +s simHuman_chr6.simHuman.chr6 481419 52 + 601863 ----------GAAAAATGACATGTGTCCAGTG-------ATCTTTTAGATTTTTATCAGTCTACTAGAT +s simMouse_chr6.simMouse.chr6 500449 69 + 636262 AAAGCATATTGTAAGATAAGATGTGCCCAGTGCCCAATTATCTTTTGGGTTTTAATCACTGTGATGGAT +s simRat_chr6.simRat.chr6 513127 41 + 647215 AAAGCATATTGCAAGGTA------------TGCCCAGTCATCTTTTGGGGATT---------------- + +a +s simMouse_chr6.simMouse.chr6 501905 4 + 636262 TCGC +s Anc0.Anc0refChr3 115498 4 + 222631 TTAC +s Anc1.Anc1refChr6 149377 4 + 197743 TTAC +s Anc2.Anc2refChr1 27648 4 + 142988 TTAC +s mr.mrrefChr3 54476 4 + 181027 TCGC +s simCow_chr6.simCow.chr6 484137 4 + 602619 TTAC +s simDog_chr6.simDog.chr6 474482 4 + 593897 TTAC +s simHuman_chr6.simHuman.chr6 481471 4 + 601863 TTAT +s simMouse_chr6.simMouse.chr6 500533 4 + 636262 TCGC +s simRat_chr6.simRat.chr6 513168 3 + 647215 -TGC + +a +s simMouse_chr6.simMouse.chr6 501909 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 500537 41 + 636262 TGTGACACTGGTCTGAATGCATCTACCTCTGAGGAAACAAA +s simRat_chr6.simRat.chr6 513171 41 + 647215 TGTAACACCGATCTGACTGTTTCAACCTTTGTGGAAAAGAA + +a +s simMouse_chr6.simMouse.chr6 501950 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 500578 42 + 636262 GTTATTGTTGCATAAATAGTTAATTGACCCTACTTTTTGACC +s simRat_chr6.simRat.chr6 513214 40 + 647215 GTTGTCATTGCACA--TCGTTAATTGACTCTAGTTTTTGAGC + +a +s simMouse_chr6.simMouse.chr6 501992 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 500620 3 + 636262 CTA +s simRat_chr6.simRat.chr6 513254 3 + 647215 TTA + +a +s simMouse_chr6.simMouse.chr6 501995 15 + 636262 GCTACCTTGGTTATC +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 500623 15 + 636262 GCCACCTTAGTTATC +s simRat_chr6.simRat.chr6 513257 15 + 647215 GCTACCTTAGTTATT + +a +s simMouse_chr6.simMouse.chr6 502010 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 500638 30 + 636262 CATAGCTTTTAATAGCATGAGTCAAGAATC +s simRat_chr6.simRat.chr6 513272 30 + 647215 CATACCTTTCAATAGCATGAGTCAAGAACT + +a +s simMouse_chr6.simMouse.chr6 502040 35 + 636262 AGGGGTTATTTGGGATGGAAGTAGTTGGTTTCAGA +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 500668 35 + 636262 GGGGGTTATTTGGGATGGAAGTAGTTGGTTTCAGA +s simRat_chr6.simRat.chr6 513302 35 + 647215 GGGGGTTATTCAGGGTGAAAGTACTAGGTTTCTGA + +a +s simMouse_chr6.simMouse.chr6 502075 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 500703 25 + 636262 TCCTATGGCAAAAAAGTAAGGTGTG +s simRat_chr6.simRat.chr6 513337 11 + 647215 TCCTAAGCCAA-------------- + +a +s simMouse_chr6.simMouse.chr6 502100 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 500728 17 + 636262 GGAGCCGCAATGTATGT + +a +s simMouse_chr6.simMouse.chr6 502117 50 + 636262 TAGGTGCCACCCAAATCTACTGTGTGCCACATACAGCATGACAACTATTG +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 500745 50 + 636262 TAGGCGCCACCCAAATCTACCGTGTGCCACATACAGCATGACAACTATTG +s simRat_chr6.simRat.chr6 513348 44 + 647215 ------TCGCCCAAGTCTGCCTTGTGTCACATGCTGCATGACAAGTATTG + +a +s simMouse_chr6.simMouse.chr6 502167 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 500795 21 + 636262 AATAGCAACACAACTTCACCA +s simRat_chr6.simRat.chr6 513392 21 + 647215 AATATCAACACATCTCCACCA + +a +s simMouse_chr6.simMouse.chr6 502188 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 500816 25 + 636262 AGTCCACTGTGGGTCCAACAGAGTG +s simRat_chr6.simRat.chr6 513414 25 + 647215 AGTCCACTGTGGGTTCACCACAGTG + +a +s simMouse_chr6.simMouse.chr6 502213 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 500841 15 + 636262 TAATACTCCCCACAA +s simRat_chr6.simRat.chr6 513439 15 + 647215 TAATACTCCCCGCAA + +a +s simMouse_chr6.simMouse.chr6 502228 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 500856 19 + 636262 CAGTTTTAGGGACCATCCA +s simRat_chr6.simRat.chr6 513454 19 + 647215 GAGTTTGAGAGACCATCCA + +a +s simMouse_chr6.simMouse.chr6 502247 15 + 636262 CTTTCAAGTGCAAAA +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 500875 15 + 636262 CTTTCAAGAGCAAAA +s simRat_chr6.simRat.chr6 513473 15 + 647215 CTTTCTAGTGCGAAA + +a +s simMouse_chr6.simMouse.chr6 502262 26 + 636262 TGTGGAAGGATGTCTCAATACCATCT +s Anc0.Anc0refChr3 115836 21 + 222631 TGTGGAATGCTGTCTCATTAC----- +s Anc1.Anc1refChr6 149729 21 + 197743 TGTGGAATGCTGTCTCATTAC----- +s Anc2.Anc2refChr1 27990 21 + 142988 TGTGGAATGCTGTCTCATTAC----- +s mr.mrrefChr3 54835 26 + 181027 TGTGGAAGGATGTCTCAATACTGTCT +s simCow_chr6.simCow.chr6 484509 21 + 602619 TGAGGGATGATGTTGCATTAC----- +s simDog_chr6.simDog.chr6 474827 21 + 593897 TGTGGAATGCTGTCTCATTAC----- +s simMouse_chr6.simMouse.chr6 500890 19 + 636262 TGTGGAAGGATGTCTCAAG------- +s simRat_chr6.simRat.chr6 513488 26 + 647215 CGTGGAAGGATGTCTCAATACTGTCT a s simMouse_chr6.simMouse.chr6 502288 14 + 636262 TACCCTCTTCTCCC @@ -192748,6 +206044,48 @@ s simRat_chr6.simRat.chr6 517404 39 + 647215 ATTCCTGATAATGAAATATCTTACTCTGGGAAATCTTGA a +s simMouse_chr6.simMouse.chr6 506085 3 + 636262 TGT +s Anc0.Anc0refChr3 119683 3 + 222631 CAT +s Anc1.Anc1refChr6 153663 3 + 197743 CAT +s Anc2.Anc2refChr1 32170 3 + 142988 CAT +s mr.mrrefChr3 58654 3 + 181027 TGT +s mr.mrrefChr3 58555 3 + 181027 CGT +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 505988 3 + 636262 AGT +s simRat_chr6.simRat.chr6 517344 3 + 647215 CGT +s simRat_chr6.simRat.chr6 517443 3 + 647215 TGT + +a +s simMouse_chr6.simMouse.chr6 506088 4 + 636262 AAAC +s Anc0.Anc0refChr3 119686 4 + 222631 TTAT +s Anc1.Anc1refChr6 153666 4 + 197743 TTAT +s Anc2.Anc2refChr1 32173 4 + 142988 TTAT +s mr.mrrefChr3 58657 4 + 181027 AAAC +s mr.mrrefChr3 58558 4 + 181027 TTAT +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 505991 4 + 636262 TTAT +s simRat_chr6.simRat.chr6 517347 4 + 647215 TTAT +s simRat_chr6.simRat.chr6 517446 4 + 647215 AAAC + +a +s simMouse_chr6.simMouse.chr6 506092 30 + 636262 CAACATTTCGGGGCTTTGTGGACTCACCAA +s Anc0.Anc0refChr3 119690 30 + 222631 CAAAATTTGGAGGTTTTCTGGAAACATTAA +s Anc1.Anc1refChr6 153670 30 + 197743 CAAAATTTGGAGGTTTTCTGGAAACATTAA +s Anc2.Anc2refChr1 32177 30 + 142988 CAATATTTGGAGGTCTTCTGGAAATGTTAA +s mr.mrrefChr3 58661 30 + 181027 CAACATTTCGGGGTTTTGTGGACTCACCAA +s mr.mrrefChr3 58563 30 + 181027 CAAAATTTTAAGGCTCTCAGGATGCATTGA +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 505996 30 + 636262 CAAAATTTTAGGGCTCTCAGGATGAACTGA +s simRat_chr6.simRat.chr6 517352 30 + 647215 CACAATTTCAAGACTCTCAGGATGCCTTGA +s simRat_chr6.simRat.chr6 517450 30 + 647215 CGACATTTTGGGGTTTTCTGGACTCACCAA + +a s simMouse_chr6.simMouse.chr6 506122 4 + 636262 TACT s Anc0.Anc0refChr3 119720 4 + 222631 GAAT s Anc1.Anc1refChr6 153700 4 + 197743 GAAT @@ -192758,22 +206096,36 @@ s simRat_chr6.simRat.chr6 517480 4 + 647215 GACT a +s simMouse_chr6.simMouse.chr6 506126 5 + 636262 TGATG +s Anc0.Anc0refChr3 119724 4 + 222631 TGGT- +s Anc1.Anc1refChr6 153704 5 + 197743 TGGTG +s Anc2.Anc2refChr1 32211 4 + 142988 TGGT- +s mr.mrrefChr3 58695 5 + 181027 TGATT +s mr.mrrefChr3 58593 5 + 181027 TGGTG +s simDog_chr6.simDog.chr6 479164 4 + 593897 TGGT- +s simHuman_chr6.simHuman.chr6 485594 5 + 601863 TGATG +s simMouse_chr6.simMouse.chr6 506026 5 + 636262 TGGCA +s simRat_chr6.simRat.chr6 517382 5 + 647215 TGGTG +s simRat_chr6.simRat.chr6 517484 5 + 647215 TGATT + +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 +s simMouse_chr6.simMouse.chr6 506134 56 + 636262 CCGAAAGGCAGGCCTATTCACTTGATGCTGAGATTTCTTATTCTGGGAGATGTAGA +s Anc0.Anc0refChr3 119728 55 + 222631 -TAGAAGGCAGGCCTATTTACATGATGCTGAGATATCTTCTGTTGGAAAATGAATA +s Anc1.Anc1refChr6 153709 56 + 197743 CTAGAAGGCAGGCCTATTTACATGATGCTGAGATATCTTCTGTTGGAAAATGAATA +s Anc2.Anc2refChr1 32215 55 + 142988 -TAGAAGGCAGGCATATTTACATGATGCTGATATATCTTCTGTTGGAACATGAATA +s mr.mrrefChr3 58703 56 + 181027 CCGAAAGGCAGGCCTATTCACATGATGCTGAGATATCTTATTCTGGGAGATGTAGA +s mr.mrrefChr3 58598 56 + 181027 CCAAAAGATGGGCCTCTGTTCTTGATAATGAGATATCTTACTCTGGGAAATCTAGA +s simCow_chr6.simCow.chr6 488502 48 + 602619 --------CAGGTGTATTTACATGATGCTGTAATAGCTTCTGTTGGAACATGAATA +s simDog_chr6.simDog.chr6 479168 55 + 593897 -TAGAAGGCAGGCATCTTTACATGATGCTGATATATCTTCTGTTGGAACATGAATA +s simHuman_chr6.simHuman.chr6 485599 56 + 601863 CTAGAAGACAGGCCTATTTGCATGATAATGAGATATTTTCTGTTAGACAGTGAATA +s simMouse_chr6.simMouse.chr6 506031 54 + 636262 CCAAAAGGTGGGCCT--GTTGTTGATACTGAGATATCTTACTCTGGGAGATCTAGA +s simRat_chr6.simRat.chr6 517387 56 + 647215 CCAAAAGATGGGCCCCTATTCCTGATAATGAAATATCTTACTCTGGGAAATCTTGA +s simRat_chr6.simRat.chr6 517492 56 + 647215 CCAAAAGGCAGGCTTATTGACATGATACTGAAATATCTTACTCTGGGAGATGTCAA a s simMouse_chr6.simMouse.chr6 506190 156 + 636262 TGTAAAAGCTCTACACAACGAAGGACTTTAGCGGTCCGCGACACATTCTGCTGGACTTTTAGGACGCGACTGTTGCATCGCCTATAGCAGGGTGAAAAATAATTGGGAACATATAATGGATAGGCCTTGGGAAGGTATAATGTGGAATAATCCTAC @@ -196957,7 +210309,60 @@ s simRat_chr6.simRat.chr6 527959 11 + 647215 TCAGT--AATCG--A a -s simMouse_chr6.simMouse.chr6 516418 75 + 636262 AGGATAGGTGGTCGTCTGCGAAGCAATCACCATTGGCTGCATTTCTCCCCTGCTAGTGCTGCTAATAGTCTCAAT +s simMouse_chr6.simMouse.chr6 516405 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 349811 1 + 636262 G +s simRat_chr6.simRat.chr6 341112 1 + 647215 G +s simRat_chr6.simRat.chr6 527970 1 + 647215 G + +a +s simMouse_chr6.simMouse.chr6 516406 3 + 636262 AAA +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 349812 3 + 636262 ATA +s simRat_chr6.simRat.chr6 341116 3 + 647215 ATA +s simRat_chr6.simRat.chr6 527971 3 + 647215 ATA + +a +s simMouse_chr6.simMouse.chr6 516409 87 + 636262 AGTAATCACAGGATAGGTGGTCGTCTGCGAAGCAATCACCATTGGCTGCATTTCTCCCCTGCTAGTGCTGCTAATAGTCTCAATCCA +s Anc0.Anc0refChr0 13078 12 + 26507 GGCCACCCC---------------------------------------------------------------------------CTT +s Anc1.Anc1refChr6 13400 12 + 197743 GGCCACCCC---------------------------------------------------------------------------CTT +s Anc2.Anc2refChr17 6413 12 + 28526 GGCCACCCT---------------------------------------------------------------------------CTT +s mr.mrrefChr3 69028 12 + 181027 AGCCATCAC---------------------------------------------------------------------------CCA +s mr.mrrefChr5 197031 12 + 294540 GTCCATTGC---------------------------------------------------------------------------CTA +s simCow_chr6.simCow.chr6 322000 11 + 602619 GGCCACCTT---------------------------------------------------------------------------CT- +s simDog_chr6.simDog.chr6 313827 12 + 593897 TGCCACCCT---------------------------------------------------------------------------CTT +s simHuman_chr6.simHuman.chr6 333562 12 + 601863 GGCCACTCC---------------------------------------------------------------------------CTT +s simMouse_chr6.simMouse.chr6 349815 12 + 636262 GTCAATTGC---------------------------------------------------------------------------TTA +s simRat_chr6.simRat.chr6 341119 12 + 647215 GTACATTGC---------------------------------------------------------------------------CTA +s simRat_chr6.simRat.chr6 527974 12 + 647215 GGCCATCAC---------------------------------------------------------------------------CCA + +a +s simMouse_chr6.simMouse.chr6 516496 16 + 636262 TTGGCCCACATGCATT +s Anc0.Anc0refChr0 13092 15 + 26507 CTAGTTCACTT-CACT +s Anc1.Anc1refChr6 13414 16 + 197743 CTAGTTCACTTCCACT +s Anc2.Anc2refChr17 6427 15 + 28526 CTAGTTCACTT-CACT +s mr.mrrefChr3 69042 16 + 181027 CTAGTTCACTTGCATT +s mr.mrrefChr5 197045 16 + 294540 CTAGTTCACTTCCATC +s simCow_chr6.simCow.chr6 322011 10 + 602619 -----TCACTT-CACT +s simDog_chr6.simDog.chr6 313841 15 + 593897 CTAGTTCTCTG-CAAT +s simHuman_chr6.simHuman.chr6 333576 15 + 601863 CTTGTTCACATC-ACG +s simMouse_chr6.simMouse.chr6 349829 16 + 636262 TTAGTTCACTTCCATC +s simRat_chr6.simRat.chr6 341133 16 + 647215 CTAGTGTACTTCCTTC +s simRat_chr6.simRat.chr6 527988 15 + 647215 CTAGTTCACTCG-ATT a s simMouse_chr6.simMouse.chr6 516512 1 + 636262 A @@ -196971,6 +210376,62 @@ s simRat_chr6.simRat.chr6 528003 1 + 647215 A a +s simMouse_chr6.simMouse.chr6 516513 12 + 636262 CTGTCTCATTGG +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 349845 12 + 636262 AAGGATCACTTT +s simRat_chr6.simRat.chr6 341149 12 + 647215 AAGGATCACTTT +s simRat_chr6.simRat.chr6 528004 12 + 647215 ATGGGTCATTCT + +a +s simMouse_chr6.simMouse.chr6 516525 10 + 636262 TAGTCTTTGA +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 349864 10 + 636262 TAGTTCTTGA +s simRat_chr6.simRat.chr6 341170 10 + 647215 GAGCTCTTGA +s simRat_chr6.simRat.chr6 528016 10 + 647215 TAGGACGTAA + +a +s simMouse_chr6.simMouse.chr6 516535 12 + 636262 GAGCTGCCACTT +s Anc0.Anc0refChr0 13141 12 + 26507 CAACTGCCACTT +s Anc1.Anc1refChr6 13464 12 + 197743 CAACTGCCACTT +s Anc2.Anc2refChr17 6476 12 + 28526 CAACTGCCACTT +s mr.mrrefChr3 69081 12 + 181027 GAGCTGCCACTT +s mr.mrrefChr5 197092 12 + 294540 CATCTGTCGATT +s simCow_chr6.simCow.chr6 322055 12 + 602619 GAATAGTCACTT +s simDog_chr6.simDog.chr6 313890 12 + 593897 CAACTGCCACTT +s simHuman_chr6.simHuman.chr6 333625 12 + 601863 CAACTGTTGATT +s simMouse_chr6.simMouse.chr6 349876 12 + 636262 TGTCCATCGATT +s simRat_chr6.simRat.chr6 341182 12 + 647215 CATCTGTCAATT +s simRat_chr6.simRat.chr6 528026 4 + 647215 --------AGTT + +a +s simMouse_chr6.simMouse.chr6 516547 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 349888 1 + 636262 T +s simRat_chr6.simRat.chr6 341194 1 + 647215 T +s simRat_chr6.simRat.chr6 528030 1 + 647215 T + +a s simMouse_chr6.simMouse.chr6 516548 2 + 636262 CA s Anc0.Anc0refChr0 13154 2 + 26507 CA s Anc1.Anc1refChr6 13477 2 + 197743 CA @@ -196981,17 +210442,32 @@ 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 +s simMouse_chr6.simMouse.chr6 516550 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 349889 3 + 636262 CTT +s simRat_chr6.simRat.chr6 341195 3 + 647215 CTT +s simRat_chr6.simRat.chr6 528033 3 + 647215 CTT + +a +s simMouse_chr6.simMouse.chr6 516553 18 + 636262 TTAGGAAGTATAGTTTTT +s Anc0.Anc0refChr0 13159 18 + 26507 TCTTAATGCAGCTTTCTT +s Anc1.Anc1refChr6 13482 18 + 197743 TCTTAATGCAGCTTTCTT +s Anc2.Anc2refChr17 6499 18 + 28526 TCTTAATGGAGCTTTCTT +s mr.mrrefChr3 69099 18 + 181027 TTAGAAAGTAGATTTTTT +s mr.mrrefChr5 197108 18 + 294540 AGTGAAACCTCTTCTCTT +s simCow_chr6.simCow.chr6 322090 18 + 602619 CCTTAATGGAACTTTCTT +s simDog_chr6.simDog.chr6 313913 18 + 593897 TTTTAATAGAGTTTTCTT +s simHuman_chr6.simHuman.chr6 333641 18 + 601863 GCTTAATGCACCTTTCTT +s simMouse_chr6.simMouse.chr6 349892 17 + 636262 AGTGGAAC-TCTCCTCTT +s simRat_chr6.simRat.chr6 341198 18 + 647215 AGTGAACCCTCTTCTCTT +s simRat_chr6.simRat.chr6 528036 18 + 647215 TTAGAAAGTAGATTTTTT a s simMouse_chr6.simMouse.chr6 516571 19 + 636262 GAGGTGACCATCAGTCAGC @@ -196999,7 +210475,88 @@ s simRat_chr6.simRat.chr6 528054 19 + 647215 AAGGTGACCGCCAGTCAGC a -s simMouse_chr6.simMouse.chr6 516629 74 + 636262 AGCTACAGAGACCCTGAACCATGCGCGTTACTGTAATGAACATGTTAATCTATAACTGTGAACCACTGGCCACC +s simMouse_chr6.simMouse.chr6 516590 13 + 636262 TTGGGGCTTAATG +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 349909 13 + 636262 TGGAAGTTTAAAG +s simRat_chr6.simRat.chr6 341216 13 + 647215 TGGAGATTTAAAG +s simRat_chr6.simRat.chr6 528073 13 + 647215 CTGGGGCTTAGTG + +a +s simMouse_chr6.simMouse.chr6 516603 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 349922 1 + 636262 G +s simRat_chr6.simRat.chr6 341229 1 + 647215 G +s simRat_chr6.simRat.chr6 528086 1 + 647215 G + +a +s simMouse_chr6.simMouse.chr6 516604 15 + 636262 GACCCTCCTCCCTTT +s Anc0.Anc0refChr0 13197 15 + 26507 AGTCTTGTGCTGAGT +s Anc1.Anc1refChr6 13520 15 + 197743 AGTCTTGTGCTGAGT +s Anc2.Anc2refChr17 6537 15 + 28526 AGTCTTGTGCTGAGT +s mr.mrrefChr3 69150 15 + 181027 AACCCTCCTCCCTTT +s mr.mrrefChr5 197141 15 + 294540 AACCTTGTCATGGGT +s simCow_chr6.simCow.chr6 322128 15 + 602619 AGTCTTGTGGTGGAT +s simDog_chr6.simDog.chr6 313951 15 + 593897 AGTCCTCTGCTGAGT +s simHuman_chr6.simHuman.chr6 333679 15 + 601863 AGTCTTGTAATGAGT +s simMouse_chr6.simMouse.chr6 349924 15 + 636262 AACCTTGTCCTGGGT +s simRat_chr6.simRat.chr6 341231 15 + 647215 AACCTTGTCATGGGT +s simRat_chr6.simRat.chr6 528087 15 + 647215 AACTCTCCTCCCTTT + +a +s simMouse_chr6.simMouse.chr6 516619 8 + 636262 GAAAGTTT +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 350098 8 + 636262 GCAGGGCT +s simRat_chr6.simRat.chr6 341403 8 + 647215 CCAGGTTT +s simRat_chr6.simRat.chr6 528263 8 + 647215 GCAAGTTG + +a +s simMouse_chr6.simMouse.chr6 516627 78 + 636262 AAAGCTACAGAGACCCTGAACCATGCGCGTTACTGTAATGAACATGTTAATCTATAACTGTGAACCACTGGCCACCCT +s Anc0.Anc0refChr0 13382 4 + 26507 AG--------------------------------------------------------------------------CT +s Anc1.Anc1refChr6 13709 4 + 197743 AG--------------------------------------------------------------------------CT +s Anc2.Anc2refChr17 6724 4 + 28526 AG--------------------------------------------------------------------------GT +s mr.mrrefChr3 69328 4 + 181027 AA--------------------------------------------------------------------------CT +s mr.mrrefChr5 197324 4 + 294540 AG--------------------------------------------------------------------------CT +s simCow_chr6.simCow.chr6 322272 4 + 602619 CG--------------------------------------------------------------------------AT +s simDog_chr6.simDog.chr6 314146 4 + 593897 AA--------------------------------------------------------------------------GT +s simHuman_chr6.simHuman.chr6 333897 4 + 601863 AG--------------------------------------------------------------------------CT +s simMouse_chr6.simMouse.chr6 350107 4 + 636262 AG--------------------------------------------------------------------------CT +s simRat_chr6.simRat.chr6 341412 4 + 647215 AG--------------------------------------------------------------------------CT +s simRat_chr6.simRat.chr6 528271 4 + 647215 GG--------------------------------------------------------------------------CT + +a +s simMouse_chr6.simMouse.chr6 516705 9 + 636262 AAATTCTTT +s Anc0.Anc0refChr0 13386 9 + 26507 CAATACCTT +s Anc1.Anc1refChr6 13713 9 + 197743 CAATACCTT +s Anc2.Anc2refChr17 6728 9 + 28526 CAAAACCGT +s mr.mrrefChr3 69332 9 + 181027 AAATTCTTA +s mr.mrrefChr5 197328 9 + 294540 CCATACCTA +s simCow_chr6.simCow.chr6 322276 9 + 602619 TAAAACCAT +s simDog_chr6.simDog.chr6 314150 9 + 593897 CAAAAGCGT +s simHuman_chr6.simHuman.chr6 333901 9 + 601863 CAATACCTT +s simMouse_chr6.simMouse.chr6 350116 9 + 636262 CCATACCTA +s simRat_chr6.simRat.chr6 341416 9 + 647215 CCCTACCTA +s simRat_chr6.simRat.chr6 528275 9 + 647215 AAATTCTTA a s simMouse_chr6.simMouse.chr6 516714 1 + 636262 T @@ -197007,6 +210564,62 @@ s simRat_chr6.simRat.chr6 528287 1 + 647215 T a +s simMouse_chr6.simMouse.chr6 516715 17 + 636262 TTCACATGAAACAAAGT +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 350126 17 + 636262 TTCACACCAAAAGAATT +s simRat_chr6.simRat.chr6 341426 17 + 647215 TTCACAGCAAAAGAAGT +s simRat_chr6.simRat.chr6 528288 17 + 647215 TTCCCATTAAATGAGGT + +a +s simMouse_chr6.simMouse.chr6 516732 14 + 636262 CATGCAGCCCGCAA +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 350143 14 + 636262 CAGGCATCCCACAA +s simRat_chr6.simRat.chr6 341443 14 + 647215 TAGGCTGCCCACAA +s simRat_chr6.simRat.chr6 528305 14 + 647215 CATGCAGCCCACAA + +a +s simMouse_chr6.simMouse.chr6 516746 6 + 636262 AAAATA +s Anc0.Anc0refChr0 13427 6 + 26507 AAAATA +s Anc1.Anc1refChr6 13754 6 + 197743 AAAATA +s Anc2.Anc2refChr17 6769 6 + 28526 AAAATA +s mr.mrrefChr3 69376 6 + 181027 AAAATA +s mr.mrrefChr5 197369 6 + 294540 TGAAAA +s simCow_chr6.simCow.chr6 322326 6 + 602619 AAGATA +s simDog_chr6.simDog.chr6 314191 6 + 593897 AAAATA +s simHuman_chr6.simHuman.chr6 333955 6 + 601863 AAAAAA +s simMouse_chr6.simMouse.chr6 350157 6 + 636262 TGAAAA +s simRat_chr6.simRat.chr6 341457 6 + 647215 TGAAAA +s simRat_chr6.simRat.chr6 528319 6 + 647215 AAAATA + +a +s simMouse_chr6.simMouse.chr6 516752 44 + 636262 CTGCAATAACCCTGGTCTGCTCATAGAGCAGTCAGAGTACTGCA +s Anc0.Anc0refChr0 13434 44 + 26507 CTGCAATAACTCTGATTTGCACATAAGAATCTCAGATTACTGCA +s Anc1.Anc1refChr6 13761 44 + 197743 CTGCAATAACTCTGATTTGCACATAAGAATCTCAGATTACTGCA +s Anc2.Anc2refChr17 6776 44 + 28526 CTGCAATAACTCTGATTTGCACACCAGAATTTCAGACTACTGCA +s mr.mrrefChr3 69383 44 + 181027 CTGTAATAACCCTGGTCTGCACATAGGGCTGTCAGAGTACTGCA +s mr.mrrefChr5 197376 44 + 294540 TTGTAACAACTCTGGTCTGCCCATAAGAATCTCAGATTACTGCA +s simCow_chr6.simCow.chr6 322333 41 + 602619 ---CTATAGCTCTGTTTTCCACACCAGTATTACAGACTACTACA +s simDog_chr6.simDog.chr6 314198 44 + 593897 CTGTAATAACCCTGACCTGCACACCAGAATTTCAGACAACTGCA +s simHuman_chr6.simHuman.chr6 333962 44 + 601863 TTACAATAACTCTAATTGGCACATGAGATTCCCAGATTACTGCA +s simMouse_chr6.simMouse.chr6 350164 44 + 636262 TTGTAACAACTCTGGTCTGCCCATAAGAATCTCAGTGTACTGCA +s simRat_chr6.simRat.chr6 341464 44 + 647215 TTGTAACAACTCTGGTCAGCCCATAAGAATCTCAGATTATTGCA +s simRat_chr6.simRat.chr6 528326 44 + 647215 CTGTAACAACCCTGGTCTGCACATGGGGCTCTCAGAGTACTGCA + +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 @@ -197037,15 +210650,20 @@ 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 +s simMouse_chr6.simMouse.chr6 518088 74 + 636262 GCATATGAGAAGATGCTGACCTGTGACAAAGGGGAGCCCATCTCTCTCACTATCCAAATAAGCTTGTATGCTGT +s mr.mrrefChr3 70479 71 + 181027 ACATATGAGAAGATTTTGACC---GACAAAGGGGAGCCCATCTCTCTCACTATCCAAATAAGCTTGTATGCTGT +s simRat_chr6.simRat.chr6 529483 71 + 647215 ACGTATGAGAAGATTTTGACC---GACAAAGGGTAGCCCATCTTACGCACTATCCAAATAAGCTTGTATGTTGT + +a +s simMouse_chr6.simMouse.chr6 518162 15 + 636262 ACGTGCTTCCCTCCT +s Anc0.Anc0refChr3 130030 15 + 222631 AAGACCTCCCTTTCT +s Anc1.Anc1refChr6 164422 15 + 197743 AAGACCTCCCTTTCT +s Anc2.Anc2refChr1 43120 15 + 142988 AAGACCTCCCTTTCT +s mr.mrrefChr3 70550 15 + 181027 ACGTGCTTCCCTCCT +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 529554 15 + 647215 ATGTGCTTCCACCCT a s simMouse_chr6.simMouse.chr6 518177 8 + 636262 ACACTCCA @@ -197741,12 +211359,168 @@ s simRat_chr6.simRat.chr6 531007 83 + 647215 ATCTTGCCTAACCATTATTAGGTAATATA-CCCTTATGAATCAGGTATAGTGATTTTATGCTGGCCATTGAACCATCAAATAGA a +s simMouse_chr6.simMouse.chr6 519708 8 + 636262 catttggc +s Anc1.Anc1refChr6 165891 8 + 197743 catttgct +s mr.mrrefChr3 72092 8 + 181027 catttggc +s mr.mrrefChr5 61106 8 - 294540 cattctct +s simMouse_chr6.simMouse.chr6 313890 8 - 636262 cattctct +s simMouse_chr6.simMouse.chr6 256250 8 - 636262 catcctct +s simRat_chr6.simRat.chr6 267994 8 - 647215 cgttctct +s simRat_chr6.simRat.chr6 452693 8 + 647215 cattccct +s simRat_chr6.simRat.chr6 531090 8 + 647215 CACTCACT + +a +s simMouse_chr6.simMouse.chr6 519716 3 + 636262 tgt +s Anc1.Anc1refChr6 165899 3 + 197743 tac +s mr.mrrefChr3 72100 3 + 181027 tgt +s mr.mrrefChr5 61114 3 - 294540 tac +s simMouse_chr6.simMouse.chr6 313898 3 - 636262 tgc +s simMouse_chr6.simMouse.chr6 256258 3 - 636262 tac +s simRat_chr6.simRat.chr6 268002 3 - 647215 cac +s simRat_chr6.simRat.chr6 531098 3 + 647215 TGC + +a +s simMouse_chr6.simMouse.chr6 519719 11 + 636262 tagagaagaag +s Anc1.Anc1refChr6 165902 11 + 197743 tagacaagaag +s mr.mrrefChr3 72103 11 + 181027 tagagaagaag +s mr.mrrefChr5 61117 11 - 294540 tacacaagaag +s simMouse_chr6.simMouse.chr6 313901 11 - 636262 tggagaagaag +s simMouse_chr6.simMouse.chr6 256261 11 - 636262 tacacaagaag +s simRat_chr6.simRat.chr6 268005 11 - 647215 tacacaagaag +s simRat_chr6.simRat.chr6 452701 11 + 647215 tgcaagagaag +s simRat_chr6.simRat.chr6 531101 11 + 647215 CAAAGAAGAAG + +a +s simMouse_chr6.simMouse.chr6 519730 10 + 636262 tccacgctcc +s Anc1.Anc1refChr6 165913 10 + 197743 tctacgtttc +s mr.mrrefChr3 72114 10 + 181027 tccacgctcc +s mr.mrrefChr5 61128 10 - 294540 tctacatttc +s simMouse_chr6.simMouse.chr6 313912 10 - 636262 tctacactcc +s simMouse_chr6.simMouse.chr6 256272 10 - 636262 tctacatttc +s simRat_chr6.simRat.chr6 268016 10 - 647215 tctacatttt +s simRat_chr6.simRat.chr6 452712 10 + 647215 tttacgctcc +s simRat_chr6.simRat.chr6 531127 10 + 647215 tctacgctcc + +a +s simMouse_chr6.simMouse.chr6 519740 1 + 636262 a +s Anc1.Anc1refChr6 165923 1 + 197743 a +s mr.mrrefChr3 72124 1 + 181027 a +s mr.mrrefChr5 61138 1 - 294540 a +s simMouse_chr6.simMouse.chr6 313922 1 - 636262 a +s simMouse_chr6.simMouse.chr6 256282 1 - 636262 a +s simRat_chr6.simRat.chr6 452722 1 + 647215 a +s simRat_chr6.simRat.chr6 531137 1 + 647215 a + +a +s simMouse_chr6.simMouse.chr6 519741 23 + 636262 aagaagcatttacaaaagtgtac +s Anc1.Anc1refChr6 165924 23 + 197743 aagaagcatttacaaaagtgtac +s mr.mrrefChr3 72125 23 + 181027 aagaagcatttacaaaagtgtac +s mr.mrrefChr5 61139 23 - 294540 aagaagcatttacaaaagtgtac +s simMouse_chr6.simMouse.chr6 313923 23 - 636262 aagaagcatttacaaaagtgttt +s simMouse_chr6.simMouse.chr6 256283 23 - 636262 aagaagcacttacaaaagtatac +s simRat_chr6.simRat.chr6 268026 23 - 647215 aagaagcatttacaaaagtatcc +s simRat_chr6.simRat.chr6 452723 23 + 647215 aagaagcatttacaaaagtgtac +s simRat_chr6.simRat.chr6 531138 23 + 647215 aagaagcatctacaaaagtgtac + +a +s simMouse_chr6.simMouse.chr6 519764 1 + 636262 a +s Anc1.Anc1refChr6 165947 1 + 197743 a +s mr.mrrefChr3 72148 1 + 181027 a +s mr.mrrefChr5 61162 1 - 294540 a +s simMouse_chr6.simMouse.chr6 256306 1 - 636262 a +s simRat_chr6.simRat.chr6 268049 1 - 647215 a +s simRat_chr6.simRat.chr6 452746 1 + 647215 a +s simRat_chr6.simRat.chr6 531161 1 + 647215 a + +a +s simMouse_chr6.simMouse.chr6 519765 1 + 636262 t +s Anc1.Anc1refChr6 165948 1 + 197743 t +s mr.mrrefChr3 72149 1 + 181027 t +s mr.mrrefChr5 61163 1 - 294540 t +s simMouse_chr6.simMouse.chr6 313946 1 - 636262 t +s simMouse_chr6.simMouse.chr6 256307 1 - 636262 t +s simRat_chr6.simRat.chr6 268050 1 - 647215 t +s simRat_chr6.simRat.chr6 452747 1 + 647215 t +s simRat_chr6.simRat.chr6 531162 1 + 647215 t + +a +s simMouse_chr6.simMouse.chr6 519766 2 + 636262 tc +s Anc1.Anc1refChr6 165949 2 + 197743 tc +s mr.mrrefChr3 72150 2 + 181027 tc +s mr.mrrefChr5 61164 2 - 294540 tc +s simMouse_chr6.simMouse.chr6 313947 2 - 636262 gt +s simMouse_chr6.simMouse.chr6 256308 2 - 636262 tc +s simRat_chr6.simRat.chr6 268051 2 - 647215 tc +s simRat_chr6.simRat.chr6 452763 2 + 647215 tC +s simRat_chr6.simRat.chr6 531163 2 + 647215 gc + +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 +s simMouse_chr6.simMouse.chr6 519772 17 + 636262 aactcgtctcaTGAAGC +s Anc1.Anc1refChr6 165951 17 + 197743 aactcgtcccaataagc +s mr.mrrefChr3 72156 17 + 181027 aactcgtctcaTGAAGC +s mr.mrrefChr5 61166 17 - 294540 agctcgtcccaataaga +s simMouse_chr6.simMouse.chr6 313949 17 - 636262 agctcattccaataaga +s simMouse_chr6.simMouse.chr6 256310 17 - 636262 agcttgtcccaataaga +s simRat_chr6.simRat.chr6 268053 17 - 647215 agctcgtcccaataagA +s simRat_chr6.simRat.chr6 452765 17 + 647215 TACCTGTCCTCTTGAGA +s simRat_chr6.simRat.chr6 531169 17 + 647215 aacccgtcCCATGAGGA + +a +s simMouse_chr6.simMouse.chr6 519789 9 + 636262 TTGTAAGGG +s Anc1.Anc1refChr6 165968 9 + 197743 ttGTAAGGG +s mr.mrrefChr3 72173 9 + 181027 TTGTAAGGG +s mr.mrrefChr5 61183 9 - 294540 ttGTAGGGG +s simMouse_chr6.simMouse.chr6 313966 9 - 636262 ttTTAGGGG +s simMouse_chr6.simMouse.chr6 256327 9 - 636262 ttgTAGGGG +s simRat_chr6.simRat.chr6 268070 9 - 647215 TAGTAGGGG +s simRat_chr6.simRat.chr6 452783 9 + 647215 TTGTAAGGG +s simRat_chr6.simRat.chr6 531186 9 + 647215 TTGTAAGGG + +a +s simMouse_chr6.simMouse.chr6 519798 4 + 636262 ATGT +s Anc1.Anc1refChr6 165977 4 + 197743 ATGT +s mr.mrrefChr3 72182 4 + 181027 ATGT +s mr.mrrefChr5 61202 4 - 294540 ATGC +s simMouse_chr6.simMouse.chr6 256346 4 - 636262 ATGC +s simRat_chr6.simRat.chr6 268089 4 - 647215 ATGC +s simRat_chr6.simRat.chr6 452794 4 + 647215 ACAC +s simRat_chr6.simRat.chr6 531195 4 + 647215 ATGT + +a +s simMouse_chr6.simMouse.chr6 519802 26 + 636262 GCGTGCAACAGAGGTGAAGCAGTTGA +s Anc1.Anc1refChr6 165981 4 + 197743 ACGT---------------------- +s mr.mrrefChr3 72186 4 + 181027 GCGT---------------------- +s mr.mrrefChr5 61206 4 - 294540 ATGT---------------------- +s simMouse_chr6.simMouse.chr6 313984 4 - 636262 GTTT---------------------- +s simMouse_chr6.simMouse.chr6 256350 4 - 636262 ATGC---------------------- +s simRat_chr6.simRat.chr6 268093 4 - 647215 ATGT---------------------- +s simRat_chr6.simRat.chr6 452798 4 + 647215 GTGC---------------------- +s simRat_chr6.simRat.chr6 531199 4 + 647215 ACGT---------------------- + +a +s simMouse_chr6.simMouse.chr6 519828 5 + 636262 TGGTG +s Anc1.Anc1refChr6 165985 5 + 197743 TGGAT +s mr.mrrefChr3 72190 5 + 181027 TGGTG +s mr.mrrefChr5 61212 5 - 294540 TGGAT +s simMouse_chr6.simMouse.chr6 313990 5 - 636262 GTGGT +s simMouse_chr6.simMouse.chr6 256356 5 - 636262 TGGAG +s simRat_chr6.simRat.chr6 268099 5 - 647215 TGGAG +s simRat_chr6.simRat.chr6 452804 5 + 647215 GGGAT +s simRat_chr6.simRat.chr6 531203 5 + 647215 TGGAG + +a +s simMouse_chr6.simMouse.chr6 519833 21 + 636262 AAGCCGCTGATATCTGCACTA +s Anc1.Anc1refChr6 165990 21 + 197743 AAACCGTTGATATCTGCACTG +s mr.mrrefChr3 72195 21 + 181027 AAGCCGCTGATATCTGCACTA +s mr.mrrefChr5 61217 21 - 294540 AAACGGTTGATATCTGAACTG +s simMouse_chr6.simMouse.chr6 256361 21 - 636262 AAACGGTTGATATCTGAACTG +s simRat_chr6.simRat.chr6 268104 21 - 647215 AAGTGGTTGATTTCTGGACTG +s simRat_chr6.simRat.chr6 531208 21 + 647215 AAGCAGTCGATATGTGCACAT a s simMouse_chr6.simMouse.chr6 519854 35 + 636262 CAGTCTGCCCACTATAATTTCCCACACCCCACAAC @@ -197754,18 +211528,86 @@ s simRat_chr6.simRat.chr6 531229 35 + 647215 AGGTCTGCCCACTATAAGTTCCCACACCTTTCTAC a +s simMouse_chr6.simMouse.chr6 519889 2 + 636262 TG +s Anc1.Anc1refChr6 166011 2 + 197743 TG +s mr.mrrefChr3 72251 2 + 181027 TG +s mr.mrrefChr5 61238 2 - 294540 TG +s simMouse_chr6.simMouse.chr6 256382 2 - 636262 TG +s simRat_chr6.simRat.chr6 268125 2 - 647215 AA +s simRat_chr6.simRat.chr6 531264 2 + 647215 TA + +a +s simMouse_chr6.simMouse.chr6 519891 1 + 636262 A +s Anc1.Anc1refChr6 166013 1 + 197743 A +s mr.mrrefChr3 72253 1 + 181027 A +s mr.mrrefChr5 61240 1 - 294540 A +s simMouse_chr6.simMouse.chr6 256384 1 - 636262 A +s simRat_chr6.simRat.chr6 268127 1 - 647215 A +s simRat_chr6.simRat.chr6 452809 1 + 647215 A +s simRat_chr6.simRat.chr6 531266 1 + 647215 A + +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 +s simMouse_chr6.simMouse.chr6 519893 13 + 636262 GTGGGAGCGATAC +s Anc1.Anc1refChr6 166014 13 + 197743 GTGGGAGTGATAC +s mr.mrrefChr3 72255 13 + 181027 GTGGGAGCGATAC +s mr.mrrefChr5 61241 13 - 294540 GTGGGGGTGATAC +s simMouse_chr6.simMouse.chr6 256385 13 - 636262 GGAGAGGTGATAC +s simRat_chr6.simRat.chr6 268128 13 - 647215 GTGGGGGTGATAC +s simRat_chr6.simRat.chr6 452810 13 + 647215 GTGGGGCCGATAC +s simRat_chr6.simRat.chr6 531269 13 + 647215 GTGGGGGTGTTAC + +a +s simMouse_chr6.simMouse.chr6 519906 19 + 636262 TCTGAAGAGCCATTAGAAG +s Anc1.Anc1refChr6 166027 19 + 197743 TCTGAAGAGCCATTAGAAG +s mr.mrrefChr3 72268 19 + 181027 TCTGAAGAGCCATTAGAAG +s mr.mrrefChr5 61254 19 - 294540 TCTGAAGAGCCATAAGAAG +s simMouse_chr6.simMouse.chr6 256398 19 - 636262 TCTGAAGAGCCATAAGAAG +s simRat_chr6.simRat.chr6 268141 19 - 647215 TCTGAAGAGCCATAAGAAG +s simRat_chr6.simRat.chr6 452824 19 + 647215 TCTGAAGAGCCATAAGAAG +s simRat_chr6.simRat.chr6 531282 19 + 647215 TCTGAAGACCCATGAAAAG + +a +s simMouse_chr6.simMouse.chr6 519925 3 + 636262 GAC +s Anc1.Anc1refChr6 166046 3 + 197743 GAC +s mr.mrrefChr3 72287 3 + 181027 GAC +s mr.mrrefChr5 61273 3 - 294540 GAC +s simMouse_chr6.simMouse.chr6 256417 3 - 636262 GAC +s simRat_chr6.simRat.chr6 268160 3 - 647215 AGC +s simRat_chr6.simRat.chr6 531301 3 + 647215 GAC + +a +s simMouse_chr6.simMouse.chr6 519928 4 + 636262 TTAA +s Anc1.Anc1refChr6 166049 4 + 197743 TTAA +s mr.mrrefChr3 72290 4 + 181027 TTAA +s mr.mrrefChr5 61278 4 - 294540 TTAA +s simMouse_chr6.simMouse.chr6 256422 4 - 636262 TTAA +s simRat_chr6.simRat.chr6 268165 4 - 647215 TTAA +s simRat_chr6.simRat.chr6 531304 4 + 647215 TTAA + +a +s simMouse_chr6.simMouse.chr6 519932 9 + 636262 GAAGCCTAA +s Anc1.Anc1refChr6 166053 9 + 197743 AAAACCTGA +s mr.mrrefChr3 72294 9 + 181027 GAAGCCTAA +s mr.mrrefChr5 61282 9 - 294540 AAAACCTGA +s simMouse_chr6.simMouse.chr6 256426 7 - 636262 AAAACCT-- +s simRat_chr6.simRat.chr6 268169 9 - 647215 AAAACTTCA +s simRat_chr6.simRat.chr6 452843 9 + 647215 GAGACCCGA +s simRat_chr6.simRat.chr6 531308 9 + 647215 GAAACCTAA + +a +s simMouse_chr6.simMouse.chr6 519941 1 + 636262 T +s Anc1.Anc1refChr6 166062 1 + 197743 T +s mr.mrrefChr3 72303 1 + 181027 T +s mr.mrrefChr5 61291 1 - 294540 T +s simMouse_chr6.simMouse.chr6 313995 1 - 636262 T +s simRat_chr6.simRat.chr6 268178 1 - 647215 T +s simRat_chr6.simRat.chr6 452852 1 + 647215 T +s simRat_chr6.simRat.chr6 531317 1 + 647215 G a s simMouse_chr6.simMouse.chr6 519942 29 + 636262 ATATGAGAAGGACAGTACAGAAACCTATC @@ -197773,7 +211615,235 @@ s simRat_chr6.simRat.chr6 531318 29 + 647215 ATATAAGAAGGATGTTTCAGAAGCCTAAT a -s simMouse_chr6.simMouse.chr6 520057 7 + 636262 AACAAAC +s simMouse_chr6.simMouse.chr6 519971 1 + 636262 A +s Anc1.Anc1refChr6 166063 1 + 197743 A +s mr.mrrefChr3 72333 1 + 181027 A +s mr.mrrefChr5 61292 1 - 294540 A +s simMouse_chr6.simMouse.chr6 313996 1 - 636262 A +s simRat_chr6.simRat.chr6 268179 1 - 647215 A +s simRat_chr6.simRat.chr6 452853 1 + 647215 A +s simRat_chr6.simRat.chr6 531347 1 + 647215 G + +a +s simMouse_chr6.simMouse.chr6 519972 18 + 636262 TAGTGGAAAAGCACATGA +s Anc1.Anc1refChr6 166064 18 + 197743 TAGTGGAAAAGCACATGA +s mr.mrrefChr3 72334 18 + 181027 TAGTGGAAAAGCACATGA +s mr.mrrefChr5 61293 18 - 294540 TAGTGGAGAAGCATACGA +s simMouse_chr6.simMouse.chr6 313997 18 - 636262 CAGTGGAGAAGCATACGG +s simMouse_chr6.simMouse.chr6 256433 18 - 636262 TACTGGATAAGTGTACGA +s simRat_chr6.simRat.chr6 268180 18 - 647215 AACCGGAGAAACGTATGT +s simRat_chr6.simRat.chr6 452854 18 + 647215 TAGGGGAAAAGCACACGA +s simRat_chr6.simRat.chr6 531348 18 + 647215 CAGTGGAGAAGCACACGA + +a +s simMouse_chr6.simMouse.chr6 519990 14 + 636262 AGAGGACCAGCACT +s Anc1.Anc1refChr6 166082 14 + 197743 AGAAGGCCAGCACT +s mr.mrrefChr3 72352 14 + 181027 AGAGGACCAGCACT +s mr.mrrefChr5 61311 14 - 294540 AAAAGGCCAGCAGT +s simMouse_chr6.simMouse.chr6 256451 14 - 636262 AAAAGGCCAGCAGT +s simRat_chr6.simRat.chr6 268198 14 - 647215 AAAAAGCCTGCAGT +s simRat_chr6.simRat.chr6 452872 14 + 647215 AAAGGAACAGTGGT +s simRat_chr6.simRat.chr6 531366 14 + 647215 AGAGGACCAGCAGT + +a +s simMouse_chr6.simMouse.chr6 520004 3 + 636262 CAA +s Anc1.Anc1refChr6 166096 3 + 197743 AAA +s mr.mrrefChr3 72366 3 + 181027 CAA +s mr.mrrefChr5 61325 3 - 294540 AAA +s simMouse_chr6.simMouse.chr6 314015 3 - 636262 AAA +s simMouse_chr6.simMouse.chr6 256465 3 - 636262 AAA +s simRat_chr6.simRat.chr6 268212 3 - 647215 AAA +s simRat_chr6.simRat.chr6 452886 3 + 647215 AAA +s simRat_chr6.simRat.chr6 531380 3 + 647215 GAA + +a +s simMouse_chr6.simMouse.chr6 520007 2 + 636262 AC +s Anc1.Anc1refChr6 166099 2 + 197743 AC +s mr.mrrefChr3 72369 2 + 181027 AC +s mr.mrrefChr5 61342 2 - 294540 AC +s simMouse_chr6.simMouse.chr6 314032 2 - 636262 AC +s simMouse_chr6.simMouse.chr6 256482 2 - 636262 AC +s simRat_chr6.simRat.chr6 268229 2 - 647215 AT +s simRat_chr6.simRat.chr6 531383 2 + 647215 AC + +a +s simMouse_chr6.simMouse.chr6 520009 24 + 636262 TCTGAAGAGCCATAACGTGGACAA +s Anc1.Anc1refChr6 166101 24 + 197743 TCTGAAGAGCCATAAGACAGACAA +s mr.mrrefChr3 72371 24 + 181027 TCTGAAGAGCCATAACGTGGACAA +s mr.mrrefChr5 61344 24 - 294540 TCTGAAGAGCCATAAGACAGACAA +s simMouse_chr6.simMouse.chr6 314034 24 - 636262 TCTGAGGAGACATAAGACACACAA +s simMouse_chr6.simMouse.chr6 256484 14 - 636262 TCTGGTGAGCC----------AAG +s simRat_chr6.simRat.chr6 268231 24 - 647215 TCTGAAGAGCCATAAGATGGAAAA +s simRat_chr6.simRat.chr6 452891 24 + 647215 TCTGAAAAGCCATAACACAGACGA +s simRat_chr6.simRat.chr6 531385 24 + 647215 TCTGAAGAGTCATAACACGGACAA + +a +s simMouse_chr6.simMouse.chr6 520033 1 + 636262 T +s Anc1.Anc1refChr6 166125 1 + 197743 T +s mr.mrrefChr3 72395 1 + 181027 T +s mr.mrrefChr5 61368 1 - 294540 T +s simMouse_chr6.simMouse.chr6 314058 1 - 636262 T +s simMouse_chr6.simMouse.chr6 256498 1 - 636262 T +s simRat_chr6.simRat.chr6 268255 1 - 647215 T +s simRat_chr6.simRat.chr6 531409 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 520034 13 + 636262 CAAGAAACACAAT +s Anc1.Anc1refChr6 166126 13 + 197743 CAAGAAATATAAT +s mr.mrrefChr3 72396 13 + 181027 CAAGAAACACAAT +s mr.mrrefChr5 61369 13 - 294540 CAAGAAATCTAAT +s simMouse_chr6.simMouse.chr6 314075 13 - 636262 CAAGAAATCTAAT +s simMouse_chr6.simMouse.chr6 256499 13 - 636262 CAAAAAATCTAAT +s simRat_chr6.simRat.chr6 268256 13 - 647215 CAGCAAATCTAAT +s simRat_chr6.simRat.chr6 531453 13 + 647215 CAAGGACAATCAT + +a +s simMouse_chr6.simMouse.chr6 520047 17 + 636262 ATAGTGGAGAAACAAAC +s Anc1.Anc1refChr6 166139 10 + 197743 ATAGTGGAGA------- +s mr.mrrefChr3 72409 10 + 181027 ATAGTGGAGA------- +s mr.mrrefChr5 61382 10 - 294540 ATTGTGGAGA------- +s simMouse_chr6.simMouse.chr6 314088 10 - 636262 ATTGTGGAGA------- +s simMouse_chr6.simMouse.chr6 256512 10 - 636262 GTCGTGGAGA------- +s simRat_chr6.simRat.chr6 268269 10 - 647215 ATTGTGGAGA------- +s simRat_chr6.simRat.chr6 452915 10 + 647215 ATAGTGGGGA------- +s simRat_chr6.simRat.chr6 531466 10 + 647215 ATATTGGGGA------- + +a +s simMouse_chr6.simMouse.chr6 520064 4 + 636262 GAAA +s Anc1.Anc1refChr6 166149 4 + 197743 AAAA +s mr.mrrefChr3 72419 4 + 181027 GAAA +s mr.mrrefChr5 61399 4 - 294540 AAAA +s simMouse_chr6.simMouse.chr6 256529 4 - 636262 ATAA +s simRat_chr6.simRat.chr6 268286 4 - 647215 AAAA +s simRat_chr6.simRat.chr6 452932 4 + 647215 AAAA +s simRat_chr6.simRat.chr6 531476 4 + 647215 GAGA + +a +s simMouse_chr6.simMouse.chr6 520068 27 + 636262 GCGGTCATGGTCATAAGTGCCATCTCC +s Anc1.Anc1refChr6 166153 27 + 197743 ATGGTCATAGTCAGAAGTGCCACCTCC +s mr.mrrefChr3 72423 27 + 181027 GCGGTCATGGTCATAAGTGCCATCTCC +s mr.mrrefChr5 61403 27 - 294540 ATGGCCATACTCAGAAGTGCCACCTTC +s simMouse_chr6.simMouse.chr6 314103 27 - 636262 ATGGAAATAATCAGAAGTGCGACAGTC +s simMouse_chr6.simMouse.chr6 256533 27 - 636262 ATGGCCATACTCAGAAGTGCCACCTTC +s simRat_chr6.simRat.chr6 268290 27 - 647215 ATGGCCATACTCAGAAGTGCCACCCTC +s simRat_chr6.simRat.chr6 452936 27 + 647215 ACGGCCATACTCAAAAGTGCCACCTTC +s simRat_chr6.simRat.chr6 531480 27 + 647215 ACGGCCATACTCAAAAGTGCCACCTTC + +a +s simMouse_chr6.simMouse.chr6 520095 7 + 636262 AAGTACA +s Anc1.Anc1refChr6 166180 7 + 197743 AAATACA +s mr.mrrefChr3 72450 7 + 181027 AAGTACA +s mr.mrrefChr5 61430 7 - 294540 AAATACA +s simMouse_chr6.simMouse.chr6 314130 7 - 636262 AAATACA +s simRat_chr6.simRat.chr6 452963 7 + 647215 AAGTACA +s simRat_chr6.simRat.chr6 531507 7 + 647215 AAGTACA + +a +s simMouse_chr6.simMouse.chr6 520102 8 + 636262 CCTAATAT +s Anc1.Anc1refChr6 166187 8 + 197743 CCTAATAT +s mr.mrrefChr3 72457 8 + 181027 CCTAATAT +s mr.mrrefChr5 61437 8 - 294540 CCTAATAT +s simMouse_chr6.simMouse.chr6 314137 8 - 636262 CCTAAGAT +s simMouse_chr6.simMouse.chr6 256560 8 - 636262 CCTAATAT +s simRat_chr6.simRat.chr6 268317 8 - 647215 CCTAATAT +s simRat_chr6.simRat.chr6 452970 8 + 647215 CCTAATAT +s simRat_chr6.simRat.chr6 531514 8 + 647215 CCTAATAT + +a +s simMouse_chr6.simMouse.chr6 520110 35 + 636262 GGTGAGGGAACAAAAACAGTCAAGTAATCCTCACA +s Anc1.Anc1refChr6 166195 35 + 197743 GGTGAGGGAACAAAAACAGTCAAGTAAACCTCACA +s mr.mrrefChr3 72465 35 + 181027 GGTGAGGGAACAAAAACAGTCAAGTAATCCTCACA +s mr.mrrefChr5 61445 35 - 294540 GGTGAGGGAACAAAAACAGTCAAGTAAACCTTATA +s simMouse_chr6.simMouse.chr6 314145 35 - 636262 GGTGAGGGAATAAAAACAGTCCAGTAAATCTCATA +s simMouse_chr6.simMouse.chr6 256568 35 - 636262 GGTGAGGGAACAAAAACAGTCAAGTAAACCTTGTA +s simRat_chr6.simRat.chr6 268325 35 - 647215 GGTGAGGGAACAAAAACAGTCAAGTAAACCTTGTA +s simRat_chr6.simRat.chr6 453051 35 + 647215 GGTGATGGAACAAAAACAGTCAAGTAAACCTTATA +s simRat_chr6.simRat.chr6 531522 35 + 647215 AGTGAGTGAACAAAAAGAGTCTAGTAAACCTCTCA + +a +s simMouse_chr6.simMouse.chr6 520145 1 + 636262 T +s Anc1.Anc1refChr6 166230 1 + 197743 T +s mr.mrrefChr3 72500 1 + 181027 T +s mr.mrrefChr5 61480 1 - 294540 T +s simMouse_chr6.simMouse.chr6 314180 1 - 636262 T +s simMouse_chr6.simMouse.chr6 256603 1 - 636262 T +s simRat_chr6.simRat.chr6 453086 1 + 647215 T +s simRat_chr6.simRat.chr6 531557 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 520146 6 + 636262 GGCATG +s Anc1.Anc1refChr6 166231 6 + 197743 GGCATG +s mr.mrrefChr3 72501 6 + 181027 GGCATG +s mr.mrrefChr5 61481 6 - 294540 GGTATG +s simMouse_chr6.simMouse.chr6 314181 6 - 636262 GGTATG +s simMouse_chr6.simMouse.chr6 256604 6 - 636262 GGCATG +s simRat_chr6.simRat.chr6 268360 6 - 647215 CGGTTG +s simRat_chr6.simRat.chr6 453087 6 + 647215 TGTTTG +s simRat_chr6.simRat.chr6 531558 6 + 647215 AGCATG + +a +s simMouse_chr6.simMouse.chr6 520152 25 + 636262 ATGGACAGGAGAATGCAGGTAAAAG +s Anc1.Anc1refChr6 166237 25 + 197743 AAGGACAGGAACATGCAAGTAAAAG +s mr.mrrefChr3 72507 25 + 181027 ATGGACAGGAGAATGCAGGTAAAAG +s mr.mrrefChr5 61487 25 - 294540 AAGGACAGGAACATTCAAGTAAAAG +s simMouse_chr6.simMouse.chr6 314191 25 - 636262 GAGGACAAGAACATTCACGTAAAAG +s simMouse_chr6.simMouse.chr6 256610 25 - 636262 AAGGACAGGAACATTCAAGTAAGAG +s simRat_chr6.simRat.chr6 268366 25 - 647215 AAGGACTGGAACATTCAAATAAAAG +s simRat_chr6.simRat.chr6 453093 25 + 647215 AAGCACAGGGACATTTGAGTAAAAG +s simRat_chr6.simRat.chr6 531564 25 + 647215 ATGGACAAGAGCATTCAAGTAAGAA + +a +s simMouse_chr6.simMouse.chr6 520177 12 + 636262 CAAGCAAACCTC +s Anc1.Anc1refChr6 166262 12 + 197743 CAAGCAAACCTC +s mr.mrrefChr3 72532 12 + 181027 CAAGCAAACCTC +s mr.mrrefChr5 61524 12 - 294540 CAGGTAAACCTC +s simMouse_chr6.simMouse.chr6 314228 12 - 636262 CAAGTAAACCTC +s simMouse_chr6.simMouse.chr6 256644 12 - 636262 CAGGTGAACCTC +s simRat_chr6.simRat.chr6 268403 12 - 647215 CAGGTAAACCTC +s simRat_chr6.simRat.chr6 453137 12 + 647215 CAGGTAAACCTC +s simRat_chr6.simRat.chr6 531602 12 + 647215 CAAGTAAACCTC + +a +s simMouse_chr6.simMouse.chr6 520189 2 + 636262 AT +s Anc1.Anc1refChr6 166274 2 + 197743 AT +s mr.mrrefChr3 72544 2 + 181027 AT +s mr.mrrefChr5 61536 2 - 294540 AT +s simMouse_chr6.simMouse.chr6 314240 2 - 636262 AT +s simMouse_chr6.simMouse.chr6 256656 2 - 636262 AC +s simRat_chr6.simRat.chr6 268415 2 - 647215 AT +s simRat_chr6.simRat.chr6 531614 2 + 647215 AT + +a +s simMouse_chr6.simMouse.chr6 520191 33 + 636262 CTGGTATAAAGGAGCATAAGAGATAGATTGTAT +s Anc1.Anc1refChr6 166276 33 + 197743 CCGGTGTGAAGGAGCATAAGAGATAGATTGTAT +s mr.mrrefChr3 72546 33 + 181027 CTGGTATAAAGGAGCATAAGAGATAGATTGTAT +s mr.mrrefChr5 61538 33 - 294540 ACAGTGTGAAGGAGCATACGAAACAGATTGTAT +s simMouse_chr6.simMouse.chr6 314242 33 - 636262 ACAGTGTGAAGGAGCACACAAAAGAAATTGTAT +s simMouse_chr6.simMouse.chr6 256658 33 - 636262 ACAGTTTGAAGGAGCATACGAAACAGGTTGTAT +s simRat_chr6.simRat.chr6 268417 33 - 647215 ACAGTGGGAAGGAGCATACGGAACAGATTGTAT +s simRat_chr6.simRat.chr6 453149 33 + 647215 TCGGTATGAAGGAGCGTAAGAAATTGATTGTAT +s simRat_chr6.simRat.chr6 531616 33 + 647215 TCGGTATGAAGGAGCATAAGAAATAGATTGTAT + +a +s simMouse_chr6.simMouse.chr6 520224 2 + 636262 TA +s Anc1.Anc1refChr6 166309 2 + 197743 TA +s mr.mrrefChr3 72579 2 + 181027 TA +s mr.mrrefChr5 61571 2 - 294540 TA +s simMouse_chr6.simMouse.chr6 314275 2 - 636262 TA +s simMouse_chr6.simMouse.chr6 256691 2 - 636262 TA +s simRat_chr6.simRat.chr6 268450 2 - 647215 TA +s simRat_chr6.simRat.chr6 531649 2 + 647215 TA + +a +s simMouse_chr6.simMouse.chr6 520226 3 + 636262 TAG +s Anc1.Anc1refChr6 166311 3 + 197743 TAG +s mr.mrrefChr3 72581 3 + 181027 TAG +s mr.mrrefChr5 61573 3 - 294540 TAG +s simMouse_chr6.simMouse.chr6 314277 3 - 636262 TAG +s simMouse_chr6.simMouse.chr6 256693 3 - 636262 TAG +s simRat_chr6.simRat.chr6 268452 3 - 647215 TAG +s simRat_chr6.simRat.chr6 453182 3 + 647215 TAG +s simRat_chr6.simRat.chr6 531654 3 + 647215 TAG a s simMouse_chr6.simMouse.chr6 520229 2 + 636262 TC @@ -197781,6 +211851,49 @@ s simRat_chr6.simRat.chr6 531657 2 + 647215 TA a +s simMouse_chr6.simMouse.chr6 520231 7 + 636262 AGACTAG +s Anc1.Anc1refChr6 166314 7 + 197743 GGGCTAG +s mr.mrrefChr3 72586 7 + 181027 AGACTAG +s mr.mrrefChr5 61576 7 - 294540 GGGCAGG +s simMouse_chr6.simMouse.chr6 314280 7 - 636262 TGGGAGG +s simMouse_chr6.simMouse.chr6 256696 7 - 636262 GGGCAGG +s simRat_chr6.simRat.chr6 268455 7 - 647215 GGGCAGG +s simRat_chr6.simRat.chr6 453185 7 + 647215 AGTCAGA +s simRat_chr6.simRat.chr6 531659 7 + 647215 GGAGTAG + +a +s simMouse_chr6.simMouse.chr6 520238 1 + 636262 A +s Anc1.Anc1refChr6 166321 1 + 197743 A +s mr.mrrefChr3 72593 1 + 181027 A +s mr.mrrefChr5 61588 1 - 294540 A +s simMouse_chr6.simMouse.chr6 314292 1 - 636262 A +s simMouse_chr6.simMouse.chr6 256708 1 - 636262 A +s simRat_chr6.simRat.chr6 268467 1 - 647215 A +s simRat_chr6.simRat.chr6 453197 1 + 647215 A +s simRat_chr6.simRat.chr6 531669 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 520239 4 + 636262 TGAA +s Anc1.Anc1refChr6 166322 4 + 197743 TGAA +s mr.mrrefChr3 72594 4 + 181027 TGAA +s mr.mrrefChr5 61589 4 - 294540 TGAA +s simMouse_chr6.simMouse.chr6 314293 4 - 636262 TGTA +s simMouse_chr6.simMouse.chr6 256709 4 - 636262 TGAA +s simRat_chr6.simRat.chr6 268468 4 - 647215 TGAA +s simRat_chr6.simRat.chr6 453205 4 + 647215 TGAA +s simRat_chr6.simRat.chr6 531670 4 + 647215 TGAA + +a +s simMouse_chr6.simMouse.chr6 520243 10 + 636262 ATGCATGTGC +s Anc1.Anc1refChr6 166326 10 + 197743 GTGCCCGTGC +s mr.mrrefChr3 72598 10 + 181027 ATGCATGTGC +s mr.mrrefChr5 61593 10 - 294540 GTGCCCGTGG +s simMouse_chr6.simMouse.chr6 256713 10 - 636262 GTGCCCATGG +s simRat_chr6.simRat.chr6 268472 10 - 647215 GTGTCCGTGG +s simRat_chr6.simRat.chr6 453209 10 + 647215 ATGCTTGTGT +s simRat_chr6.simRat.chr6 531674 10 + 647215 ATGCATGTGT + +a s simMouse_chr6.simMouse.chr6 520253 18 + 636262 GATTCAGTTTTTTCATCA s Anc0.Anc0refChr3 131442 8 + 222631 -----AGTGATAC----- s Anc1.Anc1refChr6 166338 13 + 197743 -----AGTGATACCATCA @@ -200247,6 +214360,34 @@ s simRat_chr6.simRat.chr6 538057 25 + 647215 ACAATCCCGTTTTGAAAGATGTACT--- a +s simMouse_chr6.simMouse.chr6 527028 35 + 636262 CTACCTCTTTCCTGGTGACAAAGTGTCTGCCTTTC +s Anc0.Anc0refChr3 137312 27 + 222631 --------TCCCTAGAGATAAAGAGTCTGTCTTAC +s Anc1.Anc1refChr6 172529 35 + 197743 CTACCTCTTCCCTAGAGATAAAGAGTCTGTCTTAC +s Anc2.Anc2refChr1 50640 27 + 142988 --------TCCCTAGAGATCAAGAGTCTGTCTTAT +s mr.mrrefChr3 78856 35 + 181027 CTACCTCTTTCCTGGTGACAAAGTGTCTGCCTTTC +s mr.mrrefChr5 117913 35 - 294540 CTACTTCTTTCCTGGAGATAAAGTGTCTGCCTTTC +s simCow_chr6.simCow.chr6 507746 26 + 602619 --------TCCCTAGATATCCAGGCTCTGTCTT-T +s simDog_chr6.simDog.chr6 497021 27 + 593897 --------TCCCTACAGATCAAGAGTCAGCCTTAT +s simHuman_chr6.simHuman.chr6 504402 35 + 601863 CTACCCTTTCCCTAGAAATTTGGAGTCTGTCTTAC +s simMouse_chr6.simMouse.chr6 307687 35 - 636262 CTACTTCTTTCCTGGAGATAAAGTGTCTGCCTTTC +s simRat_chr6.simRat.chr6 327192 35 - 647215 CTACCTCTTTCCTGGAGATAAAGTGTCCGCCTACC +s simRat_chr6.simRat.chr6 538082 31 + 647215 CCCGCTCTTTCA----GACAAAGTTTCTGCCTTTC + +a +s simMouse_chr6.simMouse.chr6 527063 1 + 636262 C +s Anc0.Anc0refChr3 137339 1 + 222631 C +s Anc1.Anc1refChr6 172564 1 + 197743 C +s Anc2.Anc2refChr1 50667 1 + 142988 C +s mr.mrrefChr3 78891 1 + 181027 C +s mr.mrrefChr5 117948 1 - 294540 T +s simCow_chr6.simCow.chr6 507772 1 + 602619 C +s simDog_chr6.simDog.chr6 497048 1 + 593897 C +s simHuman_chr6.simHuman.chr6 504437 1 + 601863 C +s simMouse_chr6.simMouse.chr6 307723 1 - 636262 T +s simRat_chr6.simRat.chr6 327227 1 - 647215 T +s simRat_chr6.simRat.chr6 538113 1 + 647215 C + +a s simMouse_chr6.simMouse.chr6 527064 1 + 636262 T s Anc0.Anc0refChr3 137340 1 + 222631 C s Anc1.Anc1refChr6 172565 1 + 197743 C @@ -200258,6 +214399,145 @@ s simRat_chr6.simRat.chr6 538114 1 + 647215 C a +s simMouse_chr6.simMouse.chr6 527065 16 + 636262 GAGCTCTTTCCTTATG +s Anc0.Anc0refChr3 137341 16 + 222631 AAGCTAGTTCCTTGTT +s Anc1.Anc1refChr6 172566 16 + 197743 AAGCTAGTTCCTTGTT +s Anc2.Anc2refChr1 50669 16 + 142988 AAGCTAGTTCCTTGTT +s mr.mrrefChr3 78893 16 + 181027 GAGCTAGTTCCTTATG +s mr.mrrefChr5 117949 16 - 294540 GAGCTAGTTCCTTATA +s simCow_chr6.simCow.chr6 507774 16 + 602619 AAGCTAGTTCCTTGTG +s simDog_chr6.simDog.chr6 497050 16 + 593897 AAGCTATGTCCTTGTT +s simHuman_chr6.simHuman.chr6 504439 16 + 601863 AAGCTAGTTCTTTGTT +s simMouse_chr6.simMouse.chr6 307724 16 - 636262 GAGCTAGTTCCTTATA +s simRat_chr6.simRat.chr6 327228 16 - 647215 GAGCTAGTTCTTTGTA +s simRat_chr6.simRat.chr6 538115 16 + 647215 GAGCCAGTTCCTTATG + +a +s simMouse_chr6.simMouse.chr6 527081 22 + 636262 ATTACCTGTTCATATGCCTCAT +s Anc0.Anc0refChr3 137357 22 + 222631 ATTACCTGTTCACAAGTCTCAT +s Anc1.Anc1refChr6 172582 22 + 197743 ATTACCTGTTCACAAGTCTCAT +s Anc2.Anc2refChr1 50685 22 + 142988 ACTGTCTGTTCACAAGTCTCAT +s mr.mrrefChr3 78909 22 + 181027 ATTACCTGTTCATATGTCTCAT +s mr.mrrefChr5 117965 22 - 294540 ATTACCTGTTCATATGTCTCAT +s simCow_chr6.simCow.chr6 507790 22 + 602619 ACTGTGTGATCACCAGTCTCAT +s simDog_chr6.simDog.chr6 497067 22 + 593897 ACTGTCTGTCCACAGGTCTGAT +s simHuman_chr6.simHuman.chr6 504455 22 + 601863 ATTACCTGTTCACAAGTCTCAT +s simMouse_chr6.simMouse.chr6 307740 22 - 636262 ATTACCTGTTCATATGTCTCAT +s simRat_chr6.simRat.chr6 327244 22 - 647215 ATTACCTGTCCATATGTCTCAT +s simRat_chr6.simRat.chr6 538131 18 + 647215 AT----TGTTCAGATGTCTCAT + +a +s simMouse_chr6.simMouse.chr6 527103 7 + 636262 CAGATAG +s Anc0.Anc0refChr3 137379 7 + 222631 CAGTTAG +s Anc1.Anc1refChr6 172604 7 + 197743 CAGTTAG +s Anc2.Anc2refChr1 50707 7 + 142988 GGGTAAG +s mr.mrrefChr3 78931 7 + 181027 CAGATAG +s mr.mrrefChr5 117987 7 - 294540 CAGATAG +s simCow_chr6.simCow.chr6 507812 7 + 602619 GGGTAAG +s simDog_chr6.simDog.chr6 497090 7 + 593897 GGTTAAG +s simHuman_chr6.simHuman.chr6 504477 7 + 601863 CAGTTAG +s simMouse_chr6.simMouse.chr6 307762 7 - 636262 CAGATAG +s simRat_chr6.simRat.chr6 327266 7 - 647215 CAATTAG +s simRat_chr6.simRat.chr6 538149 7 + 647215 CAGATAG + +a +s simMouse_chr6.simMouse.chr6 527110 30 + 636262 GACCTCTAACATGATTGTGTGTTGATAGAG +s Anc0.Anc0refChr3 137386 25 + 222631 GAGATC-ATCAACATTGTG----GATAGAG +s Anc1.Anc1refChr6 172611 30 + 197743 GAGATCTATCAACATTGTGTGCTGATAGAG +s Anc2.Anc2refChr1 50714 25 + 142988 AAAATC-ATCAACATCGTG----GATAGAG +s mr.mrrefChr3 78938 30 + 181027 GAGCTCTAACATGATTGGATGTTGATAGAG +s mr.mrrefChr5 117994 30 - 294540 GAGCTCTAACATGATTGTGTGCTGATAGGG +s simCow_chr6.simCow.chr6 507819 24 + 602619 TAAACC-A-CAACCTCATG----TATAGAG +s simDog_chr6.simDog.chr6 497097 25 + 593897 AGAATC-ATCAACACCGTG----GACAGGG +s simHuman_chr6.simHuman.chr6 504484 26 + 601863 GAGATCCATTAACATTGTG----GATAAAA +s simMouse_chr6.simMouse.chr6 307769 30 - 636262 GAGCTCTAACATGATTGTGTGCTGATAGGG +s simRat_chr6.simRat.chr6 327273 30 - 647215 AAGCTCTAACATGATTGTGTGCTTATGGAG +s simRat_chr6.simRat.chr6 538158 30 + 647215 GAGTTGTAACATGATTGGATGCTGATAGAG + +a +s simMouse_chr6.simMouse.chr6 527140 10 + 636262 TGATATTAAA +s Anc0.Anc0refChr3 137411 10 + 222631 TGGTATAAGA +s Anc1.Anc1refChr6 172641 10 + 197743 TGGTATAAGA +s Anc2.Anc2refChr1 50739 10 + 142988 AGGTATAAGA +s mr.mrrefChr3 78968 10 + 181027 TGATATTAAA +s mr.mrrefChr5 118024 10 - 294540 GGGTATCAAA +s simCow_chr6.simCow.chr6 507843 10 + 602619 TGGTATAAGA +s simDog_chr6.simDog.chr6 497122 10 + 593897 AGGTATAGGG +s simHuman_chr6.simHuman.chr6 504511 10 + 601863 TGGTGTAAGA +s simMouse_chr6.simMouse.chr6 307799 10 - 636262 GGGTATCAAA +s simRat_chr6.simRat.chr6 327303 10 - 647215 TGGTATTAAA +s simRat_chr6.simRat.chr6 538188 10 + 647215 TGGTATAAAA + +a +s simMouse_chr6.simMouse.chr6 527150 3 + 636262 ATA +s Anc0.Anc0refChr3 137421 3 + 222631 GTA +s Anc1.Anc1refChr6 172651 3 + 197743 GTA +s Anc2.Anc2refChr1 50749 3 + 142988 GTA +s mr.mrrefChr3 78978 3 + 181027 ATA +s mr.mrrefChr5 118034 3 - 294540 ATA +s simCow_chr6.simCow.chr6 507853 3 + 602619 GTA +s simDog_chr6.simDog.chr6 497132 3 + 593897 GTA +s simHuman_chr6.simHuman.chr6 504521 3 + 601863 GTA +s simMouse_chr6.simMouse.chr6 307809 3 - 636262 ATA +s simRat_chr6.simRat.chr6 327359 3 - 647215 AAA +s simRat_chr6.simRat.chr6 538198 3 + 647215 ATA + +a +s simMouse_chr6.simMouse.chr6 527153 9 + 636262 CTAGTAGCT +s Anc0.Anc0refChr3 137428 9 + 222631 ATAATAGGA +s Anc1.Anc1refChr6 172658 9 + 197743 ATAATAGGA +s Anc2.Anc2refChr1 50756 9 + 142988 ATAATAGGA +s mr.mrrefChr3 78981 9 + 181027 ATAGTAGCT +s mr.mrrefChr5 118037 9 - 294540 ATGGTAGCA +s simCow_chr6.simCow.chr6 507860 9 + 602619 CTAATAAGA +s simDog_chr6.simDog.chr6 497139 9 + 593897 ATAATAGGG +s simHuman_chr6.simHuman.chr6 504528 9 + 601863 ATAATAGGA +s simMouse_chr6.simMouse.chr6 307812 9 - 636262 ATGGTAGCA +s simRat_chr6.simRat.chr6 327362 9 - 647215 ATAATAGCA +s simRat_chr6.simRat.chr6 538201 5 + 647215 ATTGT---- + +a +s simMouse_chr6.simMouse.chr6 527162 6 + 636262 GACGGC +s Anc0.Anc0refChr3 137437 6 + 222631 GAAGAC +s Anc1.Anc1refChr6 172667 6 + 197743 GAAGAC +s Anc2.Anc2refChr1 50765 6 + 142988 GAAAAC +s mr.mrrefChr3 78990 6 + 181027 GACGGC +s mr.mrrefChr5 118046 6 - 294540 GCTGGC +s simCow_chr6.simCow.chr6 507869 5 + 602619 GAA-AC +s simDog_chr6.simDog.chr6 497150 6 + 593897 GAAAAC +s simHuman_chr6.simHuman.chr6 504537 6 + 601863 GAAGAC +s simMouse_chr6.simMouse.chr6 307821 6 - 636262 GCTGGC +s simRat_chr6.simRat.chr6 327371 6 - 647215 GATGGC + +a +s simMouse_chr6.simMouse.chr6 527168 23 + 636262 CCGTAGTTTAAGTCAATGATGCC +s Anc0.Anc0refChr3 137446 18 + 222631 C-----TTTAAGTCAATGATGCC +s Anc1.Anc1refChr6 172676 23 + 197743 CAGTAGTTTAAGTCAATGATGCC +s Anc2.Anc2refChr1 50774 18 + 142988 C-----TTTAAGCCAATGATGCC +s mr.mrrefChr3 78996 23 + 181027 CCGTAGTTTAAGTCAATGATGCC +s mr.mrrefChr5 118052 23 - 294540 CAATAGTTTAAGTCAATGATGCG +s simCow_chr6.simCow.chr6 507877 18 + 602619 A-----TTTAAGGCAATAATGCC +s simDog_chr6.simDog.chr6 497159 18 + 593897 C-----TTTAAGCCAATGATGCT +s simHuman_chr6.simHuman.chr6 504546 23 + 601863 CAGTCATTTAGGTCAATGATACC +s simMouse_chr6.simMouse.chr6 307827 23 - 636262 CAATAGTTTAAGTCAATGATGCG +s simRat_chr6.simRat.chr6 327377 23 - 647215 CAGTAGTTTAAATCAATGATGTC +s simRat_chr6.simRat.chr6 538206 20 + 647215 ---TAGTTTAAGTCAATGATGTC + +a +s simMouse_chr6.simMouse.chr6 527191 15 + 636262 CACTGGCTAGAAGTC +s Anc0.Anc0refChr3 137464 14 + 222631 CACTGG-TAGAAGTC +s Anc1.Anc1refChr6 172699 15 + 197743 CACTGGCTAGAAGTC +s Anc2.Anc2refChr1 50792 14 + 142988 CACTGG-TAGAAGTC +s mr.mrrefChr3 79019 15 + 181027 CACTGGCTAGAAGTC +s mr.mrrefChr5 118075 15 - 294540 CCTTGGCCAGAGGTC +s simCow_chr6.simCow.chr6 507916 14 + 602619 AACTGG-TAGAATTA +s simDog_chr6.simDog.chr6 497177 14 + 593897 CACTAG-CAGAAGTC +s simHuman_chr6.simHuman.chr6 504569 14 + 601863 CCCTGG-TAGAAGTC +s simMouse_chr6.simMouse.chr6 307850 15 - 636262 CCTTGGCCAGAGGTC +s simRat_chr6.simRat.chr6 327400 15 - 647215 CGCCGGCCAGAGGTC +s simRat_chr6.simRat.chr6 538226 15 + 647215 TGCCGGCCAGAAGTC + +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 @@ -201171,17 +215451,55 @@ 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 +s simMouse_chr6.simMouse.chr6 529032 1 + 636262 T +s Anc1.Anc1refChr6 173995 1 + 197743 T +s mr.mrrefChr3 80986 1 + 181027 T +s mr.mrrefChr3 80640 1 + 181027 T +s simMouse_chr6.simMouse.chr6 528676 1 + 636262 T +s simRat_chr6.simRat.chr6 539768 1 + 647215 T +s simRat_chr6.simRat.chr6 540134 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 529033 41 + 636262 TTCCAAGAAAGCGGAAACCTAACTGCATATGTTACCTCAAG +s Anc0.Anc0refChr3 138727 41 + 222631 TTCCAACTAAGCTGTGACCTATCTGCATACCCTACCTCAAG +s Anc1.Anc1refChr6 174029 41 + 197743 TTCCAACTAAGCTGTGACCTATCTGCATACCCTACCTCAAG +s Anc2.Anc2refChr1 52065 41 + 142988 TTCCACCTAAGCTGTGACCTATCTACGTACCCTACCTCAAG +s mr.mrrefChr3 80987 41 + 181027 TTCCAAGAAAGCGGAAACCTAACTGCATATGTTACCTCAAG +s mr.mrrefChr3 80679 41 + 181027 TTCCAAGTAGGCTGTAACCTATCTGCATACACTACCACAAG +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 528715 41 + 636262 TTCCAAGTAGGCTGTAACCTTTCTGCATACACTACTACAAG +s simRat_chr6.simRat.chr6 539807 41 + 647215 TTCCAAGTAGGCTGTAACCTATCAGCATACACTAACACAAG +s simRat_chr6.simRat.chr6 540138 41 + 647215 TTCCCAGAAAGCACAAACCTATGTGCTTATGTTACCTCAAG + +a +s simMouse_chr6.simMouse.chr6 529074 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 81028 1 + 181027 A +s mr.mrrefChr3 80720 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 528756 1 + 636262 A +s simRat_chr6.simRat.chr6 539848 1 + 647215 A +s simRat_chr6.simRat.chr6 540183 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 529075 29 + 636262 TAATTGTATGCACCCCCTCAACAGCTAAA +s Anc0.Anc0refChr3 138773 29 + 222631 TACTTGTTGCCACCCCTTCATCAGCGATA +s Anc1.Anc1refChr6 174075 29 + 197743 TACTTGTTGCCACCCCTTCATCAGCGATA +s Anc2.Anc2refChr1 52111 29 + 142988 TACTTGTTGCCACCACTTCATCAGCGCTA +s mr.mrrefChr3 81029 29 + 181027 TAATTGTATGCACCCCCTCAACAGCTAAA +s mr.mrrefChr3 80725 29 + 181027 TACTTGTTTGCACTCCTTTAACAGCTAAT +s simCow_chr6.simCow.chr6 509329 29 + 602619 TACTTGTTGCCACCACATCATCAGCGCTA +s simDog_chr6.simDog.chr6 498365 29 + 593897 TACTTGTTGCCACCACTTTGCTTGCCCTA +s simHuman_chr6.simHuman.chr6 505923 29 + 601863 TATTTGTTGCCACGCCTTCATCATCGATA +s simMouse_chr6.simMouse.chr6 528761 28 + 636262 TACTTGTCTGCACTCCCTT-ACGGCTAAT +s simRat_chr6.simRat.chr6 539853 29 + 647215 TACTTGTTTGCACCCCTTTAACAGCTAGT +s simRat_chr6.simRat.chr6 540184 29 + 647215 TAATTGTCTGCACCCCCTCAACAGCTAGA a s simMouse_chr6.simMouse.chr6 529104 1 + 636262 A @@ -201195,21 +215513,255 @@ s simRat_chr6.simRat.chr6 540213 1 + 647215 A a +s simMouse_chr6.simMouse.chr6 529105 16 + 636262 GGAGATTGGGAAACTT +s Anc0.Anc0refChr3 138803 9 + 222631 C-------TAAGATAT +s Anc1.Anc1refChr6 174105 16 + 197743 CCACATTGTAAGATAT +s Anc2.Anc2refChr1 52141 9 + 142988 C-------TAAGATAT +s mr.mrrefChr3 81059 16 + 181027 GGAGATTGGGAAACTT +s mr.mrrefChr3 80754 16 + 181027 GCACAATGTATGACTT +s simCow_chr6.simCow.chr6 509359 9 + 602619 G-------TTGGATAT +s simDog_chr6.simDog.chr6 498395 9 + 593897 C-------TAAGATGC +s simHuman_chr6.simHuman.chr6 505953 9 + 601863 C-------TATGATAT +s simMouse_chr6.simMouse.chr6 528789 16 + 636262 GCACAATGTACAACTT +s simRat_chr6.simRat.chr6 539882 16 + 647215 GCACGATGCATGACTT +s simRat_chr6.simRat.chr6 540214 16 + 647215 GGAGATTGGGAAACTT + +a +s simMouse_chr6.simMouse.chr6 529121 1 + 636262 G +s Anc0.Anc0refChr3 138812 1 + 222631 G +s Anc1.Anc1refChr6 174121 1 + 197743 G +s Anc2.Anc2refChr1 52150 1 + 142988 G +s mr.mrrefChr3 81075 1 + 181027 G +s mr.mrrefChr3 80770 1 + 181027 G +s simCow_chr6.simCow.chr6 509368 1 + 602619 G +s simDog_chr6.simDog.chr6 498404 1 + 593897 A +s simHuman_chr6.simHuman.chr6 505962 1 + 601863 G +s simMouse_chr6.simMouse.chr6 528805 1 + 636262 G +s simRat_chr6.simRat.chr6 540230 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 529122 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 81076 7 + 181027 ACCACAA +s mr.mrrefChr3 80771 7 + 181027 ACGACAA +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 528806 7 + 636262 ACCACAA +s simRat_chr6.simRat.chr6 539898 7 + 647215 ACGAGGA +s simRat_chr6.simRat.chr6 540231 7 + 647215 ACCACAA + +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 529134 5 + 636262 GTCAA +s Anc1.Anc1refChr6 174129 5 + 197743 GTCAG +s mr.mrrefChr3 81088 5 + 181027 GTCAA +s mr.mrrefChr3 80778 5 + 181027 GTCAG +s simMouse_chr6.simMouse.chr6 528813 5 + 636262 GTCAG +s simRat_chr6.simRat.chr6 539905 5 + 647215 ATCTG +s simRat_chr6.simRat.chr6 540243 5 + 647215 GTCAA + +a +s simMouse_chr6.simMouse.chr6 529139 6 + 636262 ATGCGT +s Anc1.Anc1refChr6 174134 6 + 197743 ATTTGT +s mr.mrrefChr3 81093 6 + 181027 ATGCGT +s mr.mrrefChr3 80783 6 + 181027 TTTGGT +s simHuman_chr6.simHuman.chr6 505969 4 + 601863 --TTGT +s simMouse_chr6.simMouse.chr6 528827 6 + 636262 TTGGGT +s simRat_chr6.simRat.chr6 539910 6 + 647215 TCTGAT +s simRat_chr6.simRat.chr6 540248 6 + 647215 ATGTGT + +a +s simMouse_chr6.simMouse.chr6 529145 1 + 636262 G +s Anc1.Anc1refChr6 174140 1 + 197743 C +s mr.mrrefChr3 81099 1 + 181027 G +s mr.mrrefChr3 80789 1 + 181027 C +s simHuman_chr6.simHuman.chr6 505973 1 + 601863 C +s simMouse_chr6.simMouse.chr6 528833 1 + 636262 C +s simRat_chr6.simRat.chr6 539916 1 + 647215 C +s simRat_chr6.simRat.chr6 540256 1 + 647215 G + +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 529148 6 + 636262 AACGAG +s Anc1.Anc1refChr6 174141 6 + 197743 AATGAC +s mr.mrrefChr3 81102 6 + 181027 AACGAG +s mr.mrrefChr3 80790 6 + 181027 AATAAG +s simHuman_chr6.simHuman.chr6 505974 6 + 601863 AATGAC +s simMouse_chr6.simMouse.chr6 528834 6 + 636262 AATAAG +s simRat_chr6.simRat.chr6 539917 6 + 647215 TATATG +s simRat_chr6.simRat.chr6 540259 6 + 647215 AAGAAG + +a +s simMouse_chr6.simMouse.chr6 529154 5 + 636262 GTCTG +s Anc1.Anc1refChr6 174147 5 + 197743 GTCTG +s mr.mrrefChr3 81108 5 + 181027 GTCTG +s mr.mrrefChr3 80796 5 + 181027 ATCTG +s simMouse_chr6.simMouse.chr6 528840 5 + 636262 ATCTG +s simRat_chr6.simRat.chr6 539928 5 + 647215 GTCTG +s simRat_chr6.simRat.chr6 540265 5 + 647215 GTCCG + +a +s simMouse_chr6.simMouse.chr6 529159 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 81113 2 + 181027 AC +s mr.mrrefChr3 80801 2 + 181027 AC +s simDog_chr6.simDog.chr6 498411 1 + 593897 -C +s simMouse_chr6.simMouse.chr6 528845 2 + 636262 AC +s simRat_chr6.simRat.chr6 539933 2 + 647215 AC +s simRat_chr6.simRat.chr6 540288 2 + 647215 AC + +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 529175 1 + 636262 C +s Anc0.Anc0refChr3 138819 1 + 222631 A +s Anc1.Anc1refChr6 174154 1 + 197743 A +s Anc2.Anc2refChr1 52157 1 + 142988 T +s mr.mrrefChr3 81129 1 + 181027 C +s mr.mrrefChr3 80803 1 + 181027 A +s simDog_chr6.simDog.chr6 498412 1 + 593897 T +s simMouse_chr6.simMouse.chr6 528847 1 + 636262 A +s simRat_chr6.simRat.chr6 539935 1 + 647215 A +s simRat_chr6.simRat.chr6 540304 1 + 647215 C + +a +s simMouse_chr6.simMouse.chr6 529176 2 + 636262 TG +s Anc0.Anc0refChr3 138820 2 + 222631 TG +s Anc1.Anc1refChr6 174155 2 + 197743 TG +s Anc2.Anc2refChr1 52158 2 + 142988 TG +s mr.mrrefChr3 81130 2 + 181027 TG +s mr.mrrefChr3 80804 2 + 181027 TG +s simCow_chr6.simCow.chr6 509372 1 + 602619 -G +s simDog_chr6.simDog.chr6 498413 1 + 593897 T- +s simMouse_chr6.simMouse.chr6 528850 2 + 636262 TG +s simRat_chr6.simRat.chr6 540305 2 + 647215 TG + +a +s simMouse_chr6.simMouse.chr6 529178 17 + 636262 ACCTTGATTGTCAAACT +s Anc0.Anc0refChr3 138822 13 + 222631 AC----ATTGTCAAACT +s Anc1.Anc1refChr6 174157 17 + 197743 ACCTGGATTGTCAAACT +s Anc2.Anc2refChr1 52160 13 + 142988 AC----ACTGTCAAACT +s mr.mrrefChr3 81132 17 + 181027 ACCTTGATTGTCAAACT +s mr.mrrefChr3 80806 17 + 181027 ACCCGGATTGTTAAGCT +s simCow_chr6.simCow.chr6 509373 13 + 602619 AC----ACTATCAAACT +s simDog_chr6.simDog.chr6 498414 12 + 593897 -C----ACTGTCAAGTT +s simHuman_chr6.simHuman.chr6 505980 11 + 601863 ------ATTGACCAACT +s simMouse_chr6.simMouse.chr6 528852 17 + 636262 ACCCGGATTGTTAAGCT +s simRat_chr6.simRat.chr6 539936 17 + 647215 ATCCGGATCAGTAATAT +s simRat_chr6.simRat.chr6 540307 17 + 647215 ACTTTGATTGTCAAACT + +a +s simMouse_chr6.simMouse.chr6 529195 10 + 636262 GTTCCAAATA +s Anc0.Anc0refChr3 138835 10 + 222631 GTTCCATATA +s Anc1.Anc1refChr6 174174 10 + 197743 GTTCCATATA +s Anc2.Anc2refChr1 52173 10 + 142988 GTTCCATATA +s mr.mrrefChr3 81149 10 + 181027 GTTCCAAATA +s mr.mrrefChr3 80823 10 + 181027 GTTTCATTTA +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 528869 10 + 636262 GTTTCATTTA +s simRat_chr6.simRat.chr6 539966 10 + 647215 ATCTCATTCA +s simRat_chr6.simRat.chr6 540324 10 + 647215 GTTCCAAACA + +a +s simMouse_chr6.simMouse.chr6 529205 6 + 636262 AATCAC +s Anc0.Anc0refChr3 138845 6 + 222631 AATCAC +s Anc1.Anc1refChr6 174184 6 + 197743 AATCAC +s Anc2.Anc2refChr1 52183 6 + 142988 GACCAC +s mr.mrrefChr3 81159 6 + 181027 AATCAC +s mr.mrrefChr3 80833 6 + 181027 CATCAG +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 528879 6 + 636262 CATCAG +s simRat_chr6.simRat.chr6 539979 6 + 647215 CATTAA +s simRat_chr6.simRat.chr6 540334 6 + 647215 AATGAC + +a +s simMouse_chr6.simMouse.chr6 529211 2 + 636262 AC +s Anc0.Anc0refChr3 138851 2 + 222631 AC +s Anc1.Anc1refChr6 174190 2 + 197743 AC +s Anc2.Anc2refChr1 52195 2 + 142988 AC +s mr.mrrefChr3 81165 2 + 181027 AC +s mr.mrrefChr3 80839 2 + 181027 AC +s simCow_chr6.simCow.chr6 509408 2 + 602619 AC +s simDog_chr6.simDog.chr6 498448 1 + 593897 A- +s simHuman_chr6.simHuman.chr6 506007 2 + 601863 AC +s simMouse_chr6.simMouse.chr6 528885 2 + 636262 AC +s simRat_chr6.simRat.chr6 539985 2 + 647215 AC +s simRat_chr6.simRat.chr6 540340 2 + 647215 AC + +a +s simMouse_chr6.simMouse.chr6 529213 1 + 636262 A +s Anc0.Anc0refChr3 138853 1 + 222631 A +s Anc1.Anc1refChr6 174192 1 + 197743 A +s Anc2.Anc2refChr1 52197 1 + 142988 A +s mr.mrrefChr3 81167 1 + 181027 A +s mr.mrrefChr3 80841 1 + 181027 A +s simCow_chr6.simCow.chr6 509410 1 + 602619 A +s simHuman_chr6.simHuman.chr6 506009 1 + 601863 A +s simMouse_chr6.simMouse.chr6 528887 1 + 636262 A +s simRat_chr6.simRat.chr6 540342 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 529214 1 + 636262 G +s Anc0.Anc0refChr3 138859 1 + 222631 G +s Anc1.Anc1refChr6 174198 1 + 197743 G +s Anc2.Anc2refChr1 52203 1 + 142988 G +s mr.mrrefChr3 81168 1 + 181027 G +s mr.mrrefChr3 80842 1 + 181027 G +s simCow_chr6.simCow.chr6 509416 1 + 602619 G +s simDog_chr6.simDog.chr6 498451 1 + 593897 G +s simHuman_chr6.simHuman.chr6 506015 1 + 601863 G +s simMouse_chr6.simMouse.chr6 528888 1 + 636262 G +s simRat_chr6.simRat.chr6 540343 1 + 647215 G + +a +s simMouse_chr6.simMouse.chr6 529215 9 + 636262 ATCCCTTGT +s Anc0.Anc0refChr3 138860 9 + 222631 ATTTCTTGT +s Anc1.Anc1refChr6 174199 9 + 197743 ATTTCTTGT +s Anc2.Anc2refChr1 52204 9 + 142988 ATTTCTTGT +s mr.mrrefChr3 81169 9 + 181027 ATCCCTTGT +s mr.mrrefChr3 80843 9 + 181027 ATTCCTTGT +s simCow_chr6.simCow.chr6 509417 9 + 602619 ATTTCTTGT +s simDog_chr6.simDog.chr6 498452 9 + 593897 ATTTCTTGT +s simHuman_chr6.simHuman.chr6 506016 9 + 601863 ATTTCTTGT +s simMouse_chr6.simMouse.chr6 528889 9 + 636262 ATTCCTTGT +s simRat_chr6.simRat.chr6 539987 9 + 647215 CTGGCTTGT +s simRat_chr6.simRat.chr6 540344 9 + 647215 ATCCCTTGT + +a +s simMouse_chr6.simMouse.chr6 529224 11 + 636262 CTGTACATCTT +s Anc0.Anc0refChr3 138869 11 + 222631 CTGAACACCTT +s Anc1.Anc1refChr6 174208 11 + 197743 CTGAACACCTT +s Anc2.Anc2refChr1 52213 11 + 142988 CTGAGCACCTT +s mr.mrrefChr3 81178 11 + 181027 CTGTACATCTT +s mr.mrrefChr3 80852 11 + 181027 CTGAATACCTT +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 528898 11 + 636262 CTGAAAACCTT +s simRat_chr6.simRat.chr6 540000 11 + 647215 CTGAATGCCTT +s simRat_chr6.simRat.chr6 540353 11 + 647215 CTGTAGGTCTT + +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-- @@ -201221,11 +215773,137 @@ s simRat_chr6.simRat.chr6 540364 18 + 647215 ACTCTACCTTTGGCAGAT a +s simMouse_chr6.simMouse.chr6 529253 38 + 636262 GCTCTACATAGTTAAGTGTATTAATCAAGGGCAGCAGG +s Anc0.Anc0refChr3 138893 38 + 222631 GATCTATATAGTTATGTGTATTGATAAGAGAGAGAAGG +s Anc1.Anc1refChr6 174232 38 + 197743 GATCTATATAGTTATGTGTATTGATAAGAGAGAGAAGG +s Anc2.Anc2refChr1 52237 38 + 142988 GATTTATCTAGTTATTTGTATTGATAAGTGAGAGAAAG +s mr.mrrefChr3 81207 38 + 181027 GCTCTACATAGTTAAGTGTATTAATCAAGGGCAGCAGG +s mr.mrrefChr3 80863 38 + 181027 GATCTACATAGTTAAGTCTATGGATGAAAGACAGAAGG +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 528909 38 + 636262 AATCTGCATAGTTAATTCTATGGATGAAAGACAAAAGG +s simRat_chr6.simRat.chr6 540011 38 + 647215 GATCCACACAGTTAAGTCTATGAATGAAAGACAGAAGG +s simRat_chr6.simRat.chr6 540382 38 + 647215 GCTCTACATAGTTAAGTGTCTTAATCAAAGGCAGAATG + +a +s simMouse_chr6.simMouse.chr6 529291 15 + 636262 CTGCAGCTTTCATGT +s Anc0.Anc0refChr3 138947 15 + 222631 CTACAGCCTTTACGG +s Anc1.Anc1refChr6 174286 15 + 197743 CTACAGCCTTTACGG +s Anc2.Anc2refChr1 52291 15 + 142988 CTACAGCCTTTACGG +s mr.mrrefChr3 81245 15 + 181027 CTGCAGCTTTCATGT +s mr.mrrefChr3 80916 15 + 181027 CTACAGCCTTTGTGG +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 528962 15 + 636262 CTACTGCCTTTGTGG +s simRat_chr6.simRat.chr6 540064 15 + 647215 CTACAGCCTTTTTGG +s simRat_chr6.simRat.chr6 540420 15 + 647215 ATGCAACTTTCATGT + +a +s simMouse_chr6.simMouse.chr6 529306 2 + 636262 CT +s Anc0.Anc0refChr3 138962 2 + 222631 TT +s Anc1.Anc1refChr6 174301 2 + 197743 TT +s Anc2.Anc2refChr1 52308 2 + 142988 TT +s mr.mrrefChr3 81260 2 + 181027 CT +s mr.mrrefChr3 80931 2 + 181027 TT +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 528977 2 + 636262 TT +s simRat_chr6.simRat.chr6 540079 2 + 647215 GT +s simRat_chr6.simRat.chr6 540435 2 + 647215 CT + +a +s simMouse_chr6.simMouse.chr6 529308 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 81262 1 + 181027 A +s mr.mrrefChr3 80942 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 528988 1 + 636262 A +s simRat_chr6.simRat.chr6 540090 1 + 647215 A +s simRat_chr6.simRat.chr6 540437 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 529309 6 + 636262 TAGCCT +s Anc0.Anc0refChr3 138968 6 + 222631 TATCCT +s Anc1.Anc1refChr6 174307 6 + 197743 TATCCT +s Anc2.Anc2refChr1 52314 6 + 142988 TATCCT +s mr.mrrefChr3 81263 6 + 181027 TAGCCT +s mr.mrrefChr3 80943 6 + 181027 TATCCT +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 528989 6 + 636262 TATCCT +s simRat_chr6.simRat.chr6 540091 6 + 647215 TATCCT +s simRat_chr6.simRat.chr6 540438 6 + 647215 TAGCCT + +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 529318 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 81272 2 + 181027 TG +s mr.mrrefChr3 80949 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 528995 2 + 636262 TG +s simRat_chr6.simRat.chr6 540097 2 + 647215 TG +s simRat_chr6.simRat.chr6 540447 2 + 647215 TG + +a +s simMouse_chr6.simMouse.chr6 529320 3 + 636262 TCT +s Anc0.Anc0refChr3 138976 3 + 222631 GCC +s Anc1.Anc1refChr6 174315 3 + 197743 GCC +s Anc2.Anc2refChr1 52322 3 + 142988 GCC +s mr.mrrefChr3 81274 3 + 181027 TCT +s mr.mrrefChr3 80951 3 + 181027 GCT +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 528997 3 + 636262 GCT +s simRat_chr6.simRat.chr6 540099 3 + 647215 GCT +s simRat_chr6.simRat.chr6 540504 3 + 647215 TCT + +a +s simMouse_chr6.simMouse.chr6 529323 4 + 636262 CCTA +s Anc0.Anc0refChr3 138998 4 + 222631 CTTA +s Anc1.Anc1refChr6 174337 4 + 197743 CTTA +s Anc2.Anc2refChr1 52344 4 + 142988 ATTA +s mr.mrrefChr3 81277 4 + 181027 CCTA +s mr.mrrefChr3 80973 4 + 181027 CTTA +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 529019 4 + 636262 CTTA +s simRat_chr6.simRat.chr6 540121 4 + 647215 CTTA +s simRat_chr6.simRat.chr6 540507 4 + 647215 CCTA + +a +s simMouse_chr6.simMouse.chr6 529327 9 + 636262 TTTTATCAG +s Anc0.Anc0refChr3 139002 9 + 222631 TTTTATCAG +s Anc1.Anc1refChr6 174341 9 + 197743 TTTTATCAG +s Anc2.Anc2refChr1 52348 9 + 142988 TTATATTAG +s mr.mrrefChr3 81281 9 + 181027 TTTTATCAG +s mr.mrrefChr3 80977 9 + 181027 CTTTATCAG +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 529023 9 + 636262 CTTTATCAG +s simRat_chr6.simRat.chr6 540125 9 + 647215 TGTTATCAG +s simRat_chr6.simRat.chr6 540511 9 + 647215 TTTTATCAG + +a s simMouse_chr6.simMouse.chr6 529336 39 + 636262 TATATCTTCTAGGGTTCATCACAACTGTTGCGGGACTCT s Anc0.Anc0refChr3 139011 39 + 222631 TATATCTCCTGTGCTTCATCCTAAATCTTGGAGGCATTA s Anc1.Anc1refChr6 174350 39 + 197743 TATATCTCCTGTGCTTCATCCTAAATCTTGGAGGCATTA @@ -201741,6 +216419,34 @@ s simRat_chr6.simRat.chr6 542083 15 + 647215 TAAGTCCTTGAGCGG a +s simMouse_chr6.simMouse.chr6 531014 5 + 636262 CACCT +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 20843 5 + 636262 ATCTT +s simRat_chr6.simRat.chr6 12768 5 + 647215 ATCTT +s simRat_chr6.simRat.chr6 542098 5 + 647215 TACCC + +a +s simMouse_chr6.simMouse.chr6 531019 1 + 636262 G +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 20848 1 + 636262 A +s simRat_chr6.simRat.chr6 12773 1 + 647215 A +s simRat_chr6.simRat.chr6 542103 1 + 647215 A + +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 @@ -201911,6 +216617,180 @@ s simRat_chr6.simRat.chr6 546803 336 + 647215 atggattaattcgatatatttcagtcagcagtggattatgagctattcatgtaactcagccgaagggtatcatcagatacttggatacaatgagc-agataggattgggtgaacaggataactctggataaaattttggctgacactggcagtacatgtttcatgctaggagtacatca--atctgtacatccaaaagaa----gctccaaattgaactattaaaaagacattgcagggatttatagtgctggccatggtgttggtggtaaacacaggtatagatggtcctttcttggggtggtt-------tggtttggccactcgaaggggtccatggctctggaact a +s simMouse_chr6.simMouse.chr6 536345 20 + 636262 CAATTCACCTCTGGTCAGCA +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 20849 20 + 636262 AGCATTCTCTCTAGTCAGCA +s simRat_chr6.simRat.chr6 12778 20 + 647215 AGCACTCCCTCTAGTCAGCA +s simRat_chr6.simRat.chr6 547139 20 + 647215 aagtttgccTCTAGTCAGCA + +a +s simMouse_chr6.simMouse.chr6 536365 6 + 636262 ATCCAA +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 20869 6 + 636262 GTCTAA +s simRat_chr6.simRat.chr6 12798 6 + 647215 ATATAA +s simRat_chr6.simRat.chr6 547159 6 + 647215 ATCTAA + +a +s simMouse_chr6.simMouse.chr6 536371 15 + 636262 TTAGACAAGACTGAC +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 20875 15 + 636262 TTAGATTAGACTAAC +s simRat_chr6.simRat.chr6 12804 15 + 647215 TTAGATAGGACTGAC +s simRat_chr6.simRat.chr6 547165 15 + 647215 TTAGATAAGACTGAC + +a +s simMouse_chr6.simMouse.chr6 536386 3 + 636262 ACA +s Anc0.Anc0refChr2 15198 3 + 17989 ACA +s Anc1.Anc1refChr2 122727 3 - 144309 ACA +s Anc2.Anc2refChr0 13699 3 - 56053 ACA +s mr.mrrefChr0 19202 3 + 130230 ACA +s mr.mrrefChr3 86994 3 + 181027 ACA +s simCow_chr6.simCow.chr6 556677 3 - 602619 ACT +s simDog_chr6.simDog.chr6 554076 3 - 593897 ACA +s simHuman_chr6.simHuman.chr6 561890 3 - 601863 ACA +s simMouse_chr6.simMouse.chr6 20890 3 + 636262 ACA +s simRat_chr6.simRat.chr6 12819 3 + 647215 ACA +s simRat_chr6.simRat.chr6 547187 3 + 647215 ACA + +a +s simMouse_chr6.simMouse.chr6 536389 21 + 636262 TTTGTAAGCTTGTTCTTTATA +s Anc0.Anc0refChr2 15201 21 + 17989 TTTCTAAGCTTATGCTTTATA +s Anc1.Anc1refChr2 122730 21 - 144309 TTTCTAAGCTTATGCTTTATA +s Anc2.Anc2refChr0 13702 21 - 56053 TTTCTGAGCTGATCCTTTATG +s mr.mrrefChr0 19205 21 + 130230 TTTGTAATCTTGTGCTTTATA +s mr.mrrefChr3 86997 21 + 181027 TTTGTAAGCTTGTTCTTTATA +s simCow_chr6.simCow.chr6 556680 21 - 602619 TTTCTGAGCTGACACTTTATG +s simDog_chr6.simDog.chr6 554079 21 - 593897 TCTCTGAGCTGGTCCTTTATG +s simHuman_chr6.simHuman.chr6 561893 21 - 601863 TTTCTAAGCTAATGCTTTATA +s simMouse_chr6.simMouse.chr6 20894 21 + 636262 TTTGTAATCTTGTGCTTTATA +s simRat_chr6.simRat.chr6 12822 21 + 647215 TTTGTAATCTTGTGCCTAATA +s simRat_chr6.simRat.chr6 547190 21 + 647215 CTTGTAATCTTGTGCTTTTTA + +a +s simMouse_chr6.simMouse.chr6 536410 51 + 636262 ACAAAGTTATGTGACATACATATAAATTGTGTAATGACCTTTAGTGTCAAC +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 20915 51 + 636262 ACAAAGGTGTGTGACATACATATAAATTGTGTAATGAGCTGCAGTATCAAC +s simRat_chr6.simRat.chr6 12843 51 + 647215 GCAAAGGTGTGTGACGTACATCTAGATTGTGTAATGACCTGTAGTGTCAAC +s simRat_chr6.simRat.chr6 547211 51 + 647215 ACAAAGGTGTATGTCATACATATAAATTGTGTGTTGACCTGTAGTGTCCAC + +a +s simMouse_chr6.simMouse.chr6 536461 1 + 636262 C +s Anc0.Anc0refChr2 15272 1 + 17989 C +s Anc1.Anc1refChr2 122802 1 - 144309 C +s Anc2.Anc2refChr0 13773 1 - 56053 C +s mr.mrrefChr0 19277 1 + 130230 C +s mr.mrrefChr3 87069 1 + 181027 C +s simCow_chr6.simCow.chr6 556757 1 - 602619 C +s simDog_chr6.simDog.chr6 554150 1 - 593897 C +s simHuman_chr6.simHuman.chr6 561970 1 - 601863 C +s simMouse_chr6.simMouse.chr6 20966 1 + 636262 C +s simRat_chr6.simRat.chr6 12894 1 + 647215 C +s simRat_chr6.simRat.chr6 547262 1 + 647215 C + +a +s simMouse_chr6.simMouse.chr6 536462 24 + 636262 AATTGGGTCCTTATAATGCTTCAG +s Anc0.Anc0refChr2 15273 24 + 17989 AATTGGAAGCTTATAATGCTTCAG +s Anc1.Anc1refChr2 122803 24 - 144309 AATTGGAAGCTTATAATGCTTCAG +s Anc2.Anc2refChr0 13774 24 - 56053 AATTGGAAGCTTATAATGCTTCAG +s mr.mrrefChr0 19278 24 + 130230 AATTGGGACCTTATAATGCTTCAG +s mr.mrrefChr3 87070 24 + 181027 AATTGGGACCTTATAATGCTTCAG +s simCow_chr6.simCow.chr6 556758 24 - 602619 AATTGGGAGCTTGTAATACTTCAG +s simDog_chr6.simDog.chr6 554151 24 - 593897 AATTGGAAGTTTACACCGCTTCTG +s simHuman_chr6.simHuman.chr6 561971 24 - 601863 AATCAAAAGCTTATGATGCTTCAG +s simMouse_chr6.simMouse.chr6 20969 24 + 636262 AATTGGGACCTCGTAACGCTTCAG +s simRat_chr6.simRat.chr6 12895 24 + 647215 AATTGGGATCTTATAATGCTTCAG +s simRat_chr6.simRat.chr6 547263 24 + 647215 AATTGGGACCTTATAATGTGTCCG + +a +s simMouse_chr6.simMouse.chr6 536486 50 + 636262 AAAATCATCTTATGAACCATGTGAAATCAATAATGTCAGACCCATTGGTA +s Anc0.Anc0refChr2 15300 46 + 17989 AGAACCATTTTATGGACCATGTGAAATTAATAATGTCAGACACATT---- +s Anc1.Anc1refChr2 122830 50 - 144309 AGAACCATTTTATGGACCATGTGAAATTAATAATGTCAGACACATTGGTG +s Anc2.Anc2refChr0 13801 46 - 56053 AGGACCATTCTATGGACCATGTGAAATTAATATTGTCAGATGCTTT---- +s mr.mrrefChr0 19305 50 + 130230 AGAATCATCTTATAAACCATGTGAAATCAATAATGTCAGACACATTGGTC +s mr.mrrefChr3 87097 50 + 181027 AGAATCATCTTATGAACCATGTGAAATCAATAATGTCAGACCCATTGGTA +s simCow_chr6.simCow.chr6 556785 46 - 602619 AGGACCACTATATGTACCATGTGAAATCAATATTGTCAGATGCTTT---- +s simDog_chr6.simDog.chr6 554178 45 - 593897 AGGACCATTCTATGGA-CATGTGAGACTAATATTGTCAGATGCTTT---- +s simHuman_chr6.simHuman.chr6 561998 49 - 601863 AGA-CCATTGTATGGACCAGGTGCAAttaataatgtctgacaccttggtg +s simMouse_chr6.simMouse.chr6 20996 50 + 636262 AGAATCAACTTATAAACTATGTGAAATCAATAATGTCAGACACATTGGTC +s simRat_chr6.simRat.chr6 12922 50 + 647215 AGAAACATCTTATAAACCATGTGAAATCAATAATGTCAGACATATTGGTC +s simRat_chr6.simRat.chr6 547290 50 + 647215 AGAAACATCTTATGAACCCCGTGAAATGAATTCTGTCAGACACATTGGTC + +a +s simMouse_chr6.simMouse.chr6 536536 21 + 636262 ATATACCCTAAAGTTTTGTGT +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 21047 21 + 636262 GTATATCTTAAAGTTATGTGT +s simRat_chr6.simRat.chr6 12973 21 + 647215 ATATATCGTAAAGTTATGTGC +s simRat_chr6.simRat.chr6 547341 21 + 647215 ATATCTTCCAAAGTTATGTGT + +a +s simMouse_chr6.simMouse.chr6 536557 14 + 636262 ATATGACGCCTCAA +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 21068 14 + 636262 ATGTGACCCCTAAA +s simRat_chr6.simRat.chr6 12994 14 + 647215 ATGTGACCCCTCGA +s simRat_chr6.simRat.chr6 547362 14 + 647215 ATGTGACCCTTCAA + +a +s simMouse_chr6.simMouse.chr6 536571 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 21082 6 + 636262 GTGTCT +s simRat_chr6.simRat.chr6 13008 6 + 647215 GTGTCT +s simRat_chr6.simRat.chr6 547376 6 + 647215 GTGTCT + +a +s simMouse_chr6.simMouse.chr6 536577 2 + 636262 gc +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 21088 2 + 636262 AC +s simRat_chr6.simRat.chr6 13014 2 + 647215 GC +s simRat_chr6.simRat.chr6 547382 2 + 647215 gc + +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 @@ -208959,15 +223839,147 @@ 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 +s simMouse_chr6.simMouse.chr6 554208 33 + 636262 TCACTCCAGAGGTTAGGGCACACACATTGCATA +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 474426 33 + 636262 GCATTTGAGAGGTTAGGGCACACACATTGCATA +s simRat_chr6.simRat.chr6 29355 33 - 647215 TCACTCCAGGGGTTCGGGCACACACATTGTGTA + +a +s simMouse_chr6.simMouse.chr6 554241 2 + 636262 AA +s Anc0.Anc0refChr3 156022 2 + 222631 AA +s Anc1.Anc1refChr6 192196 2 + 197743 AA +s Anc2.Anc2refChr1 70230 2 + 142988 AA +s mr.mrrefChr3 104237 2 + 181027 AA +s simCow_chr6.simCow.chr6 528471 2 + 602619 GC +s simDog_chr6.simDog.chr6 517236 2 + 593897 AA +s simHuman_chr6.simHuman.chr6 524166 2 + 601863 AA +s simMouse_chr6.simMouse.chr6 474459 2 + 636262 AA +s simRat_chr6.simRat.chr6 29388 2 - 647215 AA + +a +s simMouse_chr6.simMouse.chr6 554243 4 + 636262 TAAA +s Anc0.Anc0refChr3 156024 4 + 222631 TAAA +s Anc1.Anc1refChr6 192198 4 + 197743 TAAA +s Anc2.Anc2refChr1 70232 4 + 142988 TAAA +s mr.mrrefChr3 104239 4 + 181027 TAAA +s simCow_chr6.simCow.chr6 528473 4 + 602619 TAAC +s simDog_chr6.simDog.chr6 517238 4 + 593897 TAAA +s simHuman_chr6.simHuman.chr6 524168 4 + 601863 TAAA +s simMouse_chr6.simMouse.chr6 474462 4 + 636262 TAAA +s simRat_chr6.simRat.chr6 29390 4 - 647215 TAAA + +a +s simMouse_chr6.simMouse.chr6 554247 94 + 636262 GGCAGGTGGTCCTGAAAGATTACGCTCCAGTAAACAGGTTCATGTGGTAAGCAGCATCCCTAATCTCAAGGGAGGATATTCAAGCAGTGGAGCA +s Anc0.Anc0refChr3 156034 92 + 222631 GGCACATGGTCCAAAGAGAAAAAGCTACAGTAGTCAG--CACTGTCGTTAGCCGTTTCCCTAATCTCAAGGGAGTATATTCTATCTGTGGAGTC +s Anc1.Anc1refChr6 192208 94 + 197743 GGCACATGGTCCAAAGAGAAAAAGCTACAGTAGTCAGGACACTGTCGTTAGCCGTTTCCCTAATCTCAAGGGAGTATATTCTATCTGTGGAGTC +s Anc2.Anc2refChr1 70242 92 + 142988 GGCACATGGTCTAAAGAGAAAAAGCTACAGTAGTCAG--CACTGCCGTTCACCGTTTCCCTGATCTCAAGGGAGTATATTCTGTCTGTGGAGTC +s mr.mrrefChr3 104249 94 + 181027 GGCAGGTGGTCCTGAAAGAATAAGCTCCAGTAATCAGGTTCATGTGGTTAGCAGCATCCCTAATCTCAAGGGAGGATATTCAAGTGGTGGAGCA +s simCow_chr6.simCow.chr6 528483 92 + 602619 GGCATATGGCCTAAAGAGAATACGCTCCAATCTTCAG--CACTGCCATTGATCACCTATCTGATCTCAAGGGAGTATATTCTGTCTGGGGAATC +s simDog_chr6.simDog.chr6 517248 83 + 593897 GGCGCATGGTCTAAAGCGGAAAAGCTACAGTAGTCAG---------GTTCACGGTTTCCCTGATCTCAAGGGAACTTATTCTGTCTGTGGAG-- +s simHuman_chr6.simHuman.chr6 524178 94 + 601863 GAAACATGATCCAAAGAGAACAAACTAGAGTAGTCGGGACACTGTAGTCAGCCGTTTCCCTAATCTCAAGGGAGTAGATTCTATCTGTGGAGTC +s simMouse_chr6.simMouse.chr6 474472 94 + 636262 GGCAGGTGGCCTTGAAAGAATAGGCTCCAGTAATCAGGTTCATGTGGTTAGCAGCATCCCTAATCTCAAGGGAGGATATTCAAGTGGTGGAGCA +s simRat_chr6.simRat.chr6 29400 94 - 647215 GGCAGGTGGTCCTGAAAGAATAAGCTGCAGTGCTCAGTTTCCTGTGGCTAGCAGTTTCCCTAATCTCAAGGGAGTATATTTAACTGGTGGAGCA + +a +s simMouse_chr6.simMouse.chr6 554341 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 474566 5 + 636262 AGTAA +s simRat_chr6.simRat.chr6 29494 5 - 647215 TGTAA + +a +s simMouse_chr6.simMouse.chr6 554346 4 + 636262 CCAT +s Anc0.Anc0refChr3 156142 4 + 222631 CAAA +s Anc1.Anc1refChr6 192318 4 + 197743 CAAA +s Anc2.Anc2refChr1 70350 4 + 142988 CAAA +s mr.mrrefChr3 104348 4 + 181027 CCAT +s simCow_chr6.simCow.chr6 528626 4 + 602619 CAAG +s simDog_chr6.simDog.chr6 517341 4 + 593897 CAAA +s simHuman_chr6.simHuman.chr6 524288 4 + 601863 CAAA +s simMouse_chr6.simMouse.chr6 474571 4 + 636262 CCAT +s simRat_chr6.simRat.chr6 29499 4 - 647215 CCTT + +a +s simMouse_chr6.simMouse.chr6 554350 48 + 636262 TCTGCCATTGCTCTTGCTCTCAAACTCTGTGATTTATGAGTCCCCAAA +s Anc0.Anc0refChr3 156149 48 + 222631 TCTCCCATTGCTCTTCCTCTCAAACTCCCTAATTTCTGGCTTCCCACA +s Anc1.Anc1refChr6 192325 48 + 197743 TCTCCCATTGCTCTTCCTCTCAAACTCCCTAATTTCTGGCTTCCCACA +s Anc2.Anc2refChr1 70357 48 + 142988 TCTCCCATTGCTCTTCCTCCCAGACTCCCTAATTACTGGCTTGCCACA +s mr.mrrefChr3 104355 48 + 181027 TCTGCCATTGCTCTTGCTCTCAAACTCTGTGATTTATGAGTCCCCAAA +s simCow_chr6.simCow.chr6 528633 48 + 602619 TCTCCCAATGCTCTTTCTCCCACACTCCCTAATTACTGGCGTGCCTCA +s simDog_chr6.simDog.chr6 517348 43 + 593897 TCTCCCATTGCTCTTCC-----GACTCCCAACTTACTGGCTTGCTACA +s simHuman_chr6.simHuman.chr6 524295 48 + 601863 CGTCCCATTGCATGCACTCTGAAACTCCCTAATTTCTGGCTTCCCACA +s simMouse_chr6.simMouse.chr6 474578 48 + 636262 TCTGCCATTGCTCTTGCTCTCAAACTCTGTGATTTATGAGTCCCCAAA +s simRat_chr6.simRat.chr6 29506 48 - 647215 TTTGCCAGTGCTCTTGCTCTCAAACTCTGTGATATATAAGTCCCCAAA + +a +s simMouse_chr6.simMouse.chr6 554398 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 474626 10 + 636262 GCTGCTCATA +s simRat_chr6.simRat.chr6 29555 10 - 647215 GCTGTTCATG + +a +s simMouse_chr6.simMouse.chr6 554408 5 + 636262 GTATG +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 474636 5 + 636262 GTATA +s simRat_chr6.simRat.chr6 29565 5 - 647215 GTATA + +a +s simMouse_chr6.simMouse.chr6 554413 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 474641 25 + 636262 ACTAAATTCTAATGTCTATATCTAG +s simRat_chr6.simRat.chr6 29570 25 - 647215 GCTGAATTCTAATGTCCATATCTGG + +a +s simMouse_chr6.simMouse.chr6 554438 12 + 636262 AAATGGGTTGTG +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 474666 12 + 636262 AAATGGGTTGTA +s simRat_chr6.simRat.chr6 29595 12 - 647215 AAATAGGTTGCA + +a +s simMouse_chr6.simMouse.chr6 554450 97 + 636262 CCATTGTGACAATGACCCTGCCTTAATCACCAACCAGGGGAAAAAAGATGTAACTGTGCATATCGAGGTATAATTCTTGAGTTAATTCCTTGCAACG +s Anc0.Anc0refChr3 156271 85 + 222631 GCATGGTGAGAATGACCCTCTCTTAATTAACAACCAGGGCAAAAAAGATGTAC------------AGGGATAATCTGTTTGTTAATTCCTTGCAATA +s Anc1.Anc1refChr6 192449 85 + 197743 GCATGGTGAGAATGACCCTCTCTTAATTAACAACCAGGGCAAAAAAGATGTAC------------AGGGATAATCTGTTTGTTAATTCCTTGCAATA +s Anc2.Anc2refChr1 70479 85 + 142988 GCATGGTGAGAATGACCTTCTCTTAATTAACAACCTGGACAAAAAAGATGTAC------------AGCGGTAAACTGTTTGTTAATTCCTTGCAACA +s mr.mrrefChr3 104456 97 + 181027 CCATTGTGACAATGACCCTGCCTTAATTACCAACCAGGGGGAAAAAGATGTACCTGTGCATATCGAGGTATAATTCTTGAGTTAATTCCTTGCAATG +s simCow_chr6.simCow.chr6 528761 81 + 602619 GTATGGTGAGAATGACCTTCTCTTAATTAACAGCTTGGACAAAAAGGATGTAC------------AGTGGT----TGTTTGTCAACTCTTTGCAGCA +s simDog_chr6.simDog.chr6 517465 85 + 593897 GCATGGTGAGAATGGCCTTCTGTTAATTAGCAAACTGGACCAAAAAGATCTAC------------AGCAGTAAACTGTTTGTTAATTCCTTGTAACA +s simHuman_chr6.simHuman.chr6 524420 85 + 601863 GCTTGGTGAGTATGATCCCCTCTTGATTAACGACAAGGGCAAAAAAGATGTAC------------AGGGATAATCAGGTTGTTGATTCCTTGCAATA +s simMouse_chr6.simMouse.chr6 474678 44 + 636262 CCATTGTGACAATGACCCTGCCTTAATTACCGACCAGGGGGAAA----------------------------------------------------- +s simRat_chr6.simRat.chr6 29615 97 - 647215 CCATGATGACAGTGACCCTACCTTAATTAATAACCACGGGGAAAAAGATGTACCTGTGCACATCAAGGTATGGTTTCTGAGGTAATCCCCTACAATG a s simMouse_chr6.simMouse.chr6 554547 62 + 636262 GGTGATGACAATCTTAGCCTATCCAAGAATTAGTGTGGTTTACATGTGACCTAAAACCCACA @@ -210344,17 +225356,16 @@ 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 +s simMouse_chr6.simMouse.chr6 558136 144 + 636262 AATGATTGGTTGATAACACATGAGGTGGATAGGCTCCTTCTAGAGATGCCTGTGATTACTTGACAGCACATGAAGCGGGCAGGCTTCAGCAGCCAAGTAATGACTACATGCACATGGCCGTGTTTGCCCTTAATGGGAGCTTTG +s mr.mrrefChr3 108058 143 + 181027 AGTGATTGGTTGATAACACATGAGGTGGATAGGCTCCTTCTAGAGATGCCTGTGATTACTTGACAGCACATGAAGCGGGCAGGCT-CAGCAGCCAAGTAATGACTGCATGCACATGGCCGTGTTTGCCTTTAATGGGAGCTTTG +s simMouse_chr6.simMouse.chr6 439423 136 + 636262 AGCGT-------GTAACACATGAGGTGGATAGGTTCCTTCTTGAGATGCCTGTGATTACTTGACAGCACATGAAGCGGGCAGGCT-CAGCAGCCAAGTAATGACCGCATGCACATGGCCGTGTTTGCCTTTGATGGGAGCTTGG +s simRat_chr6.simRat.chr6 33294 143 - 647215 AGTGGTTGCTTGACAACACATGAGGTGGATAGGCTCCTTCTACAGATGCTGGTGATTATTTGGCAGCACATGAGGCAGGTGGGCT-CACCAGCCAAGTAATGACAGCACGCACATGGCCATGTTTTCCTTTAATGGGAGCTTTG + +a +s simMouse_chr6.simMouse.chr6 558280 129 + 636262 CACATGGGGCACTTGAAATTTCGACAACATTAAGGAGGTCCGAAAAGAGTTTAAGAATGTAGGAAACCCTGGACTTGCCTTAAAGGTACTTCACCAATGCAATAGTGAATAGGCCAAATGTTTGATCAC +s mr.mrrefChr3 108201 112 + 181027 CACAAGGGGCACTTGAAATTTCGACAACATTAAGGAGGTCCGAAAAGAGTTTAAGAATGTAGGAAACCCTGGACTTGCCTTAAAGGTACTT-----------------ATAGGCCAAATGTTTGATCAC +s simMouse_chr6.simMouse.chr6 439559 67 + 636262 CACAAGGGGCACTTGAAATTTCGACAACATTAAGGAGGTCCGAAAAGAGTTTAAGAATGTAGGATAT-------------------------------------------------------------- +s simRat_chr6.simRat.chr6 33438 112 - 647215 CACAAGGAGCACTTGAAATCTTGACAACATTAAGGAGGTCCAAAAAGAGTTTAAGAATGTAGGAAACCCTGGACTTGCCTTAAAGGTACTT-----------------ATAAGCCAAATGTTGGATATC a s simMouse_chr6.simMouse.chr6 558409 115 + 636262 ATTGATGAGGTTACAGGGTTTCAGAGGCATGATTGAAAGCCTGAGTTACAACCCTGGGGCAACACAATATGTGTACTCTCTACTCTCTTCAATTTCTGAGGTAGTCAGGATCATA @@ -210773,6 +225784,34 @@ s simRat_chr6.simRat.chr6 34615 6 - 647215 GTCCGG a +s simMouse_chr6.simMouse.chr6 559441 22 + 636262 CTCTTCGTAAACAGCTTATGAA +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 266483 22 + 636262 CCCTTCAGAGATATGCTGTGAA +s simRat_chr6.simRat.chr6 255286 22 + 647215 CCTTTCAGAGATTTGCTGTGAA +s simRat_chr6.simRat.chr6 34621 22 - 647215 CCCTTCGCCAACATGCTATGAA + +a +s simMouse_chr6.simMouse.chr6 559463 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 266505 3 + 636262 GGG +s simRat_chr6.simRat.chr6 255309 3 + 647215 GGG +s simRat_chr6.simRat.chr6 34643 3 - 647215 GGG + +a s simMouse_chr6.simMouse.chr6 559466 5 + 636262 AAGCA s Anc0.Anc0refChr3 160831 5 + 222631 ATCCG s Anc1.Anc1refChr6 197095 5 + 197743 ATCCG @@ -210784,11 +225823,357 @@ s simRat_chr6.simRat.chr6 34646 5 - 647215 AAGCA a +s simMouse_chr6.simMouse.chr6 559471 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 266508 3 + 636262 TCA +s simRat_chr6.simRat.chr6 255312 3 + 647215 TCA +s simRat_chr6.simRat.chr6 34651 3 - 647215 TCA + +a +s simMouse_chr6.simMouse.chr6 559474 33 + 636262 TCGAAAGAAGGGCTCCACGACAAACATGTATCA +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 266511 33 + 636262 CTGAGAGAAAAACTCCTAGATGCAAATGTATTG +s simRat_chr6.simRat.chr6 255315 33 + 647215 CTGAGAAAAGAATTCCTATATGTAAATGTATTG +s simRat_chr6.simRat.chr6 34654 33 - 647215 TCGAAAGAAGGTCTCTAGGACACACATGTATCG + +a +s simMouse_chr6.simMouse.chr6 559507 5 + 636262 GGCGG +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 266562 5 + 636262 GGTGG +s simRat_chr6.simRat.chr6 255366 5 + 647215 GGCGA +s simRat_chr6.simRat.chr6 34687 5 - 647215 GACGG + +a +s simMouse_chr6.simMouse.chr6 559512 23 + 636262 TCTTCGACCACTTCTGGATCGGC +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 266571 23 + 636262 ATTTTGCCCACTAATGAATAAGC +s simRat_chr6.simRat.chr6 255375 23 + 647215 GTGTTGTCCACTAATAAAGACAC +s simRat_chr6.simRat.chr6 34692 23 - 647215 TCTTCTACCACTTATGGATCGGC + +a +s simMouse_chr6.simMouse.chr6 559535 10 + 636262 AGGGACGAAT +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 266595 10 + 636262 AAGGATGGAT +s simRat_chr6.simRat.chr6 255399 10 + 647215 AAGGATGGGT +s simRat_chr6.simRat.chr6 34715 10 - 647215 AGGGACGAAT + +a +s simMouse_chr6.simMouse.chr6 559545 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 266605 1 + 636262 T +s simRat_chr6.simRat.chr6 255412 1 + 647215 T +s simRat_chr6.simRat.chr6 34725 1 - 647215 T + +a +s simMouse_chr6.simMouse.chr6 559546 10 + 636262 GATCCCTCTA +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 266616 10 + 636262 AATCCCTTTG +s simRat_chr6.simRat.chr6 255423 10 + 647215 AATCCCATTG +s simRat_chr6.simRat.chr6 34726 10 - 647215 AATCCCTCTA + +a +s simMouse_chr6.simMouse.chr6 559556 16 + 636262 ACCACATGGAAGCCAT +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 266627 16 + 636262 AACACATGGAGCTCTT +s simRat_chr6.simRat.chr6 255434 16 + 647215 AACACATGGAGCCCTT +s simRat_chr6.simRat.chr6 34736 16 - 647215 ACCAGATGGCAGTCTT + +a +s simMouse_chr6.simMouse.chr6 559572 17 + 636262 AATTTAATTGCTACGCG +s Anc0.Anc0refChr3 160959 17 + 222631 AATTTAACTGTTACGTG +s Anc1.Anc1refChr6 197223 17 + 197743 AATTTAACTGTTACGTG +s Anc2.Anc2refChr1 75584 17 + 142988 AATTTAACTGTTACGTG +s mr.mrrefChr3 109517 17 + 181027 AATTTAATTGCTACGCG +s mr.mrrefChr5 118268 17 + 294540 AATTTGAATGCAATGTG +s simCow_chr6.simCow.chr6 534309 17 + 602619 GAGTTAACTGCTACGTG +s simDog_chr6.simDog.chr6 522535 17 + 593897 ATTTTAACTCTTACGTG +s simHuman_chr6.simHuman.chr6 529362 17 + 601863 AATAAAACTGTTACTTG +s simMouse_chr6.simMouse.chr6 266660 17 + 636262 AATTTGAATGCAATGTG +s simRat_chr6.simRat.chr6 255460 17 + 647215 AATTTGAGTGCAATGTG +s simRat_chr6.simRat.chr6 34752 17 - 647215 AATTCAATTACTACGCG + +a +s simMouse_chr6.simMouse.chr6 559589 12 + 636262 TGTCTTGCACGG +s Anc0.Anc0refChr3 160976 12 + 222631 TGTCTTGCGCGG +s Anc1.Anc1refChr6 197240 12 + 197743 TGTCTTGCGCGG +s Anc2.Anc2refChr1 75601 12 + 142988 TGTCTTGCGCAG +s mr.mrrefChr3 109534 12 + 181027 TGTCTTGCGCGG +s mr.mrrefChr5 118285 12 + 294540 TTTCTTGCATGG +s simCow_chr6.simCow.chr6 534326 12 + 602619 TGCCTTGCGTAG +s simDog_chr6.simDog.chr6 522552 12 + 593897 TGTCTTGCGCAT +s simHuman_chr6.simHuman.chr6 529379 12 + 601863 TGTCTTGCGCCG +s simMouse_chr6.simMouse.chr6 266678 12 + 636262 TTTCTTGCATGG +s simRat_chr6.simRat.chr6 255477 12 + 647215 TTTCTTGCATGG +s simRat_chr6.simRat.chr6 34769 12 - 647215 TGTCTTGCGCGT + +a +s simMouse_chr6.simMouse.chr6 559601 1 + 636262 A +s Anc0.Anc0refChr3 160988 1 + 222631 A +s Anc1.Anc1refChr6 197252 1 + 197743 A +s Anc2.Anc2refChr1 75613 1 + 142988 A +s mr.mrrefChr3 109546 1 + 181027 A +s mr.mrrefChr5 118297 1 + 294540 A +s simCow_chr6.simCow.chr6 534338 1 + 602619 A +s simDog_chr6.simDog.chr6 522564 1 + 593897 A +s simHuman_chr6.simHuman.chr6 529391 1 + 601863 A +s simMouse_chr6.simMouse.chr6 266690 1 + 636262 A +s simRat_chr6.simRat.chr6 255497 1 + 647215 G +s simRat_chr6.simRat.chr6 34781 1 - 647215 A + +a +s simMouse_chr6.simMouse.chr6 559602 1 + 636262 A +s Anc0.Anc0refChr3 160992 1 + 222631 A +s Anc1.Anc1refChr6 197256 1 + 197743 A +s Anc2.Anc2refChr1 75617 1 + 142988 A +s mr.mrrefChr3 109550 1 + 181027 A +s mr.mrrefChr5 118301 1 + 294540 A +s simCow_chr6.simCow.chr6 534342 1 + 602619 A +s simDog_chr6.simDog.chr6 522568 1 + 593897 A +s simHuman_chr6.simHuman.chr6 529395 1 + 601863 A +s simMouse_chr6.simMouse.chr6 266694 1 + 636262 A +s simRat_chr6.simRat.chr6 255501 1 + 647215 A +s simRat_chr6.simRat.chr6 34785 1 - 647215 A + +a +s simMouse_chr6.simMouse.chr6 559603 7 + 636262 CACGTTG +s Anc0.Anc0refChr3 160993 7 + 222631 CACGTGG +s Anc1.Anc1refChr6 197257 7 + 197743 CACGTGG +s Anc2.Anc2refChr1 75618 7 + 142988 CACGTGG +s mr.mrrefChr3 109551 7 + 181027 CACGTTG +s mr.mrrefChr5 118302 7 + 294540 CCTGAAG +s simCow_chr6.simCow.chr6 534343 7 + 602619 CGCGTGG +s simDog_chr6.simDog.chr6 522569 7 + 593897 CACGTGG +s simHuman_chr6.simHuman.chr6 529400 7 + 601863 CAGGTGG +s simMouse_chr6.simMouse.chr6 266695 7 + 636262 CCTGAAG +s simRat_chr6.simRat.chr6 255502 7 + 647215 CCTGAAG +s simRat_chr6.simRat.chr6 34786 7 - 647215 TACGTTG + +a +s simMouse_chr6.simMouse.chr6 559610 4 + 636262 TTTC +s Anc0.Anc0refChr3 161002 4 + 222631 TTTC +s Anc1.Anc1refChr6 197266 4 + 197743 TTTC +s Anc2.Anc2refChr1 75627 4 + 142988 TTTA +s mr.mrrefChr3 109560 4 + 181027 TTTC +s mr.mrrefChr5 118311 4 + 294540 TTTC +s simCow_chr6.simCow.chr6 534352 4 + 602619 TTTT +s simDog_chr6.simDog.chr6 522578 4 + 593897 TTTA +s simHuman_chr6.simHuman.chr6 529409 4 + 601863 TTTC +s simMouse_chr6.simMouse.chr6 266704 4 + 636262 TTTC +s simRat_chr6.simRat.chr6 255511 4 + 647215 TTTC +s simRat_chr6.simRat.chr6 34795 4 - 647215 TTTA + +a +s simMouse_chr6.simMouse.chr6 559614 4 + 636262 CTGA +s Anc0.Anc0refChr3 161009 4 + 222631 GTGT +s Anc1.Anc1refChr6 197273 4 + 197743 GTGT +s Anc2.Anc2refChr1 75634 4 + 142988 GTGT +s mr.mrrefChr3 109567 4 + 181027 CTGA +s mr.mrrefChr5 118318 4 + 294540 GTGG +s simCow_chr6.simCow.chr6 534359 4 + 602619 GTGT +s simDog_chr6.simDog.chr6 522585 4 + 593897 GTGC +s simHuman_chr6.simHuman.chr6 529416 4 + 601863 GTTT +s simMouse_chr6.simMouse.chr6 266711 4 + 636262 GTGG +s simRat_chr6.simRat.chr6 255518 4 + 647215 GTGG +s simRat_chr6.simRat.chr6 34802 4 - 647215 CTGA + +a +s simMouse_chr6.simMouse.chr6 559618 9 + 636262 TTCATCGAT +s Anc0.Anc0refChr3 161013 9 + 222631 ATTGGCTTA +s Anc1.Anc1refChr6 197277 9 + 197743 ATTGGCTTA +s Anc2.Anc2refChr1 75638 9 + 142988 ATTGGCTTA +s mr.mrrefChr3 109571 9 + 181027 ATCATCGAT +s mr.mrrefChr5 118324 9 + 294540 ATTGACTTA +s simCow_chr6.simCow.chr6 534363 9 + 602619 GCTGTCTTA +s simDog_chr6.simDog.chr6 522589 9 + 593897 ATTGGCTTA +s simHuman_chr6.simHuman.chr6 529420 9 + 601863 ATTGGCTTA +s simMouse_chr6.simMouse.chr6 266717 9 + 636262 ATTGACTTA +s simRat_chr6.simRat.chr6 255524 9 + 647215 ATTGACTTA +s simRat_chr6.simRat.chr6 34806 9 - 647215 ATCAACGAT + +a +s simMouse_chr6.simMouse.chr6 559627 7 + 636262 TTCCCTA +s Anc0.Anc0refChr3 161022 7 + 222631 CCCACGA +s Anc1.Anc1refChr6 197286 7 + 197743 CCCACGA +s Anc2.Anc2refChr1 75647 7 + 142988 CCCACGA +s mr.mrrefChr3 109580 7 + 181027 TCCCCTA +s mr.mrrefChr5 118333 7 + 294540 CCTATGA +s simCow_chr6.simCow.chr6 534372 7 + 602619 CCTGCGA +s simDog_chr6.simDog.chr6 522598 7 + 593897 CCCACAA +s simHuman_chr6.simHuman.chr6 529429 7 + 601863 CCCACGA +s simMouse_chr6.simMouse.chr6 266727 7 + 636262 CCTATGA +s simRat_chr6.simRat.chr6 255533 7 + 647215 CCTACGA +s simRat_chr6.simRat.chr6 34815 7 - 647215 TCCCCTA + +a +s simMouse_chr6.simMouse.chr6 559634 2 + 636262 CT +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 266734 2 + 636262 TT +s simRat_chr6.simRat.chr6 255540 2 + 647215 TT +s simRat_chr6.simRat.chr6 34822 2 - 647215 CT + +a +s simMouse_chr6.simMouse.chr6 559636 32 + 636262 CAAAACATAGCTTCACACCGCTGTAAAGGGCG +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 266738 32 + 636262 CCCAACATAATTCCAGAATGCTATAGAGTATG +s simRat_chr6.simRat.chr6 255543 32 + 647215 CCCAACATAACTCCAGAATGCTTTAGAGTATG +s simRat_chr6.simRat.chr6 34824 32 - 647215 CAAAACATCGCTTCACAACGCTGTAAAGGGCG + +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 559669 36 + 636262 AAACCTTGACGACAGTTCGGTAGGGAGGCGAACTTC +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 266770 36 + 636262 AAACCTCCACAACAGTGCGTTGGGGTAGTGAACTTC +s simRat_chr6.simRat.chr6 255575 36 + 647215 AAACCTCCCCAATAGTGGGTTAGGGTAGTGTACTTC +s simRat_chr6.simRat.chr6 34857 36 - 647215 AAACTTTGACTACAGTTCGATAGGGAGGCGAACTTC + +a +s simMouse_chr6.simMouse.chr6 559705 9 + 636262 TATGATGAC +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 266807 9 + 636262 TATTAGCAC +s simRat_chr6.simRat.chr6 255613 9 + 647215 TATTAGCAT +s simRat_chr6.simRat.chr6 34893 9 - 647215 TATGATGAC + +a +s simMouse_chr6.simMouse.chr6 559714 5 + 636262 GTACG +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 266816 5 + 636262 CTCTG +s simRat_chr6.simRat.chr6 255622 5 + 647215 CACTG +s simRat_chr6.simRat.chr6 34902 5 - 647215 GTGCG + +a +s simMouse_chr6.simMouse.chr6 559719 4 + 636262 GGAG +s Anc1.Anc1refChr6 197381 4 + 197743 GGAG +s mr.mrrefChr3 109672 4 + 181027 GGAG +s mr.mrrefChr5 118429 4 + 294540 GAAG +s simHuman_chr6.simHuman.chr6 529523 4 + 601863 GGAC +s simMouse_chr6.simMouse.chr6 266824 4 + 636262 GAAG +s simRat_chr6.simRat.chr6 255630 4 + 647215 GAAG +s simRat_chr6.simRat.chr6 34907 4 - 647215 GGAG + +a +s simMouse_chr6.simMouse.chr6 559723 58 + 636262 TGCTCCGATACCATTAAGTGTGGGCCGTCTTTATGGGTCGACAATATCGTCTAACGAC +s Anc0.Anc0refChr3 161102 45 + 222631 -------------CAATGCGTGAACTAACTATATGGAGCGACAGTCGTGTTTAACAAC +s Anc1.Anc1refChr6 197385 58 + 197743 ATCGGTGAAACGGCAATGCGTGAACTAACTATATGGAGCGACAGTCGTGTTTAACAAC +s Anc2.Anc2refChr1 75727 45 + 142988 -------------CAATGCGTGAACTAACTAATTAGAGCGACAGTCGTGTTTGACAAC +s mr.mrrefChr3 109676 58 + 181027 TGCTCCGATACCATGAGCTGTGGACCGACTTTATGGGTCGACAATATTGTTTAACGAC +s mr.mrrefChr5 118433 58 + 294540 ATTGAAGACACTGTAATACACGAACTGGCTTTATGAAATAACAATAGTGTTTAACAAC +s simCow_chr6.simCow.chr6 534446 45 + 602619 -------------CAATATGTAGACTAACTTTTTAGAGCGACAGTCGTGTTCTATGAC +s simDog_chr6.simDog.chr6 522678 41 + 593897 -------------CAATGCGTGAACTAACTAA----AACGACGGTCGTGTTTGACAAC +s simHuman_chr6.simHuman.chr6 529527 58 + 601863 ATCGGTGAAACGGCAGCGGTTGAACTAACTACCTGTAGCGACAGTCTTGTTTAACAAC +s simMouse_chr6.simMouse.chr6 266832 58 + 636262 ATTGAAGACACTGTAATACACGAACTGGCTTTATGAAATAACAATAGTGTTTAACAAC +s simRat_chr6.simRat.chr6 255634 58 + 647215 ATGGGAGACCCTGTAATACATAAACTGATGTTATGAAACAACAATAGTGTTTAACAAC +s simRat_chr6.simRat.chr6 34911 58 - 647215 AGCTCCGATACCATGAGCTGCGGACCGACTTTATGGGACGACAATATTGTTTAACTAC + +a +s simMouse_chr6.simMouse.chr6 559781 1 + 636262 T +s Anc0.Anc0refChr3 161147 1 + 222631 T +s Anc1.Anc1refChr6 197443 1 + 197743 T +s Anc2.Anc2refChr1 75772 1 + 142988 T +s mr.mrrefChr3 109734 1 + 181027 T +s mr.mrrefChr5 118491 1 + 294540 T +s simCow_chr6.simCow.chr6 534491 1 + 602619 T +s simDog_chr6.simDog.chr6 522719 1 + 593897 T +s simHuman_chr6.simHuman.chr6 529585 1 + 601863 C +s simMouse_chr6.simMouse.chr6 266891 1 + 636262 T +s simRat_chr6.simRat.chr6 255692 1 + 647215 C +s simRat_chr6.simRat.chr6 34969 1 - 647215 T + +a s simMouse_chr6.simMouse.chr6 559782 1 + 636262 T s Anc0.Anc0refChr3 161148 1 + 222631 T s Anc1.Anc1refChr6 197444 1 + 197743 T @@ -210800,6 +226185,48 @@ s simRat_chr6.simRat.chr6 34970 1 - 647215 T a +s simMouse_chr6.simMouse.chr6 559783 9 + 636262 GGCTTCCCT +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 266892 9 + 636262 GGCTTGATG +s simRat_chr6.simRat.chr6 255693 9 + 647215 AGCTTGACA +s simRat_chr6.simRat.chr6 34971 9 - 647215 GGCTTCCCT + +a +s simMouse_chr6.simMouse.chr6 559792 5 + 636262 GCATC +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 266901 5 + 636262 GCCTC +s simRat_chr6.simRat.chr6 255702 5 + 647215 GTCTC +s simRat_chr6.simRat.chr6 34980 5 - 647215 GCTTC + +a +s simMouse_chr6.simMouse.chr6 559797 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 266906 2 + 636262 TT +s simRat_chr6.simRat.chr6 255708 2 + 647215 TT +s simRat_chr6.simRat.chr6 34985 2 - 647215 TT + +a s simMouse_chr6.simMouse.chr6 559799 4 + 636262 ATTC s Anc0.Anc0refChr3 161173 4 + 222631 ATTC s Anc1.Anc1refChr6 197472 4 + 197743 ATTC @@ -210811,11 +226238,53 @@ s simRat_chr6.simRat.chr6 34987 4 - 647215 AATC a +s simMouse_chr6.simMouse.chr6 559803 25 + 636262 TTCTGGCGAAGCCTTAAGCGGAGGG +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 266908 25 + 636262 TGCTGGCAAGTTGCAAAGTGGGGAG +s simRat_chr6.simRat.chr6 255710 25 + 647215 TGCTGTCAAGTTACAAAGTGGGGGG +s simRat_chr6.simRat.chr6 34991 25 - 647215 TGCTGGCGAAGCCTTAAGCGGAGGG + +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 559888 5 + 636262 ATACT +s Anc0.Anc0refChr3 161202 5 + 222631 ACCCT +s Anc1.Anc1refChr6 197501 5 + 197743 ACCCT +s Anc2.Anc2refChr1 75827 5 + 142988 ACCCT +s mr.mrrefChr3 109841 5 + 181027 ATACT +s mr.mrrefChr5 118533 5 + 294540 ATCCT +s simCow_chr6.simCow.chr6 534546 5 + 602619 CCCCT +s simDog_chr6.simDog.chr6 522759 5 + 593897 ACCCT +s simHuman_chr6.simHuman.chr6 529718 5 + 601863 ACCCC +s simMouse_chr6.simMouse.chr6 266933 5 + 636262 ATCCT +s simRat_chr6.simRat.chr6 255735 5 + 647215 ACCCT +s simRat_chr6.simRat.chr6 35076 5 - 647215 ATACT + +a +s simMouse_chr6.simMouse.chr6 559893 30 + 636262 TCTGTTGTCGGCTGTCATTGAGCAACATAT +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 266940 30 + 636262 TCTGTTGTCCATTATCTTTGAGCAATGTCT +s simRat_chr6.simRat.chr6 255742 30 + 647215 TCTGTTGTCGGCAATCTTTGGGCAATGTCT +s simRat_chr6.simRat.chr6 35086 30 - 647215 TCTGTTGTCTGCAGTCATTGAGCACCATGT + +a s simMouse_chr6.simMouse.chr6 559923 7 + 636262 TGCTCAG s Anc0.Anc0refChr3 161234 7 + 222631 CTTTAAG s Anc1.Anc1refChr6 197538 7 + 197743 CTTTAAG @@ -210827,7 +226296,46 @@ s simRat_chr6.simRat.chr6 35116 7 - 647215 CGCTCAG a -s simMouse_chr6.simMouse.chr6 559955 2 + 636262 GC +s simMouse_chr6.simMouse.chr6 559930 21 + 636262 AGAGACATCTATCCATAGATC +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 266970 21 + 636262 AGAACCCTCTATTCAGATACC +s simRat_chr6.simRat.chr6 255772 21 + 647215 AGAACCCTCTATTCAGATACC +s simRat_chr6.simRat.chr6 35123 21 - 647215 AGAGACATCTATCCAGAGACC + +a +s simMouse_chr6.simMouse.chr6 559951 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 266991 1 + 636262 T +s simRat_chr6.simRat.chr6 255793 1 + 647215 T +s simRat_chr6.simRat.chr6 35144 1 - 647215 T + +a +s simMouse_chr6.simMouse.chr6 559952 47 + 636262 ATGGCCTTTGTGATTGAGCCTGATGTGTGATGCAACCATGAAAATTG +s Anc0.Anc0refChr3 161262 45 + 222631 AAT--CCTTGAGATTGAGCCTTATTTGTGAGCCAGCCAGGAAAATCA +s Anc1.Anc1refChr6 197569 45 + 197743 AAT--CCTTGAGATTGAGCCTTATTTGTGAGCCAGCCAGGAAAATCA +s Anc2.Anc2refChr1 75887 45 + 142988 AAT--CCTAGAGATTGAGCCTTATTTGTGAGCCAGCCAGGAAAATCA +s mr.mrrefChr3 109910 45 + 181027 ATG--CTTTGAGATTGAGCCTTATGTGTGATGCAGCCATGAAAATTG +s mr.mrrefChr5 118594 45 + 294540 AAC--CCTTGCTCTTTTGCCTCATTTGTAACACAGTCAGGACATCCA +s simCow_chr6.simCow.chr6 534602 38 + 602619 --C--AATAGAGATTGAG-----TTTGTGAGCCAGCCAGGAAACTTT +s simDog_chr6.simDog.chr6 522812 45 + 593897 AAT--CCTAGAGATTGAGCCTTATTTGTGAGCCAGCCAAGAAAATCA +s simHuman_chr6.simHuman.chr6 529783 45 + 601863 TAT--CTTGGAGATTGAACCTTTTCTGTGAGCCAGCCAGGAAAATGG +s simMouse_chr6.simMouse.chr6 266994 45 + 636262 AAC--CCTTGCTCTTTTGCCTCATTTGTAACACAGTCAGGACATCCA +s simRat_chr6.simRat.chr6 255796 45 + 647215 GAC--CCTTGCCCCTGTGTCTTATTTGTAATATGGCCTGGACATCCA +s simRat_chr6.simRat.chr6 35145 45 - 647215 ATG--CTTTGAGATTGAGCCTTCTATGTAATACAGCCACAAAAAGTG a s simMouse_chr6.simMouse.chr6 559999 12 + 636262 GGTTGTTTTAAC @@ -210873,6 +226381,90 @@ s simRat_chr6.simRat.chr6 35273 27 - 647215 TGATTATTGTCAATATATGTAATGGGG a +s simMouse_chr6.simMouse.chr6 560091 3 + 636262 CAT +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 267039 3 + 636262 CTT +s simRat_chr6.simRat.chr6 255878 3 + 647215 CTT +s simRat_chr6.simRat.chr6 35300 3 - 647215 CAT + +a +s simMouse_chr6.simMouse.chr6 560094 18 + 636262 CTGCATTGACTGTGAATG +s Anc0.Anc0refChr3 161354 18 + 222631 CTGTATTGACTGTTAGCT +s Anc1.Anc1refChr6 197662 18 + 197743 CTGTATTGACTGTTAGCT +s Anc2.Anc2refChr1 75979 18 + 142988 CTGTATTAACTGTTAGCT +s mr.mrrefChr3 110050 18 + 181027 CTGCATTGACTGTGAGTG +s mr.mrrefChr5 118642 18 + 294540 CCGCATTGACTGTTAGCT +s simCow_chr6.simCow.chr6 534684 13 + 602619 CTGTA-----TGTCAGCT +s simDog_chr6.simDog.chr6 522904 18 + 593897 CTGTATTAACTGTTAGCT +s simHuman_chr6.simHuman.chr6 529884 18 + 601863 TTGTATTGACTGTTAGCT +s simMouse_chr6.simMouse.chr6 267042 18 + 636262 CCGCATTGACTGTTAGCT +s simRat_chr6.simRat.chr6 255881 18 + 647215 CTGCATTGACTATAAGCT +s simRat_chr6.simRat.chr6 35303 18 - 647215 CTGCATTGACTGTGAGTG + +a +s simMouse_chr6.simMouse.chr6 560112 25 + 636262 TTATGTATCTGTATGATTTGGTGGG +s Anc0.Anc0refChr3 161373 25 + 222631 TTATCTATCTCTATGATCTGGTGGG +s Anc1.Anc1refChr6 197681 25 + 197743 TTATCTATCTCTATGATCTGGTGGG +s Anc2.Anc2refChr1 75998 25 + 142988 TTGTCCATCTTTATGATCTGGTGGG +s mr.mrrefChr3 110069 25 + 181027 TTATGTATCTGTATGATTTGGTGGG +s mr.mrrefChr5 118661 25 + 294540 TTAACTGTCTCTATAATCTGTTGGG +s simCow_chr6.simCow.chr6 534698 25 + 602619 TTGTCCATCCTCATGATTTGGTGGT +s simDog_chr6.simDog.chr6 522923 21 + 593897 TT----ATCTTTATGCTCTGCTGGG +s simHuman_chr6.simHuman.chr6 529903 25 + 601863 TCATCTTTCTCTATTATCTGGTGGG +s simMouse_chr6.simMouse.chr6 267061 25 + 636262 TTAACTGTCTCTATAATCTGTTGGG +s simRat_chr6.simRat.chr6 255900 25 + 647215 TTAACAATCTTTATAATCTGTTGAG +s simRat_chr6.simRat.chr6 35322 25 - 647215 TTATGTATCTTTATGATTTGGTGAG + +a +s simMouse_chr6.simMouse.chr6 560137 5 + 636262 CTTAT +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 267092 5 + 636262 CTCAT +s simRat_chr6.simRat.chr6 255931 5 + 647215 CTCAT +s simRat_chr6.simRat.chr6 35347 5 - 647215 CTTAT + +a +s simMouse_chr6.simMouse.chr6 560142 26 + 636262 CAAGGATTATGATGTGAATACTGTTC +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 267098 26 + 636262 CAGGAAGCGTAATGTGATTACTGTTC +s simRat_chr6.simRat.chr6 255937 26 + 647215 CAGGAAGCATAATGTGGTTACTGTTT +s simRat_chr6.simRat.chr6 35352 26 - 647215 CAAAAAAAATAATGTGAATACTATTC + +a +s simMouse_chr6.simMouse.chr6 560168 4 + 636262 ACTC +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 267705 4 + 636262 ATTT +s simRat_chr6.simRat.chr6 256630 4 + 647215 ATTT +s simRat_chr6.simRat.chr6 35378 4 - 647215 ACTC + +a s simMouse_chr6.simMouse.chr6 560172 12 + 636262 AAACTGTAATTC s Anc0.Anc0refChr3 161434 12 + 222631 AATCTGTAATCT s Anc1.Anc1refChr1 0 12 + 69767 AATCTGTAATCT @@ -219367,7 +234959,114 @@ s simRat_chr6.simRat.chr6 57151 15 - 647215 GTGGTGACTAAGGAT a -s simMouse_chr6.simMouse.chr6 581591 46 + 636262 AGTTGCTGAGTCCTGGTCCTAGTGCTAGGTTTTACTTTTGCTTACC +s simMouse_chr6.simMouse.chr6 581583 6 + 636262 TGTTTG +s Anc0.Anc0refChr3 183048 6 + 222631 TATCTG +s Anc1.Anc1refChr1 22385 6 + 69767 TATCTG +s Anc2.Anc2refChr1 98567 6 + 142988 TATCTG +s mr.mrrefChr3 131443 6 + 181027 TGTTTG +s mr.mrrefChr3 157700 6 - 181027 TGTTTC +s simCow_chr6.simCow.chr6 556458 6 + 602619 TATCTG +s simDog_chr6.simDog.chr6 545046 6 + 593897 TTTCTG +s simHuman_chr6.simHuman.chr6 553592 6 + 601863 TATCTG +s simMouse_chr6.simMouse.chr6 168631 6 - 636262 TGTTTC +s simRat_chr6.simRat.chr6 169715 6 - 647215 TGTTTG +s simRat_chr6.simRat.chr6 57166 6 - 647215 TGTTTG + +a +s simMouse_chr6.simMouse.chr6 581589 50 + 636262 AGAGTTGCTGAGTCCTGGTCCTAGTGCTAGGTTTTACTTTTGCTTACCCC +s Anc0.Anc0refChr3 183057 4 + 222631 GC----------------------------------------------CT +s Anc1.Anc1refChr1 22394 4 + 69767 GC----------------------------------------------CT +s Anc2.Anc2refChr1 98576 4 + 142988 GC----------------------------------------------CT +s mr.mrrefChr3 131449 4 + 181027 AG----------------------------------------------CT +s mr.mrrefChr3 157706 4 - 181027 CC----------------------------------------------CT +s simCow_chr6.simCow.chr6 556467 4 + 602619 GC----------------------------------------------CT +s simDog_chr6.simDog.chr6 545055 4 + 593897 GC----------------------------------------------CT +s simHuman_chr6.simHuman.chr6 553601 4 + 601863 GC----------------------------------------------CT +s simMouse_chr6.simMouse.chr6 168637 4 - 636262 CC----------------------------------------------CT +s simRat_chr6.simRat.chr6 169721 4 - 647215 CC----------------------------------------------CT +s simRat_chr6.simRat.chr6 57172 4 - 647215 AG----------------------------------------------CT + +a +s simMouse_chr6.simMouse.chr6 581639 13 + 636262 GAATTTCACCACA +s Anc0.Anc0refChr3 183061 13 + 222631 GAATGTCAGCACA +s Anc1.Anc1refChr1 22398 13 + 69767 GAATGTCAGCACA +s Anc2.Anc2refChr1 98580 13 + 142988 GAATGTCAGCATA +s mr.mrrefChr3 131453 13 + 181027 GAATTTCACCACA +s mr.mrrefChr3 157710 13 - 181027 GGGTGTCACCACA +s simCow_chr6.simCow.chr6 556471 13 + 602619 GAATGTCACTTTA +s simDog_chr6.simDog.chr6 545062 13 + 593897 GAATGTTAGCATA +s simHuman_chr6.simHuman.chr6 553605 13 + 601863 GAATGTCAGCACA +s simMouse_chr6.simMouse.chr6 168641 13 - 636262 GGGTGTCACCACA +s simRat_chr6.simRat.chr6 169725 13 - 647215 GAATGTCACCACA +s simRat_chr6.simRat.chr6 57176 12 - 647215 GAATTT-ACCACA + +a +s simMouse_chr6.simMouse.chr6 581652 40 + 636262 GCACCTTAGAATTTCATATCAGAGGTATGCTTAACAGCCA +s Anc0.Anc0refChr3 183074 40 + 222631 GCACCTTAGAATTTGATACTATAGTTATGCTTAACAGCCA +s Anc1.Anc1refChr1 22411 40 + 69767 GCACCTTAGAATTTGATACTATAGTTATGCTTAACAGCCA +s Anc2.Anc2refChr1 98593 40 + 142988 GCACCTTAGAACTTGAGACTATAGTTATGCTTAACCGTCA +s mr.mrrefChr3 131466 40 + 181027 GCACCTTAGAATTTCATATCAGAGGTATGCTTAACAGCCA +s mr.mrrefChr3 157723 40 - 181027 GCACCCTGGAATTTGATACCAGTAGCATGCTTAATAACCA +s simCow_chr6.simCow.chr6 556484 40 + 602619 GCACTTTGGGACTTGAGACTATAGTCATGCTTGACCGTCA +s simDog_chr6.simDog.chr6 545075 34 + 593897 GCACCTTAGAACTTGAGACCATAGTTATGCTTAA------ +s simHuman_chr6.simHuman.chr6 553628 40 + 601863 GAGCCTCAGAATTTGATACTATGATTATGATTAACAGCCA +s simMouse_chr6.simMouse.chr6 168654 40 - 636262 GCACCCTGGAATTTGATACCAGTAGCATGCTTAATAACCA +s simRat_chr6.simRat.chr6 169738 40 - 647215 GCGCCCTAGGATTTGATATCAGTAGCATGCTTAATAATGA +s simRat_chr6.simRat.chr6 57188 40 - 647215 ACACCTTAGAATTTCATATCAGAGGTATGCTTAATTGCCA + +a +s simMouse_chr6.simMouse.chr6 581692 9 + 636262 ATACATGCC +s Anc0.Anc0refChr3 183117 7 + 222631 AGACATG-- +s Anc1.Anc1refChr1 22454 9 + 69767 AGACATGGC +s Anc2.Anc2refChr1 98636 7 + 142988 AGACACG-- +s mr.mrrefChr3 131506 9 + 181027 ATACATGGC +s mr.mrrefChr3 157763 9 - 181027 ATACATTCC +s simCow_chr6.simCow.chr6 556527 7 + 602619 AGACACG-- +s simHuman_chr6.simHuman.chr6 553671 8 + 601863 AGCCATGG- +s simMouse_chr6.simMouse.chr6 168694 9 - 636262 ATACATTCC +s simRat_chr6.simRat.chr6 169778 9 - 647215 ATATATGCC +s simRat_chr6.simRat.chr6 57228 9 - 647215 ATGCATGGC + +a +s simMouse_chr6.simMouse.chr6 581701 20 + 636262 AGCCCCCTGCTAACAGTAGG +s Anc0.Anc0refChr3 183124 20 + 222631 AGCACCCTGCTAATAGTAAG +s Anc1.Anc1refChr1 22463 20 + 69767 AGCACCCTGCTAATAGTAAG +s Anc2.Anc2refChr1 98643 20 + 142988 AGCACCCTGCTAATAATAAG +s mr.mrrefChr3 131515 20 + 181027 AGCCCCCTGCTAACAGTAGG +s mr.mrrefChr3 157772 20 - 181027 AGCCCCCTGGTAACAGTGAG +s simCow_chr6.simCow.chr6 556536 20 + 602619 AGCACCCTGCTAATAATAAG +s simHuman_chr6.simHuman.chr6 553679 19 + 601863 -GCACCCTGCTAATAGTAAG +s simMouse_chr6.simMouse.chr6 168703 20 - 636262 AGCCCCCTGGTAACAGTGAG +s simRat_chr6.simRat.chr6 169787 20 - 647215 AGCCCCCTGCTAACAGTGAG +s simRat_chr6.simRat.chr6 57237 19 - 647215 AGCCCC-TGCTAACGGTAGG + +a +s simMouse_chr6.simMouse.chr6 581721 22 + 636262 GGGGAAGGAATGCATAGGTACC +s Anc0.Anc0refChr3 183149 22 + 222631 GGGGAAGAAATGCATAGGACCC +s Anc1.Anc1refChr1 22488 22 + 69767 GGGGAAGAAATGCATAGGACCC +s Anc2.Anc2refChr1 98668 22 + 142988 GGGAAAGAAATGCATAGGACTC +s mr.mrrefChr3 131535 22 + 181027 GGGGAAGGAATGCATAGGTACC +s mr.mrrefChr3 157802 22 - 181027 GGGGAAGGAATGCATAGGTTCC +s simCow_chr6.simCow.chr6 556561 22 + 602619 GGGAAAGGAATGCATAGGGTTC +s simDog_chr6.simDog.chr6 545109 22 + 593897 GGCAAAGAAATGCACAAGACTA +s simHuman_chr6.simHuman.chr6 553703 22 + 601863 GGGGAAAAAATGCATAGGACCC +s simMouse_chr6.simMouse.chr6 168733 22 - 636262 GGGGAAGGAATGCATAGGTTCC +s simRat_chr6.simRat.chr6 169817 22 - 647215 GGGGAAGGAATACATAGGTACC +s simRat_chr6.simRat.chr6 57256 22 - 647215 GGGGAATGAATGCACAGGTACC + +a +s simMouse_chr6.simMouse.chr6 581743 1 + 636262 C +s Anc0.Anc0refChr3 183171 1 + 222631 T +s Anc1.Anc1refChr1 22510 1 + 69767 T +s Anc2.Anc2refChr1 98690 1 + 142988 T +s mr.mrrefChr3 131557 1 + 181027 T +s mr.mrrefChr3 157825 1 - 181027 T +s simCow_chr6.simCow.chr6 556583 1 + 602619 T +s simDog_chr6.simDog.chr6 545131 1 + 593897 T +s simHuman_chr6.simHuman.chr6 553725 1 + 601863 T +s simMouse_chr6.simMouse.chr6 168756 1 - 636262 T +s simRat_chr6.simRat.chr6 169840 1 - 647215 A +s simRat_chr6.simRat.chr6 57278 1 - 647215 T a s simMouse_chr6.simMouse.chr6 581744 2 + 636262 AG @@ -219380,6 +235079,48 @@ s simRat_chr6.simRat.chr6 57279 2 - 647215 AT a +s simMouse_chr6.simMouse.chr6 581746 1 + 636262 T +s Anc0.Anc0refChr3 183174 1 + 222631 G +s Anc1.Anc1refChr1 22513 1 + 69767 G +s Anc2.Anc2refChr1 98693 1 + 142988 G +s mr.mrrefChr3 131560 1 + 181027 T +s mr.mrrefChr3 157826 1 - 181027 G +s simCow_chr6.simCow.chr6 556586 1 + 602619 T +s simDog_chr6.simDog.chr6 545134 1 + 593897 G +s simHuman_chr6.simHuman.chr6 553726 1 + 601863 G +s simMouse_chr6.simMouse.chr6 168757 1 - 636262 G +s simRat_chr6.simRat.chr6 169841 1 - 647215 G +s simRat_chr6.simRat.chr6 57281 1 - 647215 T + +a +s simMouse_chr6.simMouse.chr6 581747 12 + 636262 GCCACTGAGGGG +s Anc0.Anc0refChr3 183175 12 + 222631 GCCGTTGAGAGT +s Anc1.Anc1refChr1 22514 12 + 69767 GCCGTTGAGAGT +s Anc2.Anc2refChr1 98694 12 + 142988 GCAGTTGAGAGT +s mr.mrrefChr3 131561 12 + 181027 GCCACTGAGAGG +s mr.mrrefChr3 157827 12 - 181027 ACCATTGAGAGC +s simCow_chr6.simCow.chr6 556587 12 + 602619 GCTAATGAGAGT +s simDog_chr6.simDog.chr6 545135 12 + 593897 GCAGTTGAGAGT +s simHuman_chr6.simHuman.chr6 553727 12 + 601863 GCCGTTGAGAGT +s simMouse_chr6.simMouse.chr6 168759 12 - 636262 ACCATTGAGAGC +s simRat_chr6.simRat.chr6 169842 12 - 647215 ACCACTGAGAGC +s simRat_chr6.simRat.chr6 57282 12 - 647215 GTCACTGAGAGG + +a +s simMouse_chr6.simMouse.chr6 581759 6 + 636262 GTATCT +s Anc0.Anc0refChr3 183187 6 + 222631 GTCTCA +s Anc1.Anc1refChr1 22526 6 + 69767 GTCTCA +s Anc2.Anc2refChr1 98706 6 + 142988 GTCTTA +s mr.mrrefChr3 131573 6 + 181027 GTCTCT +s mr.mrrefChr3 157839 6 - 181027 AGTTCA +s simCow_chr6.simCow.chr6 556600 6 + 602619 GCTTTA +s simDog_chr6.simDog.chr6 545147 6 + 593897 GTCTTA +s simHuman_chr6.simHuman.chr6 553739 6 + 601863 CACTCA +s simMouse_chr6.simMouse.chr6 168771 6 - 636262 AGTTCA +s simRat_chr6.simRat.chr6 169854 6 - 647215 AGCTCA +s simRat_chr6.simRat.chr6 57294 6 - 647215 GTCTCT + +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 @@ -219402,6 +235143,73 @@ s simRat_chr6.simRat.chr6 57320 8 - 647215 AAACATTG a +s simMouse_chr6.simMouse.chr6 581793 1 + 636262 A +s Anc0.Anc0refChr3 183216 1 + 222631 A +s Anc1.Anc1refChr1 22555 1 + 69767 A +s Anc2.Anc2refChr1 98735 1 + 142988 A +s mr.mrrefChr3 131607 1 + 181027 A +s mr.mrrefChr3 157845 1 - 181027 A +s simCow_chr6.simCow.chr6 556629 1 + 602619 A +s simHuman_chr6.simHuman.chr6 553768 1 + 601863 A +s simMouse_chr6.simMouse.chr6 168777 1 - 636262 A +s simRat_chr6.simRat.chr6 169882 1 - 647215 A +s simRat_chr6.simRat.chr6 57328 1 - 647215 G + +a +s simMouse_chr6.simMouse.chr6 581794 4 + 636262 AGTC +s Anc0.Anc0refChr3 183217 4 + 222631 AGCC +s Anc1.Anc1refChr1 22556 4 + 69767 AGCC +s Anc2.Anc2refChr1 98736 4 + 142988 AGGC +s mr.mrrefChr3 131608 4 + 181027 AGTC +s mr.mrrefChr3 157846 4 - 181027 AGCC +s simCow_chr6.simCow.chr6 556630 4 + 602619 AGGC +s simHuman_chr6.simHuman.chr6 553769 3 + 601863 AGC- +s simMouse_chr6.simMouse.chr6 168778 4 - 636262 AGCC +s simRat_chr6.simRat.chr6 169883 4 - 647215 AGTG +s simRat_chr6.simRat.chr6 57330 4 - 647215 AATC + +a +s simMouse_chr6.simMouse.chr6 581798 47 + 636262 CCAATTCTAACAGCACTCTATTTGTTGGGTAAATTTTAAAGTGGAAG +s Anc0.Anc0refChr3 183221 27 + 222631 C--------------------TTATTTGGTAAATTTTAAAGTAGAAG +s Anc1.Anc1refChr1 22560 47 + 69767 CCAGTTCTGACAGCACAGTATTTATTTGGTAAATTTTAAAGTAGAAG +s Anc2.Anc2refChr1 98740 27 + 142988 C--------------------TGTTTTGGTAACTTTTAAAGTAGAAG +s mr.mrrefChr3 131612 47 + 181027 CCAATTCTAACAGCACTCTATTTATTGGGTAAATTTTAAAGTGGAAG +s mr.mrrefChr3 157850 47 - 181027 CCAGTGATAACAGCAGAGAATTTGTTTGCCCACTTTTAAAATACAAG +s simCow_chr6.simCow.chr6 556663 27 + 602619 T--------------------GGTTTTGGTAACTTTTACAATAGAAG +s simDog_chr6.simDog.chr6 545231 27 + 593897 C--------------------TGTCTCGGTAACTTTTAAAGTAGAAG +s simHuman_chr6.simHuman.chr6 553772 28 + 601863 CCAGTTCTGACAGCA-------------------TGTAATGGATTGG +s simMouse_chr6.simMouse.chr6 168782 47 - 636262 CCAGTGATAACAGCAGAGAATTTGTTTGCCCACTTTTAAAATACAAG +s simRat_chr6.simRat.chr6 169887 47 - 647215 CCAGTGATAACAGCATAGAATTTGCTCGCTAACTATTAAAATAGAAG +s simRat_chr6.simRat.chr6 57334 47 - 647215 CCAATTCTAACACCACTGGATTAATTGGGTAAGTTTTAATGGGGAAG + +a +s simMouse_chr6.simMouse.chr6 581845 5 + 636262 ATTAT +s Anc0.Anc0refChr3 183248 5 + 222631 CCCCA +s Anc1.Anc1refChr1 22607 5 + 69767 CCCCA +s Anc2.Anc2refChr1 98767 5 + 142988 CCCCA +s mr.mrrefChr3 131659 5 + 181027 ATTAT +s mr.mrrefChr3 157897 5 - 181027 CGGCA +s simCow_chr6.simCow.chr6 556690 5 + 602619 CCCCA +s simDog_chr6.simDog.chr6 545258 5 + 593897 CCCCA +s simHuman_chr6.simHuman.chr6 553800 5 + 601863 ACCTA +s simMouse_chr6.simMouse.chr6 168829 5 - 636262 CGGCA +s simRat_chr6.simRat.chr6 169934 5 - 647215 CTGCA +s simRat_chr6.simRat.chr6 57382 5 - 647215 GGCTT + +a +s simMouse_chr6.simMouse.chr6 581850 1 + 636262 C +s Anc0.Anc0refChr3 183253 1 + 222631 C +s Anc1.Anc1refChr1 22612 1 + 69767 C +s Anc2.Anc2refChr1 98772 1 + 142988 C +s mr.mrrefChr3 131664 1 + 181027 C +s mr.mrrefChr3 157902 1 - 181027 T +s simCow_chr6.simCow.chr6 556707 1 + 602619 C +s simHuman_chr6.simHuman.chr6 553805 1 + 601863 C +s simMouse_chr6.simMouse.chr6 168834 1 - 636262 T +s simRat_chr6.simRat.chr6 169939 1 - 647215 T +s simRat_chr6.simRat.chr6 57387 1 - 647215 C + +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 @@ -222770,6 +238578,69 @@ s simRat_chr6.simRat.chr6 66185 3 - 647215 TCC a +s simMouse_chr6.simMouse.chr6 591600 5 + 636262 TGGCT +s Anc1.Anc1refChr1 56829 5 - 69767 TGGCT +s mr.mrrefChr3 140347 5 + 181027 TGGCT +s mr.mrrefChr3 58560 5 - 181027 GGGAT +s simMouse_chr6.simMouse.chr6 63743 5 - 636262 GGGAT +s simRat_chr6.simRat.chr6 599177 5 + 647215 GGGAT +s simRat_chr6.simRat.chr6 66188 5 - 647215 TTGTT + +a +s simMouse_chr6.simMouse.chr6 591605 23 + 636262 TGGTGTGATCCATCATCTTAATC +s Anc1.Anc1refChr1 56834 23 - 69767 TGGTGTGATCTACCCCCTTAATC +s mr.mrrefChr3 140352 23 + 181027 TGGTGTGATCCATCATCTTAATC +s mr.mrrefChr3 58566 23 - 181027 TGGTGTGATGTACCCCCTTATTC +s simMouse_chr6.simMouse.chr6 63749 23 - 636262 TGGTGTGATGTACCCCCTTATTC +s simRat_chr6.simRat.chr6 599183 23 + 647215 TGGTATGATGTGCCCCTTTGTTC +s simRat_chr6.simRat.chr6 66193 23 - 647215 TGGTGGAATCCATCATCTTAATC + +a +s simMouse_chr6.simMouse.chr6 591628 39 + 636262 CCCCAGTCTGATAAACAGGGTGGTTCAATAAACAAGGGC +s Anc1.Anc1refChr1 56857 39 - 69767 CCTCAGTTTGACCAACAGGATAGTTCGATAAGTGAGGGT +s mr.mrrefChr3 140375 39 + 181027 CCCCAGTCTGATAAACAGGGTGGTTCAATAAACAAGGGC +s mr.mrrefChr3 58607 39 - 181027 CTTCAGTTTGACCAACAGAAGAGTTTGATAAGTGAGGGT +s simMouse_chr6.simMouse.chr6 63790 39 - 636262 CTTCAGTTTGACCAACAGAAGAGTTTGATAAGTGAGGGT +s simRat_chr6.simRat.chr6 599225 39 + 647215 CTTCAGTTTTATCAATAGAGGGGTTTAATAAGCGAGGGT +s simRat_chr6.simRat.chr6 66216 39 - 647215 CTCCAGTCTGATAAACGGGGGGGTTCAATAAACAAGAGT + +a +s simMouse_chr6.simMouse.chr6 591667 37 + 636262 GCAATCCAATGTCCCCCAGACTGATAAGCAACTAAAA +s Anc1.Anc1refChr1 56896 37 - 69767 GCAATCTAATGTCCCCCAGACTGATAGGCAACTCCAA +s mr.mrrefChr3 140414 37 + 181027 GCAATCCAATGTCCCCCAGACTGATAAGCAACTAAAA +s mr.mrrefChr3 58646 37 - 181027 GCGATCTAGTGTCCCCCCGACTGACAGCCAACTCCTA +s simMouse_chr6.simMouse.chr6 63829 37 - 636262 GCGATCTAGTGTCCCCCCGACTGACAGCCAACTCCTA +s simRat_chr6.simRat.chr6 599300 37 + 647215 GCAATCTAGTATCCCCCGGACTGACAGCCAACACCTA +s simRat_chr6.simRat.chr6 66255 37 - 647215 GCAATCCAATGTCCCCCACACCAATAACCAACTGAAA + +a +s simMouse_chr6.simMouse.chr6 591704 1 + 636262 T +s Anc1.Anc1refChr1 56933 1 - 69767 T +s mr.mrrefChr3 140451 1 + 181027 T +s mr.mrrefChr3 58683 1 - 181027 T +s simMouse_chr6.simMouse.chr6 63866 1 - 636262 T +s simRat_chr6.simRat.chr6 599337 1 + 647215 T +s simRat_chr6.simRat.chr6 66296 1 - 647215 T + +a +s simMouse_chr6.simMouse.chr6 591705 11 + 636262 CCAGTTGTAAT +s Anc1.Anc1refChr1 56934 11 - 69767 CCAGGTGCAAT +s mr.mrrefChr3 140452 11 + 181027 CCAGTTGTAAT +s mr.mrrefChr3 58688 11 - 181027 CCAGGTGCAAT +s simMouse_chr6.simMouse.chr6 63871 11 - 636262 CCAGGTGCAAT +s simRat_chr6.simRat.chr6 599342 11 + 647215 CCTGGTGCAAT +s simRat_chr6.simRat.chr6 66297 11 - 647215 CCAGCTGTAAT + +a +s simMouse_chr6.simMouse.chr6 591716 1 + 636262 A +s Anc1.Anc1refChr1 56945 1 - 69767 A +s mr.mrrefChr3 140463 1 + 181027 A +s mr.mrrefChr3 58868 1 - 181027 A +s simMouse_chr6.simMouse.chr6 64068 1 - 636262 A +s simRat_chr6.simRat.chr6 599523 1 + 647215 A +s simRat_chr6.simRat.chr6 66308 1 - 647215 A + +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 @@ -228248,6 +244119,48 @@ s simRat_chr6.simRat.chr6 83041 36 - 647215 GAACAG--TGCATA---GCTTGCA--GTTTCCAGAGAAAGATC a +s simMouse_chr6.simMouse.chr6 608527 25 + 636262 AGCTGGGCCTGAACCTTGCTCAATC +s Anc0.Anc0refChr3 205904 25 + 222631 ACCTGGGCCTGAGCCTTGCTCAATC +s Anc1.Anc1refChr1 45763 25 + 69767 ACCTGGGCCTGAGCCTTGCTCAATC +s Anc2.Anc2refChr1 122905 25 + 142988 ACCTGGGCCTGAGTCTTGCTCAATC +s mr.mrrefChr3 156463 25 + 181027 AGCTGGGCCTGAACCTTGCTCAATC +s mr.mrrefChr3 156325 25 + 181027 ACCTGGGCCTGAACCTTGCTCAATC +s simCow_chr6.simCow.chr6 581925 25 + 602619 ACCTGGGCCCGAGCCTTGCTCAATC +s simDog_chr6.simDog.chr6 573639 25 + 593897 ACCTGGACCTGGGTCTTGCTCAACC +s simHuman_chr6.simHuman.chr6 576736 25 + 601863 ACCTCAGCCTGAGGCTTGCCCAATC +s simMouse_chr6.simMouse.chr6 608381 25 + 636262 ACCTGGCCTTGAACCTTGCTCAATC +s simRat_chr6.simRat.chr6 82921 25 - 647215 ACCTTGGCCTGAACCTTGCTCAATC +s simRat_chr6.simRat.chr6 83077 25 - 647215 AGTTGGGCCTGAACCTTGCTCAATC + +a +s simMouse_chr6.simMouse.chr6 608552 4 + 636262 TCTT +s Anc0.Anc0refChr3 205938 4 + 222631 TCTT +s Anc1.Anc1refChr1 45797 4 + 69767 TCTT +s Anc2.Anc2refChr1 122939 4 + 142988 TCTT +s mr.mrrefChr3 156488 4 + 181027 TCTT +s mr.mrrefChr3 156359 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 608415 4 + 636262 TCTA +s simRat_chr6.simRat.chr6 82954 4 - 647215 TCTT +s simRat_chr6.simRat.chr6 83111 4 - 647215 CCTT + +a +s simMouse_chr6.simMouse.chr6 608556 2 + 636262 TC +s Anc0.Anc0refChr3 205942 2 + 222631 TC +s Anc1.Anc1refChr1 45801 2 + 69767 TC +s Anc2.Anc2refChr1 122945 2 + 142988 TT +s mr.mrrefChr3 156492 2 + 181027 TC +s mr.mrrefChr3 156363 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 608419 2 + 636262 CC +s simRat_chr6.simRat.chr6 82958 2 - 647215 TC +s simRat_chr6.simRat.chr6 83115 2 - 647215 TC + +a s simMouse_chr6.simMouse.chr6 608558 1 + 636262 T s Anc0.Anc0refChr3 205944 1 + 222631 T s Anc1.Anc1refChr1 45803 1 + 69767 T @@ -228258,7 +244171,60 @@ s simRat_chr6.simRat.chr6 83117 1 - 647215 T a -s simMouse_chr6.simMouse.chr6 608566 5 + 636262 AATCA +s simMouse_chr6.simMouse.chr6 608559 3 + 636262 TTT +s Anc0.Anc0refChr3 205945 3 + 222631 TTT +s Anc1.Anc1refChr1 45804 3 + 69767 TTT +s Anc2.Anc2refChr1 122948 3 + 142988 TTT +s mr.mrrefChr3 156495 3 + 181027 TTT +s mr.mrrefChr3 156365 3 + 181027 TTT +s simCow_chr6.simCow.chr6 581968 3 + 602619 TTT +s simDog_chr6.simDog.chr6 573682 3 + 593897 TTT +s simHuman_chr6.simHuman.chr6 576776 3 + 601863 TTT +s simMouse_chr6.simMouse.chr6 608421 3 + 636262 TTT +s simRat_chr6.simRat.chr6 82960 3 - 647215 TTT +s simRat_chr6.simRat.chr6 83118 3 - 647215 TTG + +a +s simMouse_chr6.simMouse.chr6 608562 1 + 636262 G +s Anc0.Anc0refChr3 205948 1 + 222631 A +s Anc1.Anc1refChr1 45807 1 + 69767 A +s Anc2.Anc2refChr1 122951 1 + 142988 A +s mr.mrrefChr3 156498 1 + 181027 G +s mr.mrrefChr3 156368 1 + 181027 G +s simCow_chr6.simCow.chr6 581971 1 + 602619 A +s simDog_chr6.simDog.chr6 573685 1 + 593897 A +s simHuman_chr6.simHuman.chr6 576779 1 + 601863 A +s simMouse_chr6.simMouse.chr6 608425 1 + 636262 G +s simRat_chr6.simRat.chr6 82963 1 - 647215 G +s simRat_chr6.simRat.chr6 83121 1 - 647215 G + +a +s simMouse_chr6.simMouse.chr6 608563 9 + 636262 AATAATCAA +s Anc0.Anc0refChr3 205960 4 + 222631 AAT-----G +s Anc1.Anc1refChr1 45819 4 + 69767 AAT-----G +s Anc2.Anc2refChr1 122963 4 + 142988 TAT-----G +s mr.mrrefChr3 156499 4 + 181027 AAT-----A +s mr.mrrefChr3 156369 4 + 181027 AAT-----A +s simCow_chr6.simCow.chr6 581983 4 + 602619 GAT-----G +s simDog_chr6.simDog.chr6 573697 4 + 593897 TAT-----G +s simHuman_chr6.simHuman.chr6 576791 4 + 601863 AAT-----G +s simMouse_chr6.simMouse.chr6 608426 4 + 636262 AAT-----A +s simRat_chr6.simRat.chr6 82964 4 - 647215 AAT-----A +s simRat_chr6.simRat.chr6 83122 4 - 647215 AAT-----A + +a +s simMouse_chr6.simMouse.chr6 608572 9 + 636262 ATCATCTCC +s Anc0.Anc0refChr3 205964 9 + 222631 GGCATCTCC +s Anc1.Anc1refChr1 45823 9 + 69767 GGCATCTCC +s Anc2.Anc2refChr1 122967 9 + 142988 GGCATCTCC +s mr.mrrefChr3 156503 9 + 181027 GTCATCTCC +s mr.mrrefChr3 156373 9 + 181027 GGCATCTCC +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 608430 9 + 636262 GGCATCTCC +s simRat_chr6.simRat.chr6 82973 9 - 647215 GGCATTTCC +s simRat_chr6.simRat.chr6 83126 9 - 647215 GTCATCTCC a s simMouse_chr6.simMouse.chr6 608581 14 + 636262 AGTAGTCACACTAT @@ -228272,7 +244238,74 @@ s simRat_chr6.simRat.chr6 83135 14 - 647215 AGTAGTTACACTAT a -s simMouse_chr6.simMouse.chr6 608628 10 + 636262 CTAGTGTAGA +s simMouse_chr6.simMouse.chr6 608595 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 156526 4 + 181027 ATAT +s mr.mrrefChr3 156382 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 608439 4 + 636262 ATAT +s simRat_chr6.simRat.chr6 82996 4 - 647215 ACAT +s simRat_chr6.simRat.chr6 83149 4 - 647215 ATAA + +a +s simMouse_chr6.simMouse.chr6 608599 5 + 636262 CATCT +s Anc0.Anc0refChr3 205991 5 + 222631 CATCT +s Anc1.Anc1refChr1 45850 5 + 69767 CATCT +s Anc2.Anc2refChr1 122994 5 + 142988 CATCT +s mr.mrrefChr3 156530 5 + 181027 CATCT +s mr.mrrefChr3 156386 5 + 181027 CATTT +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 608443 5 + 636262 CATTT +s simRat_chr6.simRat.chr6 83000 5 - 647215 TATCT +s simRat_chr6.simRat.chr6 83153 5 - 647215 TATCT + +a +s simMouse_chr6.simMouse.chr6 608604 17 + 636262 TATGTATACAAGAGCGC +s Anc0.Anc0refChr3 205996 17 + 222631 TATGTATACAAAAGGGC +s Anc1.Anc1refChr1 45855 17 + 69767 TATGTATACAAAAGGGC +s Anc2.Anc2refChr1 122999 17 + 142988 TAGGTATACTAAAGGGC +s mr.mrrefChr3 156535 17 + 181027 TATGTATACAAGAGCGC +s mr.mrrefChr3 156391 17 + 181027 TATGTATACGAGAGGGC +s simCow_chr6.simCow.chr6 582022 17 + 602619 TAGGTATACTAAAAGGC +s simDog_chr6.simDog.chr6 573737 17 + 593897 CAGGTATGCTAAAGGGC +s simHuman_chr6.simHuman.chr6 576827 17 + 601863 TAAGTATACAAAAGGAC +s simMouse_chr6.simMouse.chr6 608448 17 + 636262 TATGTATACGAGAGGGC +s simRat_chr6.simRat.chr6 83005 17 - 647215 TATGTATAGGAGAAGGC +s simRat_chr6.simRat.chr6 83158 17 - 647215 TATGTATATGAGACAGT + +a +s simMouse_chr6.simMouse.chr6 608621 21 + 636262 CCCTTAGCTAGTGTAGACTAT +s Anc0.Anc0refChr3 206016 11 + 222631 TCTCTAG----------TTAT +s Anc1.Anc1refChr1 45875 11 + 69767 TCTCTAG----------TTAT +s Anc2.Anc2refChr1 123019 11 + 142988 TCTCTTG----------TTAT +s mr.mrrefChr3 156555 11 + 181027 TCCTTAG----------CTAT +s mr.mrrefChr3 156411 11 + 181027 TCCTTAG----------ATAT +s simCow_chr6.simCow.chr6 582041 11 + 602619 CTTCTTG----------TCAT +s simDog_chr6.simDog.chr6 573757 9 + 593897 TCCC--A----------TTAT +s simHuman_chr6.simHuman.chr6 576847 11 + 601863 TCTCTGG----------TTAT +s simMouse_chr6.simMouse.chr6 608468 11 + 636262 TCCTTAG----------ATAT +s simRat_chr6.simRat.chr6 83025 11 - 647215 TCCTAAG----------ATAA +s simRat_chr6.simRat.chr6 83178 11 - 647215 TCCTTAG----------CTAT + +a +s simMouse_chr6.simMouse.chr6 608642 5 + 636262 GTGTA +s Anc0.Anc0refChr3 206028 5 + 222631 GCATT +s Anc1.Anc1refChr1 45887 5 + 69767 GCATT +s Anc2.Anc2refChr1 123031 5 + 142988 GCATT +s mr.mrrefChr3 156566 5 + 181027 GTGTA +s mr.mrrefChr3 156422 5 + 181027 AAGTA +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 608479 5 + 636262 AAGTA +s simRat_chr6.simRat.chr6 83036 5 - 647215 AAGTA +s simRat_chr6.simRat.chr6 83189 5 - 647215 GTGTA a s simMouse_chr6.simMouse.chr6 608647 42 + 636262 GAGTAGACTGTCTGTCCAATCTGCACTGCTTGCAGTTTCCAG @@ -228495,7 +244528,157 @@ s simRat_chr6.simRat.chr6 83721 55 - 647215 ATAACTATAAAATTTAAAGAGGACTCAAATGACCATGTATCAGGTATGAGGCTTC a -s simMouse_chr6.simMouse.chr6 609342 1 + 636262 C +s simMouse_chr6.simMouse.chr6 609224 1 + 636262 G +s Anc1.Anc1refChr6 121944 1 + 197743 A +s mr.mrrefChr3 157148 1 + 181027 G +s mr.mrrefChr3 24557 1 + 181027 A +s mr.mrrefChr5 95819 1 + 294540 A +s simMouse_chr6.simMouse.chr6 242724 1 + 636262 A +s simMouse_chr6.simMouse.chr6 703 1 - 636262 G +s simMouse_chr6.simMouse.chr6 468850 1 + 636262 A +s simRat_chr6.simRat.chr6 352594 1 + 647215 T +s simRat_chr6.simRat.chr6 478789 1 + 647215 A +s simRat_chr6.simRat.chr6 83776 1 - 647215 G + +a +s simMouse_chr6.simMouse.chr6 609225 17 + 636262 AAGCCGCAAACAAAGCA +s Anc1.Anc1refChr6 121945 17 + 197743 AAGTCGCAAACAAAGCA +s mr.mrrefChr3 157149 17 + 181027 AAGCCGCAAACAAAGCA +s mr.mrrefChr3 24558 17 + 181027 AAGTTGCAAACAGAGCA +s mr.mrrefChr5 95820 17 + 294540 AAGTCGCAAACAAAGCG +s simMouse_chr6.simMouse.chr6 242725 17 + 636262 AATTCACAAACAAAGCG +s simMouse_chr6.simMouse.chr6 704 17 - 636262 AAGTCGTGAACAAAGCG +s simMouse_chr6.simMouse.chr6 468851 17 + 636262 AAGTTGCAAACAGAGCA +s simRat_chr6.simRat.chr6 352595 17 + 647215 AAGTCGCAAACAATGTA +s simRat_chr6.simRat.chr6 66885 17 - 647215 AAGTCGCAAACGAAGCA +s simRat_chr6.simRat.chr6 478790 17 + 647215 AAGTTGCAAGCAAAGTA +s simRat_chr6.simRat.chr6 83777 17 - 647215 AAGTCACAAACAAGGCA + +a +s simMouse_chr6.simMouse.chr6 609242 4 + 636262 TACG +s Anc1.Anc1refChr6 121962 4 + 197743 TACG +s mr.mrrefChr3 157166 4 + 181027 TACG +s mr.mrrefChr3 24575 4 + 181027 TACG +s mr.mrrefChr5 95837 4 + 294540 TACG +s simMouse_chr6.simMouse.chr6 242742 4 + 636262 TACA +s simMouse_chr6.simMouse.chr6 721 4 - 636262 TACG +s simMouse_chr6.simMouse.chr6 468868 4 + 636262 TACG +s simRat_chr6.simRat.chr6 66902 4 - 647215 TATG +s simRat_chr6.simRat.chr6 478807 4 + 647215 TACA +s simRat_chr6.simRat.chr6 83794 4 - 647215 TACA + +a +s simMouse_chr6.simMouse.chr6 609246 61 + 636262 CAAGGCAATTGCATACTAGAGCACTCAAATGGCAAATAGTCTTGAGTTAATAATGACTGTG +s Anc1.Anc1refChr6 121966 61 + 197743 CAAGGCAATTGCATACCAGAGCCCTCAAATGGCAAATAGTCTTGAGCTAATAATGACTGTG +s mr.mrrefChr3 157170 61 + 181027 CAAGGCAATTGCATACTAGAGCACTCAAATGGCAAATAGTCTTGAGTTAATAATGACTGTG +s mr.mrrefChr3 24579 61 + 181027 CAAGTCAATTGCATACCGGAGCCCTCAAATGGCAATTAGTCCCAAGCCAACAATGATTGTG +s mr.mrrefChr5 95841 61 + 294540 CAAGGCAGTCGCATACCAGAGTGCTCAGTTAGCAAATCGTCTTGAGCGAATCATGACCGTG +s simMouse_chr6.simMouse.chr6 242746 61 + 636262 CGAGGCAGTCGTATACAAGAGTGTTCAGTTAGCAAATCGTCTCGAGCGAGTCATGACCGTG +s simMouse_chr6.simMouse.chr6 725 61 - 636262 CAAGGCGGTCGCATACCAGAGCGCTCAGTTAGCAAATCGTCTTGAGCGAATCATGACCGTG +s simMouse_chr6.simMouse.chr6 468872 61 + 636262 CAAGTCAATTGCATACCGGAGCCCTCAAATGGCAATTAGTCCCAAGCCAACAATGATTGTG +s simRat_chr6.simRat.chr6 352612 61 + 647215 CAAGGCTATAGCAGACCAGAGGACTCAAATGGTGGATAATCCCGAGCCAATAATGGCTGTG +s simRat_chr6.simRat.chr6 66906 61 - 647215 GGAGGCCATAGCATACCAGAGTGCTCAAGTGGCAGATAGTCCTGAGCTAATAATGACTGTG +s simRat_chr6.simRat.chr6 478811 61 + 647215 CAAAGCAATTGCATACTGGAGCACTCAAATGGCAGATAGCCCCAAGCCAATAATGACTGTG +s simRat_chr6.simRat.chr6 83798 61 - 647215 CAAGGCAACCGAATACCAGGATGCTTAAATGGCTAATATTCCTGAGTGATTAATGACTGTG + +a +s simMouse_chr6.simMouse.chr6 609307 13 + 636262 GGCCCACACATTA +s Anc1.Anc1refChr6 122027 13 + 197743 GGCCCACACATTA +s mr.mrrefChr3 157231 13 + 181027 GGCCCACACATTA +s mr.mrrefChr3 24640 13 + 181027 GGCCCACACGTTA +s mr.mrrefChr5 95902 13 + 294540 GGCCCAGACAGTA +s simMouse_chr6.simMouse.chr6 242807 13 + 636262 GGCCCAGACAGTA +s simMouse_chr6.simMouse.chr6 786 13 - 636262 GGCCCAGACAGTA +s simMouse_chr6.simMouse.chr6 468933 13 + 636262 GGCCCACACGTTA +s simRat_chr6.simRat.chr6 66967 13 - 647215 GGGCCACACAATT +s simRat_chr6.simRat.chr6 478872 13 + 647215 GGCCCACCCGTTA +s simRat_chr6.simRat.chr6 83859 13 - 647215 GGCCCACACATTA + +a +s simMouse_chr6.simMouse.chr6 609320 4 + 636262 ATGT +s Anc1.Anc1refChr6 122042 4 + 197743 ATGT +s mr.mrrefChr3 157244 4 + 181027 ATGT +s mr.mrrefChr3 24655 4 + 181027 TTGT +s mr.mrrefChr5 95917 4 + 294540 ATGT +s simMouse_chr6.simMouse.chr6 242822 4 + 636262 ATGT +s simMouse_chr6.simMouse.chr6 801 4 - 636262 ATGT +s simMouse_chr6.simMouse.chr6 468948 4 + 636262 TTGT +s simRat_chr6.simRat.chr6 66982 4 - 647215 ATGT +s simRat_chr6.simRat.chr6 478887 4 + 647215 ATGT +s simRat_chr6.simRat.chr6 83874 4 - 647215 ATTT + +a +s simMouse_chr6.simMouse.chr6 609324 12 + 636262 AGCACTCACTGG +s Anc1.Anc1refChr6 122046 12 + 197743 AGCACTCACTGG +s mr.mrrefChr3 157248 12 + 181027 AGCACTCACTGG +s mr.mrrefChr3 24659 12 + 181027 AGAATTCATTGG +s mr.mrrefChr5 95921 12 + 294540 AGCACTCACTGG +s simMouse_chr6.simMouse.chr6 242826 12 + 636262 AGCACTCACTGG +s simMouse_chr6.simMouse.chr6 805 12 - 636262 AGCACTCACTGG +s simMouse_chr6.simMouse.chr6 468952 12 + 636262 AGAATTCATTGG +s simRat_chr6.simRat.chr6 67036 12 - 647215 AGCACTCATTAG +s simRat_chr6.simRat.chr6 478891 12 + 647215 AGCACTGACTGG +s simRat_chr6.simRat.chr6 83878 12 - 647215 AGGACTCACTGG + +a +s simMouse_chr6.simMouse.chr6 609336 3 + 636262 TTA +s Anc1.Anc1refChr6 122058 3 + 197743 TTA +s mr.mrrefChr3 157260 3 + 181027 TTA +s mr.mrrefChr3 24671 3 + 181027 TTA +s mr.mrrefChr5 95933 3 + 294540 TTA +s simMouse_chr6.simMouse.chr6 242838 3 + 636262 TTA +s simMouse_chr6.simMouse.chr6 817 3 - 636262 TTA +s simMouse_chr6.simMouse.chr6 468964 3 + 636262 TTA +s simRat_chr6.simRat.chr6 478903 3 + 647215 TTA +s simRat_chr6.simRat.chr6 83890 3 - 647215 TTA + +a +s simMouse_chr6.simMouse.chr6 609339 9 + 636262 TAACCACTC +s Anc1.Anc1refChr6 122062 8 + 197743 TAA-GACTT +s mr.mrrefChr3 157263 8 + 181027 TAA-CACTC +s mr.mrrefChr3 24675 8 + 181027 AAC-GACTT +s mr.mrrefChr5 95937 8 + 294540 TAA-GACTT +s simMouse_chr6.simMouse.chr6 242842 8 + 636262 TAA-GACTT +s simMouse_chr6.simMouse.chr6 821 8 - 636262 AAC-GACTT +s simMouse_chr6.simMouse.chr6 468968 8 + 636262 AAC-GACTT +s simRat_chr6.simRat.chr6 478907 8 + 647215 AAC-GACTT +s simRat_chr6.simRat.chr6 83893 8 - 647215 TAG-TGCTC + +a +s simMouse_chr6.simMouse.chr6 609348 7 + 636262 ACATACC +s Anc1.Anc1refChr6 122070 7 + 197743 TCATACC +s mr.mrrefChr3 157271 7 + 181027 ACATACC +s mr.mrrefChr3 24695 7 + 181027 TCACACC +s mr.mrrefChr5 95945 7 + 294540 TCGTGCC +s simMouse_chr6.simMouse.chr6 242850 7 + 636262 TCGTGCC +s simMouse_chr6.simMouse.chr6 829 7 - 636262 TCGTGCC +s simMouse_chr6.simMouse.chr6 468996 7 + 636262 TCACACC +s simRat_chr6.simRat.chr6 478927 7 + 647215 TCACACT +s simRat_chr6.simRat.chr6 83901 7 - 647215 ACATACC + +a +s simMouse_chr6.simMouse.chr6 609355 2 + 636262 CA +s Anc1.Anc1refChr6 122077 2 + 197743 CA +s mr.mrrefChr3 157278 2 + 181027 CA +s mr.mrrefChr3 24702 2 + 181027 CC +s mr.mrrefChr5 95952 2 + 294540 CA +s simMouse_chr6.simMouse.chr6 242877 2 + 636262 CA +s simMouse_chr6.simMouse.chr6 836 2 - 636262 CA +s simMouse_chr6.simMouse.chr6 469003 2 + 636262 CC +s simRat_chr6.simRat.chr6 478934 2 + 647215 AT +s simRat_chr6.simRat.chr6 83908 2 - 647215 GG + +a +s simMouse_chr6.simMouse.chr6 609357 2 + 636262 GA +s Anc1.Anc1refChr6 122079 2 + 197743 TG +s mr.mrrefChr3 157280 2 + 181027 GA +s mr.mrrefChr3 24704 2 + 181027 TG +s mr.mrrefChr5 95954 2 + 294540 TG +s simMouse_chr6.simMouse.chr6 242879 2 + 636262 TG +s simMouse_chr6.simMouse.chr6 838 2 - 636262 CT +s simMouse_chr6.simMouse.chr6 469006 2 + 636262 TG +s simRat_chr6.simRat.chr6 478936 2 + 647215 TG +s simRat_chr6.simRat.chr6 83910 2 - 647215 GA a s simMouse_chr6.simMouse.chr6 609359 15 + 636262 TCCGACTTATCACAT @@ -228503,10 +244686,144 @@ 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 +s simMouse_chr6.simMouse.chr6 609374 19 + 636262 GTTACCAACGAACTGCGGA +s Anc1.Anc1refChr6 122081 19 + 197743 GTTACCAACGAACTGTGGA +s mr.mrrefChr3 157297 19 + 181027 GTTACCAACGAACTGCGGA +s mr.mrrefChr3 24706 19 + 181027 ATTACCAACAAACTGTGGA +s mr.mrrefChr5 95956 19 + 294540 GTTTCCAAAGAATTTTATA +s simMouse_chr6.simMouse.chr6 242881 19 + 636262 GTTACCAACGAAGTTTGTA +s simMouse_chr6.simMouse.chr6 840 19 - 636262 ATTTGCAAAGAATTTTAGA +s simMouse_chr6.simMouse.chr6 469008 18 + 636262 ATTACCAATGAA-TGTGGA +s simRat_chr6.simRat.chr6 478938 19 + 647215 GTTACCAACAAACTGTGGA +s simRat_chr6.simRat.chr6 83932 19 - 647215 GTTACCAACAAACTGCAGA + +a +s simMouse_chr6.simMouse.chr6 609393 2 + 636262 TT +s Anc1.Anc1refChr6 122100 2 + 197743 TT +s mr.mrrefChr3 157316 2 + 181027 TT +s mr.mrrefChr3 24725 2 + 181027 TT +s mr.mrrefChr5 95975 2 + 294540 TT +s simMouse_chr6.simMouse.chr6 242900 2 + 636262 TT +s simMouse_chr6.simMouse.chr6 859 2 - 636262 TT +s simMouse_chr6.simMouse.chr6 469026 2 + 636262 TT +s simRat_chr6.simRat.chr6 83951 2 - 647215 TT + +a +s simMouse_chr6.simMouse.chr6 609395 6 + 636262 TACCCA +s Anc1.Anc1refChr6 122102 6 + 197743 TACCCA +s mr.mrrefChr3 157318 6 + 181027 TACCCA +s mr.mrrefChr3 24727 6 + 181027 TACTGA +s mr.mrrefChr5 95977 6 + 294540 TCCCCA +s simMouse_chr6.simMouse.chr6 242902 6 + 636262 TCCCCA +s simMouse_chr6.simMouse.chr6 958 6 - 636262 TCTCCA +s simMouse_chr6.simMouse.chr6 469028 6 + 636262 TACTGA +s simRat_chr6.simRat.chr6 83953 6 - 647215 TACCCA + +a +s simMouse_chr6.simMouse.chr6 609401 8 + 636262 TCACATTG +s Anc1.Anc1refChr6 122108 7 + 197743 CA-CAATG +s mr.mrrefChr3 157324 7 + 181027 TC-CATTG +s mr.mrrefChr3 24734 7 + 181027 CA-CTATA +s mr.mrrefChr5 95983 7 + 294540 CA-CAAGG +s simMouse_chr6.simMouse.chr6 242908 7 + 636262 CA-CAAAG +s simMouse_chr6.simMouse.chr6 964 7 - 636262 AT-CAAGA +s simMouse_chr6.simMouse.chr6 469035 7 + 636262 CA-CTATA +s simRat_chr6.simRat.chr6 83959 7 - 647215 TC-CAATG + +a +s simMouse_chr6.simMouse.chr6 609409 6 + 636262 CAGCAC +s Anc1.Anc1refChr6 122115 6 + 197743 CAGCAC +s mr.mrrefChr3 157331 6 + 181027 CAGCAC +s mr.mrrefChr3 24741 6 + 181027 CAGCAC +s mr.mrrefChr5 95990 6 + 294540 CACAAG +s simMouse_chr6.simMouse.chr6 242915 6 + 636262 CACCAG +s simMouse_chr6.simMouse.chr6 971 6 - 636262 AACAAG +s simMouse_chr6.simMouse.chr6 469042 6 + 636262 CAGCAC +s simRat_chr6.simRat.chr6 478957 6 + 647215 CAGCAC +s simRat_chr6.simRat.chr6 83966 6 - 647215 CACAAC + +a +s simMouse_chr6.simMouse.chr6 609415 2 + 636262 TC +s Anc1.Anc1refChr6 122121 2 + 197743 TC +s mr.mrrefChr3 157337 2 + 181027 TC +s mr.mrrefChr3 24747 2 + 181027 TC +s mr.mrrefChr5 95996 2 + 294540 GC +s simMouse_chr6.simMouse.chr6 242921 2 + 636262 GC +s simMouse_chr6.simMouse.chr6 987 2 - 636262 GC +s simMouse_chr6.simMouse.chr6 469048 2 + 636262 TC +s simRat_chr6.simRat.chr6 478963 2 + 647215 TC +s simRat_chr6.simRat.chr6 83972 2 - 647215 TC + +a +s simMouse_chr6.simMouse.chr6 609417 2 + 636262 AT +s Anc1.Anc1refChr6 122123 2 + 197743 AT +s mr.mrrefChr3 157339 2 + 181027 AT +s mr.mrrefChr3 24749 2 + 181027 AT +s simMouse_chr6.simMouse.chr6 469050 2 + 636262 AT +s simRat_chr6.simRat.chr6 478965 2 + 647215 AC +s simRat_chr6.simRat.chr6 83974 2 - 647215 AT + +a +s simMouse_chr6.simMouse.chr6 609419 3 + 636262 TGG +s Anc1.Anc1refChr6 122125 2 + 197743 T-G +s mr.mrrefChr3 157341 2 + 181027 T-G +s mr.mrrefChr3 24751 2 + 181027 T-G +s mr.mrrefChr5 95998 2 + 294540 C-A +s simMouse_chr6.simMouse.chr6 242923 2 + 636262 C-A +s simMouse_chr6.simMouse.chr6 989 2 - 636262 C-A +s simMouse_chr6.simMouse.chr6 469052 2 + 636262 T-G +s simRat_chr6.simRat.chr6 478967 2 + 647215 T-G +s simRat_chr6.simRat.chr6 83976 2 - 647215 T-G + +a +s simMouse_chr6.simMouse.chr6 609422 2 + 636262 CT +s Anc1.Anc1refChr6 122127 2 + 197743 CT +s mr.mrrefChr3 157343 2 + 181027 CT +s mr.mrrefChr3 24754 2 + 181027 CT +s mr.mrrefChr5 96000 2 + 294540 CT +s simMouse_chr6.simMouse.chr6 994 2 - 636262 CT +s simMouse_chr6.simMouse.chr6 469055 2 + 636262 CC +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 +s simRat_chr6.simRat.chr6 83978 2 - 647215 TT + +a +s simMouse_chr6.simMouse.chr6 609424 7 + 636262 CATTTAT +s Anc1.Anc1refChr6 122129 7 + 197743 CGTTTAT +s mr.mrrefChr3 157345 7 + 181027 CATTTAT +s mr.mrrefChr3 24756 7 + 181027 CGTTTAT +s mr.mrrefChr5 96002 7 + 294540 CGTTTAT +s simMouse_chr6.simMouse.chr6 242925 7 + 636262 CGTTAGT +s simMouse_chr6.simMouse.chr6 996 7 - 636262 TGCTTTT +s simMouse_chr6.simMouse.chr6 469057 7 + 636262 TGTTTAT +s simRat_chr6.simRat.chr6 352675 7 + 647215 CGTTTAT +s simRat_chr6.simRat.chr6 67050 7 - 647215 CGTTTAT +s simRat_chr6.simRat.chr6 478972 7 + 647215 CGTTTAT +s simRat_chr6.simRat.chr6 83980 7 - 647215 CATTTAT + +a +s simMouse_chr6.simMouse.chr6 609431 3 + 636262 CAT +s Anc1.Anc1refChr6 122136 3 + 197743 CAT +s mr.mrrefChr3 157352 3 + 181027 CAT +s mr.mrrefChr3 24763 3 + 181027 CAT +s mr.mrrefChr5 96009 3 + 294540 CAC +s simMouse_chr6.simMouse.chr6 242932 3 + 636262 CAC +s simMouse_chr6.simMouse.chr6 469064 3 + 636262 CAT +s simRat_chr6.simRat.chr6 352682 3 + 647215 CAC +s simRat_chr6.simRat.chr6 67057 3 - 647215 CAC +s simRat_chr6.simRat.chr6 478979 3 + 647215 CAC +s simRat_chr6.simRat.chr6 83987 3 - 647215 CAC + +a +s simMouse_chr6.simMouse.chr6 609434 19 + 636262 GGTCACAGGAGTCCCCCTA +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 242935 19 + 636262 CGCCACATGAGTCCTCCTT +s simRat_chr6.simRat.chr6 352685 19 + 647215 GGTGACATGAGTCCCTTTA +s simRat_chr6.simRat.chr6 67060 19 - 647215 GGCCACGTGGGTCCCCCTA +s simRat_chr6.simRat.chr6 83990 19 - 647215 AGCTATGTGAATCCCTCTA a s simMouse_chr6.simMouse.chr6 609453 80 + 636262 TCTCCATGTCTGTATAACTAATAAGGGACTAGTTTAATTGTTCTAACATGGTCAGTAAAGAGACGCAGAGACAAGACCCT @@ -232386,6 +248703,20 @@ s simRat_chr6.simRat.chr6 630372 125 + 647215 ATGTGATTAATGATATCAGTT-----------------------ACTTTCAGGATTTCAGCACCCTCCAAAAAGGTCTCAAATAAGCCAGGCAGTACTCCGATCACTGATTGGTGTGGGGTGTACTGCTAGGAGATTGCAAC-ATTAGG a +s simMouse_chr6.simMouse.chr6 618363 15 + 636262 AAAGGTAGGTAGGGA +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 165614 15 + 181027 AAAGGTAGGTAGGGA +s mr.mrrefChr3 164447 15 + 181027 ACAGGAAAGAACTTA +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 617165 15 + 636262 ACAGGAAAGAACTTA +s simRat_chr6.simRat.chr6 629029 15 + 647215 GTGGGAAAGAACTTA +s simRat_chr6.simRat.chr6 630497 15 + 647215 AAAGATAGGTAAGGA + +a s simMouse_chr6.simMouse.chr6 618378 4 + 636262 ACTT s Anc0.Anc0refChr3 213129 4 + 222631 ACTT s Anc1.Anc1refChr1 53384 4 + 69767 ACTT @@ -232399,20 +248730,130 @@ 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 +s simMouse_chr6.simMouse.chr6 618382 6 + 636262 ACATAC +s Anc0.Anc0refChr3 213134 5 + 222631 -CACAC +s Anc1.Anc1refChr1 53390 6 + 69767 ACACAC +s Anc2.Anc2refChr1 130560 5 + 142988 -CCCAC +s mr.mrrefChr3 165633 6 + 181027 ACATAC +s mr.mrrefChr3 164468 6 + 181027 ACACAC +s simCow_chr6.simCow.chr6 589182 5 + 602619 -CCCAC +s simDog_chr6.simDog.chr6 581140 5 + 593897 -CCCAC +s simHuman_chr6.simHuman.chr6 584937 6 + 601863 GCACGC +s simMouse_chr6.simMouse.chr6 617180 3 + 636262 ---CAC +s simRat_chr6.simRat.chr6 629065 6 + 647215 ACACAC +s simRat_chr6.simRat.chr6 630516 6 + 647215 ACACAC + +a +s simMouse_chr6.simMouse.chr6 618388 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 165639 1 + 181027 A +s mr.mrrefChr3 164480 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 617189 1 + 636262 A +s simRat_chr6.simRat.chr6 629077 1 + 647215 A +s simRat_chr6.simRat.chr6 630522 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 618389 11 + 636262 AGGGCATGCCA +s Anc0.Anc0refChr3 213145 10 + 222631 GGGTCTG-CCA +s Anc1.Anc1refChr1 53402 10 + 69767 GGGTCTG-CCA +s Anc2.Anc2refChr1 130571 10 + 142988 GGATCTG-CCA +s mr.mrrefChr3 165640 10 + 181027 AGGGCAT-CCA +s mr.mrrefChr3 164481 10 + 181027 GGGTCTA-CCA +s simCow_chr6.simCow.chr6 589195 10 + 602619 GGCTCTG-CCA +s simDog_chr6.simDog.chr6 581151 10 + 593897 GGATCTG-CCA +s simHuman_chr6.simHuman.chr6 584949 10 + 601863 GGGTCTG-CCA +s simMouse_chr6.simMouse.chr6 617190 10 + 636262 GGGTCTA-CCA +s simRat_chr6.simRat.chr6 629078 10 + 647215 GGCTATA-TCA +s simRat_chr6.simRat.chr6 630529 10 + 647215 AGAGTAT-CCA + +a +s simMouse_chr6.simMouse.chr6 618400 10 + 636262 AAAGTGGTAC +s Anc0.Anc0refChr3 213155 10 + 222631 GGAGTAATAC +s Anc1.Anc1refChr1 53412 10 + 69767 GGAGTAATAC +s Anc2.Anc2refChr1 130581 10 + 142988 GGAGTAATAC +s mr.mrrefChr3 165650 10 + 181027 AAAGTGGTAC +s mr.mrrefChr3 164491 10 + 181027 AGAGTAACAC +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 617200 10 + 636262 AGAATAACAG +s simRat_chr6.simRat.chr6 629088 10 + 647215 ACAGTAACAC +s simRat_chr6.simRat.chr6 630539 10 + 647215 AGAGTGGTAG + +a +s simMouse_chr6.simMouse.chr6 618410 37 + 636262 ATTTGGTGATTACTATGACCTGTGCATCTGACTTTGT +s Anc0.Anc0refChr3 213166 37 + 222631 ATATGGTGATTACTATGCTCTTTGCATCTTACCTTCT +s Anc1.Anc1refChr1 53423 37 + 69767 ATATGGTGATTACTATGCTCTTTGCATCTTACCTTCT +s Anc2.Anc2refChr1 130592 37 + 142988 ATATGGTGATTTCTATACTGCTTGCATCTTACCTCCT +s mr.mrrefChr3 165660 37 + 181027 ATTTGGTGATTACTATGACCTGTGCATCTGACTTTGT +s mr.mrrefChr3 164502 37 + 181027 ACTTGGTAATGACTATGCTCTTTTCAATTGACCTTCT +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 617211 37 + 636262 ACTTGGTAATGACTATGCCCTTTTCAATTGACCTAAT +s simRat_chr6.simRat.chr6 629099 37 + 647215 ACTTGGTAATGACTATGCTCTTTTCAATTGACCTTCT +s simRat_chr6.simRat.chr6 630550 37 + 647215 ATTTGGTGATTACTACGACCTGTGCATCCAACTTTAT + +a +s simMouse_chr6.simMouse.chr6 618447 16 + 636262 ATAACAACATCACAAC +s Anc0.Anc0refChr3 213203 16 + 222631 ATGCTAATATCACACT +s Anc1.Anc1refChr1 53460 16 + 69767 ATGCTAATATCACACT +s Anc2.Anc2refChr1 130629 16 + 142988 CTGCTAATAGCACACT +s mr.mrrefChr3 165697 16 + 181027 ATAACAACATCACAAC +s mr.mrrefChr3 164539 16 + 181027 ACACTAACATCACACT +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 617248 16 + 636262 ACACTAACATCACACT +s simRat_chr6.simRat.chr6 629136 16 + 647215 ACACTAACATCACACT +s simRat_chr6.simRat.chr6 630587 16 + 647215 ATAACAACATCACAAC + +a +s simMouse_chr6.simMouse.chr6 618463 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 165713 1 + 181027 A +s mr.mrrefChr3 164555 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 617264 1 + 636262 A +s simRat_chr6.simRat.chr6 629152 1 + 647215 A +s simRat_chr6.simRat.chr6 630613 1 + 647215 G + +a +s simMouse_chr6.simMouse.chr6 618464 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 165714 6 + 181027 AAATCA +s mr.mrrefChr3 164557 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 617266 6 + 636262 AAATCA +s simRat_chr6.simRat.chr6 629154 6 + 647215 AAATCA +s simRat_chr6.simRat.chr6 630614 6 + 647215 AAATCA + +a +s simMouse_chr6.simMouse.chr6 618470 19 + 636262 GGGGCCTTACAACATTCAA +s Anc0.Anc0refChr3 213227 19 + 222631 GGGGGTGTAAAACACTCAG +s Anc1.Anc1refChr1 53484 19 + 69767 GGGGGTGTAAAACACTCAG +s Anc2.Anc2refChr1 130653 19 + 142988 GGGGGTGTAAAATACTCAG +s mr.mrrefChr3 165720 19 + 181027 GGGGCCTTACAACATTCAA +s mr.mrrefChr3 164563 19 + 181027 GGGGGTATAAGACATTCAA +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 617272 19 + 636262 GGGGGTATAAGACATTCAA +s simRat_chr6.simRat.chr6 629160 19 + 647215 GGGGGTATAAGACATTCAA +s simRat_chr6.simRat.chr6 630621 19 + 647215 GGGACAATACAATGTTCAA a s simMouse_chr6.simMouse.chr6 618489 3 + 636262 AAA @@ -232425,15 +248866,217 @@ s simRat_chr6.simRat.chr6 630644 36 + 647215 CAGTTACACAATCAGGGGACATGCAACGTTCGAAAG a +s simMouse_chr6.simMouse.chr6 618528 22 + 636262 ACAGTTTCACTAACAGAGTAGG +s Anc0.Anc0refChr3 213246 22 + 222631 ACAGTGTCACTAACAAAGTAGG +s Anc1.Anc1refChr1 53503 22 + 69767 ACAGTGTCACTAACAAAGTAGG +s Anc2.Anc2refChr1 130672 22 + 142988 ACAGTGTCACTAACATACTAGG +s mr.mrrefChr3 165778 22 + 181027 ACAGTTTCACTAACAGAGTAGG +s mr.mrrefChr3 164582 22 + 181027 ACAGTTTCACTAACAAAGTAGG +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 617291 22 + 636262 ACAGTTTCACTAATAAAGTAGG +s simRat_chr6.simRat.chr6 629179 22 + 647215 ACATTTTCACAAACCAAATAGG +s simRat_chr6.simRat.chr6 630680 22 + 647215 ACAGTTTCACTAATAGAGTAGG + +a +s simMouse_chr6.simMouse.chr6 618550 9 + 636262 CCAGGCGAA +s Anc0.Anc0refChr3 213268 9 + 222631 CAAGAAGAA +s Anc1.Anc1refChr1 53525 9 + 69767 CAAGAAGAA +s Anc2.Anc2refChr1 130694 9 + 142988 TAAGATGAA +s mr.mrrefChr3 165800 9 + 181027 CCAGGCGAA +s mr.mrrefChr3 164604 9 + 181027 CCAGAAGAA +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 617313 9 + 636262 CCAGAAAAA +s simRat_chr6.simRat.chr6 629201 9 + 647215 CCATTAGAA +s simRat_chr6.simRat.chr6 630702 9 + 647215 CCAGATAAA + +a +s simMouse_chr6.simMouse.chr6 618559 6 + 636262 ACAAGG +s Anc0.Anc0refChr3 213277 6 + 222631 ACAGAC +s Anc1.Anc1refChr1 53534 6 + 69767 ACAGAC +s Anc2.Anc2refChr1 130703 6 + 142988 ACAGAC +s mr.mrrefChr3 165809 6 + 181027 ACAAGG +s mr.mrrefChr3 164613 6 + 181027 ATGAGC +s simCow_chr6.simCow.chr6 589331 6 + 602619 ATAGAC +s simDog_chr6.simDog.chr6 581283 6 + 593897 ACAGAC +s simHuman_chr6.simHuman.chr6 585083 6 + 601863 ACAGAC +s simMouse_chr6.simMouse.chr6 617322 6 + 636262 ATGAGC +s simRat_chr6.simRat.chr6 629230 6 + 647215 ATGAGC +s simRat_chr6.simRat.chr6 630711 6 + 647215 ACAAGG + +a +s simMouse_chr6.simMouse.chr6 618565 19 + 636262 TCCATGACGTAGGTTGTCA +s Anc0.Anc0refChr3 213283 19 + 222631 TCTATGACCCAAGTTGTTA +s Anc1.Anc1refChr1 53540 19 + 69767 TCTATGACCCAAGTTGTTA +s Anc2.Anc2refChr1 130709 19 + 142988 TCTGTGATCCAAATTGTTA +s mr.mrrefChr3 165815 19 + 181027 TCCATGACGTAGGTTGTCA +s mr.mrrefChr3 164619 19 + 181027 TCTAAGACCCCAGTTGTTA +s simCow_chr6.simCow.chr6 589337 19 + 602619 TCTGTGATTCAAATTGTTA +s simDog_chr6.simDog.chr6 581289 19 + 593897 TCTGTGATCTAAATTGTCG +s simHuman_chr6.simHuman.chr6 585089 19 + 601863 TCCATTACCCAAGTTGTTA +s simMouse_chr6.simMouse.chr6 617331 19 + 636262 TCTAAGACCCCAGTTACTA +s simRat_chr6.simRat.chr6 629236 19 + 647215 TCTAAGACCCCAGTTGTTA +s simRat_chr6.simRat.chr6 630717 19 + 647215 TCCTTGACCTAAGTTGTCA + +a +s simMouse_chr6.simMouse.chr6 618584 4 + 636262 ATAT +s Anc0.Anc0refChr3 213306 4 + 222631 ATAA +s Anc1.Anc1refChr1 53563 4 + 69767 ATAA +s Anc2.Anc2refChr1 130732 4 + 142988 GTAA +s mr.mrrefChr3 165834 4 + 181027 ATAT +s mr.mrrefChr3 164642 4 + 181027 ATAA +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 617354 4 + 636262 ATAA +s simRat_chr6.simRat.chr6 629259 4 + 647215 ATAA +s simRat_chr6.simRat.chr6 630736 4 + 647215 TTAT + +a +s simMouse_chr6.simMouse.chr6 618588 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 165838 2 + 181027 AG +s mr.mrrefChr3 164646 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 617358 2 + 636262 AG +s simRat_chr6.simRat.chr6 629263 2 + 647215 AG +s simRat_chr6.simRat.chr6 630741 2 + 647215 AG + +a +s simMouse_chr6.simMouse.chr6 618590 4 + 636262 TCAA +s Anc0.Anc0refChr3 213312 4 + 222631 TTAA +s Anc1.Anc1refChr1 53569 4 + 69767 TTAA +s Anc2.Anc2refChr1 130738 4 + 142988 TTAA +s mr.mrrefChr3 165840 4 + 181027 TCAA +s mr.mrrefChr3 164648 4 + 181027 TTAA +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 617360 4 + 636262 TTAA +s simRat_chr6.simRat.chr6 629266 4 + 647215 TTAG +s simRat_chr6.simRat.chr6 630743 4 + 647215 TCAG + +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 +s simMouse_chr6.simMouse.chr6 618598 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 165848 3 + 181027 CTT +s mr.mrrefChr3 164652 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 617364 3 + 636262 CTT +s simRat_chr6.simRat.chr6 629270 3 + 647215 CTT +s simRat_chr6.simRat.chr6 630751 3 + 647215 CTT + +a +s simMouse_chr6.simMouse.chr6 618601 7 + 636262 ATTATAA +s Anc0.Anc0refChr3 213319 7 + 222631 ATTACTT +s Anc1.Anc1refChr1 53576 7 + 69767 ATTACTT +s Anc2.Anc2refChr1 130750 7 + 142988 AGTACTC +s mr.mrrefChr3 165851 7 + 181027 ATTATAA +s mr.mrrefChr3 164655 7 + 181027 ATTACCT +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 617367 7 + 636262 ATTACCT +s simRat_chr6.simRat.chr6 629273 7 + 647215 ATTACCT +s simRat_chr6.simRat.chr6 630754 7 + 647215 ATTACCA + +a +s simMouse_chr6.simMouse.chr6 618608 12 + 636262 ACTCTTAACTCC +s Anc0.Anc0refChr3 213326 12 + 222631 ACTATTGACTCT +s Anc1.Anc1refChr1 53583 12 + 69767 ACTATTGACTCT +s Anc2.Anc2refChr1 130757 12 + 142988 ACTATTGACACT +s mr.mrrefChr3 165858 12 + 181027 ACTCTTAACTCC +s mr.mrrefChr3 164662 12 + 181027 ATTCTTGACTCC +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 617374 12 + 636262 ACTCTTGACTCC +s simRat_chr6.simRat.chr6 629280 12 + 647215 ATTTTTGACTCC +s simRat_chr6.simRat.chr6 630762 12 + 647215 ACTGTTGACTCA + +a +s simMouse_chr6.simMouse.chr6 618620 20 + 636262 TTGAAAAAAAGCACAGCACG +s Anc0.Anc0refChr3 213358 20 + 222631 TATATGAGGAATAAAGCACG +s Anc1.Anc1refChr1 53615 20 + 69767 TATATGAGGAATAAAGCACG +s Anc2.Anc2refChr1 130790 20 + 142988 TATATGTGGAAAAAAGCACG +s mr.mrrefChr3 165870 20 + 181027 TTGAAAAAAAGCACAGCACG +s mr.mrrefChr3 164674 20 + 181027 TCCAAAAAAATTACAGCACT +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 617386 20 + 636262 TCCAAAAAAATCACAGCGCT +s simRat_chr6.simRat.chr6 629292 20 + 647215 TCCAAAAAAATTACAGTACT +s simRat_chr6.simRat.chr6 630774 20 + 647215 TTGAAGAGAAGCACAGCACA + +a +s simMouse_chr6.simMouse.chr6 618640 6 + 636262 AGATAC +s Anc0.Anc0refChr3 213380 6 + 222631 ATGTAC +s Anc1.Anc1refChr1 53637 6 + 69767 ATGTAC +s Anc2.Anc2refChr1 130814 6 + 142988 ATGTAC +s mr.mrrefChr3 165890 6 + 181027 AGATAC +s mr.mrrefChr3 164694 6 + 181027 ATGTAC +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 617406 6 + 636262 ATGTAC +s simRat_chr6.simRat.chr6 629312 6 + 647215 ATGTAC +s simRat_chr6.simRat.chr6 630794 6 + 647215 AGGTAC + +a +s simMouse_chr6.simMouse.chr6 618646 125 + 636262 TATGAACTCTTGAAAGCTATGCTTGCACGAAAACTTGACTCTTGGTAGATCAGTTGTTGAGAAGTGAAGTATCACATTTTGGTTAAAGTGAAGTATCGCATTTTGGTTACCTGATGTACCTCATC +s Anc0.Anc0refChr3 213424 9 + 222631 TA--------------------------------------------------------------------------------------------------------------------CCACATC +s Anc1.Anc1refChr1 53681 9 + 69767 TA--------------------------------------------------------------------------------------------------------------------CCACATC +s Anc2.Anc2refChr1 130858 9 + 142988 TA--------------------------------------------------------------------------------------------------------------------CCACATC +s mr.mrrefChr3 165896 9 + 181027 TA--------------------------------------------------------------------------------------------------------------------CCTCATC +s mr.mrrefChr3 164740 9 + 181027 TA--------------------------------------------------------------------------------------------------------------------CCACATT +s simCow_chr6.simCow.chr6 589489 7 + 602619 CA--------------------------------------------------------------------------------------------------------------------CCATA-- +s simDog_chr6.simDog.chr6 581420 9 + 593897 TA--------------------------------------------------------------------------------------------------------------------CCACATC +s simHuman_chr6.simHuman.chr6 585230 9 + 601863 TA--------------------------------------------------------------------------------------------------------------------CCTCATT +s simMouse_chr6.simMouse.chr6 617452 9 + 636262 TA--------------------------------------------------------------------------------------------------------------------TCACATT +s simRat_chr6.simRat.chr6 629358 9 + 647215 TA--------------------------------------------------------------------------------------------------------------------CCACATT +s simRat_chr6.simRat.chr6 630800 9 + 647215 CA--------------------------------------------------------------------------------------------------------------------CAGTAGC + +a +s simMouse_chr6.simMouse.chr6 618771 10 + 636262 TCAATTACCC +s Anc0.Anc0refChr3 213434 9 + 222631 -CAGTTTCCC +s Anc1.Anc1refChr1 53712 10 + 69767 TCAGTTTCCC +s Anc2.Anc2refChr1 130868 9 + 142988 -CAGTTTCCC +s mr.mrrefChr3 165905 10 + 181027 TCAATTACCC +s mr.mrrefChr3 164771 10 + 181027 ACCAGTTGAC +s simDog_chr6.simDog.chr6 581430 9 + 593897 -CAGTTTCCC +s simHuman_chr6.simHuman.chr6 585261 10 + 601863 TCAGTTGCCC +s simMouse_chr6.simMouse.chr6 617479 10 + 636262 ACCAGTTGAC +s simRat_chr6.simRat.chr6 629389 10 + 647215 ACCAGTTGAC +s simRat_chr6.simRat.chr6 630809 10 + 647215 TCAGTTACCC + +a +s simMouse_chr6.simMouse.chr6 618781 16 + 636262 CCCAGTTCTAATAACA +s Anc0.Anc0refChr3 213454 13 + 222631 CACATTTAAAA---CA +s Anc1.Anc1refChr1 53733 13 + 69767 CACATTTAAAA---CA +s Anc2.Anc2refChr1 130888 13 + 142988 CATATTTAAAG---CA +s mr.mrrefChr3 165915 13 + 181027 CCCAGTTCTAA---CA +s mr.mrrefChr3 164781 13 + 181027 AAAATTCAAAA---AA +s simDog_chr6.simDog.chr6 581450 13 + 593897 CATATTTAAAG---CA +s simHuman_chr6.simHuman.chr6 585282 13 + 601863 TACACTTGAAA---TA +s simMouse_chr6.simMouse.chr6 617489 13 + 636262 AAAATTCAGAA---AA +s simRat_chr6.simRat.chr6 629399 13 + 647215 AAAATTAAAAA---AA +s simRat_chr6.simRat.chr6 630819 13 + 647215 CCTGGTTCCAA---CA a s simMouse_chr6.simMouse.chr6 618797 15 + 636262 AACAATACAGGAACT @@ -232446,6 +249089,19 @@ s simRat_chr6.simRat.chr6 630832 15 + 647215 AACAATACAGGAAAT a +s simMouse_chr6.simMouse.chr6 618812 12 + 636262 AGAATAAACTGT +s Anc0.Anc0refChr3 213481 12 + 222631 AAGGTAGACTGT +s Anc1.Anc1refChr1 53761 12 + 69767 AAGGTAGACTGT +s Anc2.Anc2refChr1 130915 12 + 142988 AAGGCAGACTGT +s mr.mrrefChr3 165943 12 + 181027 AGAATAAACTGT +s mr.mrrefChr3 164794 12 + 181027 AAGGTACACTGC +s simDog_chr6.simDog.chr6 581477 12 + 593897 AAGGCAGACTGT +s simHuman_chr6.simHuman.chr6 585310 12 + 601863 AAGGTTGACTGT +s simMouse_chr6.simMouse.chr6 617502 12 + 636262 AAGGTACACTGC +s simRat_chr6.simRat.chr6 629412 12 + 647215 CAGGAACACTGC +s simRat_chr6.simRat.chr6 630847 12 + 647215 AGAGTAAAATGT + +a s simMouse_chr6.simMouse.chr6 618824 5 + 636262 TACTC s Anc0.Anc0refChr3 213493 5 + 222631 TACTC s Anc1.Anc1refChr1 53773 5 + 69767 TACTC @@ -232456,6 +249112,131 @@ s simRat_chr6.simRat.chr6 630859 5 + 647215 TACTC a +s simMouse_chr6.simMouse.chr6 618829 19 + 636262 TTACTGTATAGGTAGGTCA +s Anc0.Anc0refChr3 213498 15 + 222631 TTATTGTATGGGTAG---- +s Anc1.Anc1refChr1 53778 19 + 69767 TTATTGTATGGGTAGGTGA +s Anc2.Anc2refChr1 130932 15 + 142988 CAATCGTAAGAGTAA---- +s mr.mrrefChr3 165960 19 + 181027 TTACTGTATAGGTAGGTCA +s mr.mrrefChr3 164806 19 + 181027 TTGTTGTATGGGTAGGTTA +s simDog_chr6.simDog.chr6 581494 15 + 593897 CAATCGTAAGAGTAA---- +s simHuman_chr6.simHuman.chr6 585327 19 + 601863 TTATTGTATGGGTAGTGGT +s simMouse_chr6.simMouse.chr6 617514 19 + 636262 TTGTTGTATGGGCAGGTTA +s simRat_chr6.simRat.chr6 629424 19 + 647215 TTGTTGTACTGGTAGGCTA +s simRat_chr6.simRat.chr6 630864 19 + 647215 TTAATGTATGGGTAGGTCT + +a +s simMouse_chr6.simMouse.chr6 618848 17 + 636262 AGTTTGAGTAGACCCTC +s Anc0.Anc0refChr3 213513 15 + 222631 --TTTGAGTAGACCATC +s Anc1.Anc1refChr1 53797 17 + 69767 AGTTTGAGTAGACCATC +s Anc2.Anc2refChr1 130947 15 + 142988 --TCTGAGTAGACCATT +s mr.mrrefChr3 165979 17 + 181027 AGTTTGAGTAGACCATC +s mr.mrrefChr3 164830 17 + 181027 AGTAGAAATGGACCATG +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 617538 17 + 636262 ACCAGAAATGGACCATG +s simRat_chr6.simRat.chr6 629448 17 + 647215 AGTAGAAATGGACCATG +s simRat_chr6.simRat.chr6 630883 17 + 647215 GGTTTGAGTACACCATC + +a +s simMouse_chr6.simMouse.chr6 618865 4 + 636262 TATA +s Anc0.Anc0refChr3 213528 4 + 222631 TGTA +s Anc1.Anc1refChr1 53814 4 + 69767 TGTA +s Anc2.Anc2refChr1 130963 4 + 142988 TGTG +s mr.mrrefChr3 165996 4 + 181027 TGTA +s mr.mrrefChr3 164847 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 617555 4 + 636262 TGTA +s simRat_chr6.simRat.chr6 629465 4 + 647215 TGTA +s simRat_chr6.simRat.chr6 630900 4 + 647215 TGTA + +a +s simMouse_chr6.simMouse.chr6 618869 20 + 636262 GTATCACTATGTTAGCACAA +s Anc0.Anc0refChr3 213562 20 + 222631 ATGTCATTATTTCACCACAA +s Anc1.Anc1refChr1 53848 20 + 69767 ATGTCATTATTTCACCACAA +s Anc2.Anc2refChr1 130997 20 + 142988 ATGTCATTATATCACCACAA +s mr.mrrefChr3 166000 20 + 181027 GTATCACTATGTTACCACAA +s mr.mrrefChr3 164879 20 + 181027 ATGTCACTATTCCCCCACAA +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 617587 20 + 636262 ATGTCACTATTCCCCCACAA +s simRat_chr6.simRat.chr6 629495 20 + 647215 ATGTCACTATTTCCCCACTA +s simRat_chr6.simRat.chr6 630904 20 + 647215 GTATCACGATGTTGCCACCA + +a +s simMouse_chr6.simMouse.chr6 618889 31 + 636262 CACAAGATGGATTCATATAACAAAGATGAAA +s Anc0.Anc0refChr3 213582 31 + 222631 TACAAGGAGGTCTCATATAGTGAAAATGAAA +s Anc1.Anc1refChr1 53868 31 + 69767 TACAAGGAGGTCTCATATAGTGAAAATGAAA +s Anc2.Anc2refChr1 131017 31 + 142988 TACAAGGAGGTCTGGTATAGTGAAAGTGGAA +s mr.mrrefChr3 166020 31 + 181027 CACAAGATGGCCTCATATAATAAAAATGAAA +s mr.mrrefChr3 164908 31 + 181027 GGCAAAGTTGTCTCATATAATCTAGATGAAA +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 617624 31 + 636262 GGCAAAGTTGTCTCATATCATCTGGATGAAA +s simRat_chr6.simRat.chr6 629524 31 + 647215 GGTAAAATTGCCTCATATAATATAGATGAAA +s simRat_chr6.simRat.chr6 630924 31 + 647215 CACAAGATGGCCTCATATAATAAAAATGAAA + +a +s simMouse_chr6.simMouse.chr6 618920 19 + 636262 GGACAATCCCAGTCTCACA +s Anc0.Anc0refChr3 213613 19 + 222631 GCACAATTCCATTCTCACA +s Anc1.Anc1refChr1 53899 19 + 69767 GCACAATTCCATTCTCACA +s Anc2.Anc2refChr1 131048 19 + 142988 GCACAATTCCATTCTCACA +s mr.mrrefChr3 166051 19 + 181027 GGACAATCCCAGTCTCACA +s mr.mrrefChr3 164939 19 + 181027 GAACAATTCAATTCTCACA +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 617655 19 + 636262 GAACAATTCAATTATCACA +s simRat_chr6.simRat.chr6 629555 19 + 647215 GGACAATTCAATTCTCATA +s simRat_chr6.simRat.chr6 630955 19 + 647215 GGACGATCCCAGTCTCCCC + +a +s simMouse_chr6.simMouse.chr6 618939 8 + 636262 GTGAAGAT +s Anc0.Anc0refChr3 213634 8 + 222631 GAAGATCC +s Anc1.Anc1refChr1 53920 8 + 69767 GAAGATCC +s Anc2.Anc2refChr1 131069 8 + 142988 GAAGATTC +s mr.mrrefChr3 166070 8 + 181027 GTGAAGAT +s mr.mrrefChr3 164960 8 + 181027 ATGGAACC +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 617676 8 + 636262 ATGGAAAC +s simRat_chr6.simRat.chr6 629576 8 + 647215 ATGAAGCC +s simRat_chr6.simRat.chr6 630974 8 + 647215 GTGAAGAT + +a +s simMouse_chr6.simMouse.chr6 618947 26 + 636262 GTGCTACACTCTTAGTTTTTGTCACC +s Anc0.Anc0refChr3 213642 26 + 222631 GTGTTGTACTCTTGTTTTTTGATGGC +s Anc1.Anc1refChr1 53928 26 + 69767 GTGTTGTACTCTTGTTTTTTGATGGC +s Anc2.Anc2refChr1 131077 26 + 142988 GTGTTGTACTCTTGTTTTTTGATGGC +s mr.mrrefChr3 166078 26 + 181027 GTGCTACACTCTTAGTTTTTGTTACC +s mr.mrrefChr3 164968 26 + 181027 GTGTTGTACTCTGGTTTTTTCATGGC +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 617684 26 + 636262 ATGTTGTACACTGCTTTTTTCATGGC +s simRat_chr6.simRat.chr6 629584 26 + 647215 GTGTTATACTCTGGTTTTTTCATGGC +s simRat_chr6.simRat.chr6 630982 26 + 647215 GTGATACACTCTTAGTCTTTGTTACC + +a +s simMouse_chr6.simMouse.chr6 618973 5 + 636262 ACTGG +s Anc0.Anc0refChr3 213669 5 + 222631 ATTGG +s Anc1.Anc1refChr1 53955 5 + 69767 ATTGG +s Anc2.Anc2refChr1 131104 5 + 142988 ATGGG +s mr.mrrefChr3 166104 5 + 181027 ACTGG +s mr.mrrefChr3 164994 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 617710 5 + 636262 ACTGT +s simRat_chr6.simRat.chr6 629610 5 + 647215 ACTGG +s simRat_chr6.simRat.chr6 631008 5 + 647215 ACTGG + +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 @@ -232466,7 +249247,88 @@ s simRat_chr6.simRat.chr6 631019 2 + 647215 AC a -s simMouse_chr6.simMouse.chr6 619066 19 + 636262 TAGGTCTGATAGCTTGTTG +s simMouse_chr6.simMouse.chr6 618984 12 + 636262 GGAATCCTCCAT +s Anc0.Anc0refChr3 213674 12 + 222631 GGAACCCTACAT +s Anc1.Anc1refChr1 53960 12 + 69767 GGAACCCTACAT +s Anc2.Anc2refChr1 131109 12 + 142988 GGAACCCTACAT +s mr.mrrefChr3 166116 12 + 181027 GGAATCCTCCAT +s mr.mrrefChr3 164999 12 + 181027 GGAACCCTCCAC +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 617715 12 + 636262 GGAACTCTCCAC +s simRat_chr6.simRat.chr6 629615 12 + 647215 GGAACCTACCAC +s simRat_chr6.simRat.chr6 631021 12 + 647215 TAGATCCTCCAT + +a +s simMouse_chr6.simMouse.chr6 618996 19 + 636262 AGTTGCCAGGGATGCTAGC +s Anc0.Anc0refChr3 213686 19 + 222631 AATTGCCAGGGATGATAAC +s Anc1.Anc1refChr1 53972 19 + 69767 AATTGCCAGGGATGATAAC +s Anc2.Anc2refChr1 131121 19 + 142988 AATTGCCAGGGATGATAAC +s mr.mrrefChr3 166128 19 + 181027 AGTTGCCAGGGATGCTAGC +s mr.mrrefChr3 165011 19 + 181027 AATTGCCAGGGATAATAAC +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 617727 19 + 636262 AATTGCCAGGGATAATAAC +s simRat_chr6.simRat.chr6 629627 19 + 647215 AATTGCCAGGGGTAATAAC +s simRat_chr6.simRat.chr6 631033 19 + 647215 AGTTGCCAGGGCTGCTAGC + +a +s simMouse_chr6.simMouse.chr6 619015 1 + 636262 A +s Anc0.Anc0refChr3 213709 1 + 222631 A +s Anc1.Anc1refChr1 53995 1 + 69767 A +s Anc2.Anc2refChr1 131144 1 + 142988 A +s mr.mrrefChr3 166147 1 + 181027 A +s mr.mrrefChr3 165034 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 617750 1 + 636262 T +s simRat_chr6.simRat.chr6 629650 1 + 647215 A +s simRat_chr6.simRat.chr6 631052 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 619016 31 + 636262 TTTATCATAATTAAAAGGATGTTGCAGGGGG +s Anc0.Anc0refChr3 213717 31 + 222631 TTCATCATAATTGAAGGGAGGTTGCAAGAAG +s Anc1.Anc1refChr1 54003 31 + 69767 TTCATCATAATTGAAGGGAGGTTGCAAGAAG +s Anc2.Anc2refChr1 131152 31 + 142988 TTCATCATAATTGAAGGGAGGTTGCAATAAG +s mr.mrrefChr3 166148 31 + 181027 TTTATCATAATTAAAAGGATGTTGCAGGGGG +s mr.mrrefChr3 165035 31 + 181027 TTCTTCATAGTTAAAAAAAGATTGCAAGAAA +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 617754 31 + 636262 TTCTTCATGGTTAAAAAAAGATTGCAAGAAA +s simRat_chr6.simRat.chr6 629651 31 + 647215 TTCTTCATAGTTAAAAAAAGACTGCAAGAAA +s simRat_chr6.simRat.chr6 631053 31 + 647215 TTTATCATAATTAAAAGGACATTGGTGGGGG + +a +s simMouse_chr6.simMouse.chr6 619047 8 + 636262 CCCTGAGT +s Anc0.Anc0refChr3 213750 8 + 222631 CCCTGAGT +s Anc1.Anc1refChr1 54036 8 + 69767 CCCTGAGT +s Anc2.Anc2refChr1 131185 8 + 142988 CCCTGTGT +s mr.mrrefChr3 166179 8 + 181027 CCCTGAGT +s mr.mrrefChr3 165066 8 + 181027 GCCTGAGT +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 617785 8 + 636262 GCCTGAGT +s simRat_chr6.simRat.chr6 629682 8 + 647215 GCCTGAGT +s simRat_chr6.simRat.chr6 631084 8 + 647215 CCCGGAGT + +a +s simMouse_chr6.simMouse.chr6 619055 35 + 636262 TTTCAGTGATATAGGTCTGATAGCTTGTTGAGTAC +s Anc0.Anc0refChr3 213758 16 + 222631 TTTTACTGATA-------------------GGTTT +s Anc1.Anc1refChr1 54044 16 + 69767 TTTTACTGATA-------------------GGTTT +s Anc2.Anc2refChr1 131194 16 + 142988 TTTTACTCATA-------------------GGTTT +s mr.mrrefChr3 166187 16 + 181027 TTTTAGTGATA-------------------AGTAT +s mr.mrrefChr3 165074 16 + 181027 TTTTCCTGATA-------------------AGTTT +s simCow_chr6.simCow.chr6 589738 16 + 602619 CTTTACTCATA-------------------CATTT +s simDog_chr6.simDog.chr6 581769 16 + 593897 TTTTACTCATA-------------------GGTTT +s simHuman_chr6.simHuman.chr6 585591 16 + 601863 TTTTACTGATA-------------------GGTTT +s simMouse_chr6.simMouse.chr6 617793 16 + 636262 CTTTCCTGATA-------------------AGTTT +s simRat_chr6.simRat.chr6 629690 16 + 647215 TTTTCCTGATA-------------------AGTTT +s simRat_chr6.simRat.chr6 631092 16 + 647215 TTTTAATGATA-------------------AGTCT a s simMouse_chr6.simMouse.chr6 619090 7 + 636262 TTGTTGA @@ -233660,6 +250522,129 @@ s simRat_chr6.simRat.chr6 634140 62 + 647215 AATGCCTGTGACTAACAGTATCTCCCCTTTGACTCAAAGGGTGAAGATCAA-GAGAGAAGATG a +s simMouse_chr6.simMouse.chr6 622335 6 + 636262 CAAGTC +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 498753 6 + 636262 CAGGTC +s simRat_chr6.simRat.chr6 511337 6 + 647215 CAGGTT + +a +s simMouse_chr6.simMouse.chr6 622341 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 498759 25 + 636262 GTTATAATCTCGAGTGCATAGTGAG +s simRat_chr6.simRat.chr6 511375 25 + 647215 ATTATACTCTTGAAGGTATAGCGAG + +a +s simMouse_chr6.simMouse.chr6 622366 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 498784 22 + 636262 ATAATGCAGAAATGGACCCCAT +s simRat_chr6.simRat.chr6 511403 22 + 647215 ATAATGCAGAAATGGACCCCTT + +a +s simMouse_chr6.simMouse.chr6 622388 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 498806 18 + 636262 CACCCATCAGACCAGATA +s simRat_chr6.simRat.chr6 511425 18 + 647215 CACCTATCAGACCAGATA + +a +s simMouse_chr6.simMouse.chr6 622406 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 498824 8 + 636262 ACCCTAAA +s simRat_chr6.simRat.chr6 511443 8 + 647215 ATCCTAAA + +a +s simMouse_chr6.simMouse.chr6 622414 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 498832 194 + 636262 CCCTTTCCAATTGGTGAATACTTTTCCACTATATTAAGGTGTCACTAATAGGTACACGTGCCAATATTCTATACTACCAGTAGGGATAAGGAAGGCAGGCAACCAATTGCCTTCTATTTGCACACTTGCTTACTGAGACCTGTAGTCCTTATTTAGATGATTCTCTCATGGGCTAGGGAGGTTGGCCCAGCCCT +s simRat_chr6.simRat.chr6 511454 194 + 647215 CCCTTTCCAATTGGTGAATACTTTTCCACTATTTTAAGGTGTCCCTAACAGGTATACATGCTAATGTTCTATATTACCTGTAGGGATAAGGAAGGCAGCCAACTAATTGCCTTCTACTGGCACACTTGCTTACTGACACCTGTAGTCCTTCTTTAGACGGTTCACCCATGGGGCAGGGAGATTGGGCCATCCCT + +a +s simMouse_chr6.simMouse.chr6 622608 5 + 636262 AAGGC +s mr.mrrefChr3 52992 5 + 181027 AACCC +s simMouse_chr6.simMouse.chr6 499026 5 + 636262 AACCC +s simRat_chr6.simRat.chr6 511649 5 + 647215 AACCC + +a +s simMouse_chr6.simMouse.chr6 622613 2 + 636262 TC +s Anc0.Anc0refChr3 114648 1 + 222631 -C +s Anc1.Anc1refChr6 148496 1 + 197743 -C +s Anc2.Anc2refChr1 26796 1 + 142988 -G +s mr.mrrefChr3 52999 2 + 181027 TC +s simCow_chr6.simCow.chr6 483280 1 + 602619 -G +s simHuman_chr6.simHuman.chr6 480514 1 + 601863 -C +s simMouse_chr6.simMouse.chr6 499033 2 + 636262 TC +s simRat_chr6.simRat.chr6 511656 2 + 647215 TC + +a +s simMouse_chr6.simMouse.chr6 622615 4 + 636262 AAAT +s Anc0.Anc0refChr3 114649 4 + 222631 CAAC +s Anc1.Anc1refChr6 148497 4 + 197743 CAAC +s Anc2.Anc2refChr1 26797 4 + 142988 CAAC +s mr.mrrefChr3 53001 4 + 181027 AAAC +s simCow_chr6.simCow.chr6 483281 4 + 602619 CAAC +s simHuman_chr6.simHuman.chr6 480515 4 + 601863 CAAC +s simMouse_chr6.simMouse.chr6 499035 4 + 636262 GAAC +s simRat_chr6.simRat.chr6 511669 4 + 647215 CAAC + +a +s simMouse_chr6.simMouse.chr6 622619 9 + 636262 AACTCCTAC +s Anc0.Anc0refChr3 114660 9 + 222631 CACTTTGCC +s Anc1.Anc1refChr6 148508 9 + 197743 CACTTTGCC +s Anc2.Anc2refChr1 26808 9 + 142988 CATTTTGCT +s mr.mrrefChr3 53012 9 + 181027 CACTCCTCC +s simCow_chr6.simCow.chr6 483292 9 + 602619 CATTTTGCT +s simDog_chr6.simDog.chr6 473633 9 + 593897 cattttgct +s simHuman_chr6.simHuman.chr6 480526 9 + 601863 CACTTTGCC +s simMouse_chr6.simMouse.chr6 499046 9 + 636262 CACTCCTCC +s simRat_chr6.simRat.chr6 511680 9 + 647215 CACTTTTCC + +a +s simMouse_chr6.simMouse.chr6 622628 5 + 636262 TGATA +s Anc0.Anc0refChr3 114676 5 + 222631 TAAGA +s Anc1.Anc1refChr6 148524 5 + 197743 TAAGA +s Anc2.Anc2refChr1 26824 5 + 142988 TAAGT +s mr.mrrefChr3 53028 5 + 181027 TAAGA +s simCow_chr6.simCow.chr6 483308 5 + 602619 CAAAT +s simDog_chr6.simDog.chr6 473649 5 + 593897 TAAGT +s simHuman_chr6.simHuman.chr6 480542 5 + 601863 TAAGA +s simMouse_chr6.simMouse.chr6 499062 5 + 636262 TAAGA +s simRat_chr6.simRat.chr6 511696 5 + 647215 TAAGC + +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 @@ -237916,11 +254901,39 @@ s simRat_chr6.simRat.chr6 644328 7 + 647215 CTCCTCA a +s simMouse_chr6.simMouse.chr6 633161 6 + 636262 TTGCTT +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 21438 6 + 636262 TTTCTT +s simRat_chr6.simRat.chr6 13369 6 + 647215 TTTCTT +s simRat_chr6.simRat.chr6 644335 6 + 647215 TCAGTC + +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 633169 11 + 636262 CACCTTTTATT +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 21444 11 + 636262 CACTATGTAGA +s simRat_chr6.simRat.chr6 13375 11 + 647215 CATTATGTAGG +s simRat_chr6.simRat.chr6 644343 11 + 647215 CACCTTTTATC + +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 @@ -237936,6 +254949,20 @@ s simRat_chr6.simRat.chr6 644538 125 + 647215 GTAATCCCTTCATACCAACT-CTAGATGTCCTGAGGACAGGAGAATTGACTAAATAGATGCCTTGCAAACTAAGTGTGACGGAT---------GCTGCTTGGAGTCGTTAGCATAAACTGCTGTCAAGCGCATTT a +s simMouse_chr6.simMouse.chr6 633490 14 + 636262 TGTGTAGATCATCC +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 21455 14 + 636262 CGTGGAAGCCTTCT +s simRat_chr6.simRat.chr6 13386 14 + 647215 TGTGGAAGCCTTCT +s simRat_chr6.simRat.chr6 644663 14 + 647215 CGTGTAGATCATCC + +a s simMouse_chr6.simMouse.chr6 633504 5 + 636262 AATGA s Anc0.Anc0refChr2 15784 5 + 17989 ATTAG s Anc1.Anc1refChr2 123358 5 - 144309 ATTAG @@ -237980,18 +255007,77 @@ 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 +s simMouse_chr6.simMouse.chr6 633521 7 + 636262 AAGGGCA +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 21469 7 + 636262 GAGAGCC +s simRat_chr6.simRat.chr6 13400 7 + 647215 GAGGACC +s simRat_chr6.simRat.chr6 644694 7 + 647215 AAGGGCA + +a +s simMouse_chr6.simMouse.chr6 633528 5 + 636262 AACCT +s Anc0.Anc0refChr2 15807 5 + 17989 AAGCT +s Anc1.Anc1refChr2 123381 5 - 144309 AAGCT +s Anc2.Anc2refChr0 14335 5 - 56053 AAGCT +s mr.mrrefChr0 19786 5 + 130230 AAGCT +s mr.mrrefChr3 179608 5 + 181027 AACCT +s simCow_chr6.simCow.chr6 557293 5 - 602619 AAGCC +s simDog_chr6.simDog.chr6 554769 5 - 593897 AGGCT +s simDog_chr6.simDog.chr6 591574 5 + 593897 AATCT +s simHuman_chr6.simHuman.chr6 562587 5 - 601863 AAGCT +s simMouse_chr6.simMouse.chr6 21476 5 + 636262 AAGCT +s simRat_chr6.simRat.chr6 13407 5 + 647215 AAGCT +s simRat_chr6.simRat.chr6 644701 5 + 647215 AACCT + +a +s simMouse_chr6.simMouse.chr6 633533 8 + 636262 GTGGCGGT +s Anc0.Anc0refChr2 15812 8 + 17989 GTGTTGGC +s Anc1.Anc1refChr2 123386 8 - 144309 GTGTTGGC +s Anc2.Anc2refChr0 14340 8 - 56053 GTGTTGGC +s mr.mrrefChr0 19791 8 + 130230 GTGCTGGC +s mr.mrrefChr3 179613 8 + 181027 GTGGCGGT +s simCow_chr6.simCow.chr6 557298 8 - 602619 AACTTGGC +s simDog_chr6.simDog.chr6 554774 8 - 593897 GTGTTGGC +s simDog_chr6.simDog.chr6 591579 8 + 593897 GTGATAGC +s simHuman_chr6.simHuman.chr6 562592 8 - 601863 GTGTTGCC +s simMouse_chr6.simMouse.chr6 21482 8 + 636262 GTGCTAGC +s simRat_chr6.simRat.chr6 13412 8 + 647215 GTGATGGC +s simRat_chr6.simRat.chr6 644706 8 + 647215 GTGGTGAT + +a +s simMouse_chr6.simMouse.chr6 633541 1 + 636262 T +s Anc0.Anc0refChr2 15820 1 + 17989 T +s Anc1.Anc1refChr2 123394 1 - 144309 T +s Anc2.Anc2refChr0 14348 1 - 56053 T +s mr.mrrefChr0 19799 1 + 130230 A +s mr.mrrefChr3 179621 1 + 181027 T +s simCow_chr6.simCow.chr6 557306 1 - 602619 T +s simDog_chr6.simDog.chr6 554782 1 - 593897 T +s simDog_chr6.simDog.chr6 591587 1 + 593897 T +s simHuman_chr6.simHuman.chr6 562600 1 - 601863 T +s simMouse_chr6.simMouse.chr6 21490 1 + 636262 A +s simRat_chr6.simRat.chr6 644714 1 + 647215 T + +a +s simMouse_chr6.simMouse.chr6 633542 21 + 636262 AAAAAGGCACTAATTTCTCAA +s Anc0.Anc0refChr2 15821 21 + 17989 AAATAGATGCAAATTTATGAA +s Anc1.Anc1refChr2 123395 21 - 144309 AAATAGATGCAAATTTATGAA +s Anc2.Anc2refChr0 14349 21 - 56053 AAATAGATGCAAATTTACTAA +s mr.mrrefChr0 19800 21 + 130230 AAATAGATGCAGGAAAATGAA +s mr.mrrefChr3 179622 21 + 181027 AAAAAGGCACTAATTTCTCAA +s simCow_chr6.simCow.chr6 557307 21 - 602619 AAATAGATGCTAATTTACTAT +s simDog_chr6.simDog.chr6 554783 21 - 593897 AAATAGATTCAAATTTACTAA +s simDog_chr6.simDog.chr6 591588 21 + 593897 GGATAGATGTACATAAAGCAA +s simHuman_chr6.simHuman.chr6 562601 18 - 601863 AAATAGATGCAAAT---TGAA +s simMouse_chr6.simMouse.chr6 21491 19 + 636262 AAATGGATGCAGGAAAAT--A +s simRat_chr6.simRat.chr6 13420 21 + 647215 AAAGAGATGCTGGAAAATGAA +s simRat_chr6.simRat.chr6 644715 21 + 647215 AAAAAGGCACTAATTTCTCAA a s simMouse_chr6.simMouse.chr6 633563 3 + 636262 TGG @@ -238005,7 +255091,64 @@ s simRat_chr6.simRat.chr6 644736 3 + 647215 TTG a -s simMouse_chr6.simMouse.chr6 633615 1 + 636262 G +s simMouse_chr6.simMouse.chr6 633566 26 + 636262 ACAAAATTGTCTGATAGAAGGCTTAG +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 21510 26 + 636262 ACAAAGTTGTCTGAGGCATAACTTCA +s simRat_chr6.simRat.chr6 13441 26 + 647215 AGAAAGTTGTCTGAGGAACAACTTGA +s simRat_chr6.simRat.chr6 644739 26 + 647215 AAAAAATTGTCTGATAGAAGACTTCG + +a +s simMouse_chr6.simMouse.chr6 633592 13 + 636262 TGATTCATGATTG +s Anc0.Anc0refChr2 15871 13 + 17989 TCATGCATGATCA +s Anc1.Anc1refChr2 123445 13 - 144309 TCATGCATGATCA +s Anc2.Anc2refChr0 14399 13 - 56053 TCATACATGATCA +s mr.mrrefChr0 19847 13 + 130230 TCATGCCATATCA +s mr.mrrefChr3 179672 13 + 181027 TGATTCATGATTG +s simCow_chr6.simCow.chr6 557358 13 - 602619 TCATACAGGATCA +s simDog_chr6.simDog.chr6 554833 13 - 593897 TCACACATAATCA +s simDog_chr6.simDog.chr6 591638 13 + 593897 TCATGCATGATAA +s simHuman_chr6.simHuman.chr6 562645 13 - 601863 TCATGCATGATCA +s simMouse_chr6.simMouse.chr6 21536 13 + 636262 TCATGCCATATCA +s simRat_chr6.simRat.chr6 13467 13 + 647215 TCATGCCATATGA +s simRat_chr6.simRat.chr6 644766 13 + 647215 TGATTCATGCTTG + +a +s simMouse_chr6.simMouse.chr6 633605 15 + 636262 TGTAGAGGCAGGGAA +s Anc0.Anc0refChr2 15884 14 + 17989 TGCAAAGGTA-AGCT +s Anc1.Anc1refChr2 123458 14 - 144309 TGCAAAGGTA-AGCT +s Anc2.Anc2refChr0 14412 14 - 56053 TGCAAAAGTA-AGCT +s mr.mrrefChr0 19860 14 + 130230 TACATGGGTA-GAAA +s mr.mrrefChr3 179685 14 + 181027 TGTAGAGGCA-GGAA +s simCow_chr6.simCow.chr6 557371 1 - 602619 T-------------- +s simDog_chr6.simDog.chr6 554846 14 - 593897 TGCATATGTA-GGCT +s simDog_chr6.simDog.chr6 591651 14 + 593897 TGAAACAGGA-ATCT +s simHuman_chr6.simHuman.chr6 562658 14 - 601863 TCCAAAGGTA-AGCT +s simMouse_chr6.simMouse.chr6 21551 14 + 636262 TACATGGGTA-GAAA +s simRat_chr6.simRat.chr6 13480 14 + 647215 TGCAGGGGTA-GAAT +s simRat_chr6.simRat.chr6 644779 14 + 647215 TGTAAAGGCA-GGCA + +a +s simMouse_chr6.simMouse.chr6 633620 33 + 636262 TATGGGAATGCTCTGATTTCATGGGGGAGGCTT +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 21566 33 + 636262 TATATGAAGGTTCTTGTTTTAGTGGTATGACCT +s simRat_chr6.simRat.chr6 13502 33 + 647215 TATATGAATGTCCTTGTTTTAGGGGTATGACCT +s simRat_chr6.simRat.chr6 644793 33 + 647215 TATGGGGATGTTCTGGTTTCAGGGGGGAGGCTT a s simMouse_chr6.simMouse.chr6 633653 1 + 636262 G @@ -238020,6 +255163,35 @@ s simRat_chr6.simRat.chr6 644826 1 + 647215 G a +s simMouse_chr6.simMouse.chr6 633654 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 21599 7 + 636262 ATTGGTT +s simRat_chr6.simRat.chr6 13535 7 + 647215 ATTGGTT +s simRat_chr6.simRat.chr6 644827 7 + 647215 ATTGGCT + +a +s simMouse_chr6.simMouse.chr6 633661 4 + 636262 TTCC +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 21606 4 + 636262 TTCT +s simRat_chr6.simRat.chr6 13542 4 + 647215 TTCT +s simRat_chr6.simRat.chr6 644834 4 + 647215 TTCA + +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------------------------------------------------------------------------------ @@ -238080,6 +255252,25 @@ s simRat_chr6.simRat.chr6 645044 15 + 647215 TTCCCAGATGTTTCA a +s simMouse_chr6.simMouse.chr6 633873 6 + 636262 ATCTGA +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 562728 6 - 601863 GTTCCT +s simHuman_chr6.simHuman.chr6 599774 6 + 601863 GTCCTC +s simMouse_chr6.simMouse.chr6 21621 6 + 636262 GCCATT +s simRat_chr6.simRat.chr6 13557 6 + 647215 GCCACT +s simRat_chr6.simRat.chr6 645059 6 + 647215 ATCCAA + +a s simMouse_chr6.simMouse.chr6 633879 1 + 636262 C s Anc0.Anc0refChr2 15960 1 + 17989 C s Anc1.Anc1refChr1 67679 1 + 69767 C @@ -238090,6 +255281,25 @@ s simRat_chr6.simRat.chr6 645065 1 + 647215 C a +s simMouse_chr6.simMouse.chr6 633880 2 + 636262 AA +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 562734 2 - 601863 TG +s simHuman_chr6.simHuman.chr6 599781 2 + 601863 AA +s simMouse_chr6.simMouse.chr6 21627 2 + 636262 TA +s simRat_chr6.simRat.chr6 13563 2 + 647215 TA +s simRat_chr6.simRat.chr6 645066 2 + 647215 AA + +a s simMouse_chr6.simMouse.chr6 633882 1 + 636262 C s Anc0.Anc0refChr2 15963 1 + 17989 G s Anc1.Anc1refChr1 67682 1 + 69767 C @@ -238106,6 +255316,44 @@ s simRat_chr6.simRat.chr6 645068 1 + 647215 C a +s simMouse_chr6.simMouse.chr6 633883 3 + 636262 CTA +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 562740 3 - 601863 GTG +s simHuman_chr6.simHuman.chr6 599784 3 + 601863 ATA +s simMouse_chr6.simMouse.chr6 21631 3 + 636262 ATG +s simRat_chr6.simRat.chr6 13567 3 + 647215 AGG +s simRat_chr6.simRat.chr6 645069 3 + 647215 ATA + +a +s simMouse_chr6.simMouse.chr6 633886 3 + 636262 ATA +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 562743 3 - 601863 ATG +s simHuman_chr6.simHuman.chr6 599787 3 + 601863 ATG +s simMouse_chr6.simMouse.chr6 21634 3 + 636262 GTG +s simRat_chr6.simRat.chr6 13570 3 + 647215 GTG +s simRat_chr6.simRat.chr6 645072 3 + 647215 ACA + +a s simMouse_chr6.simMouse.chr6 633889 5 + 636262 TGACT s Anc1.Anc1refChr1 67689 5 + 69767 TGAAT s mr.mrrefChr3 179967 5 + 181027 TGACT @@ -238113,21 +255361,80 @@ 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 +s simMouse_chr6.simMouse.chr6 633894 8 + 636262 AGTCCTCA +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 562746 8 - 601863 GGTCCTAC +s simHuman_chr6.simHuman.chr6 599795 8 + 601863 AGTCCTAC +s simMouse_chr6.simMouse.chr6 21637 8 + 636262 GGTTCTAA +s simRat_chr6.simRat.chr6 13573 8 + 647215 GGTCGTAC +s simRat_chr6.simRat.chr6 645080 8 + 647215 AGTCCTAC + +a +s simMouse_chr6.simMouse.chr6 633902 5 + 636262 AAGAG +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 562754 5 - 601863 AATAG +s simHuman_chr6.simHuman.chr6 599803 5 + 601863 AAAAG +s simMouse_chr6.simMouse.chr6 21645 5 + 636262 AAAGT +s simRat_chr6.simRat.chr6 13581 5 + 647215 ACAGT +s simRat_chr6.simRat.chr6 645088 5 + 647215 AAGGG + +a +s simMouse_chr6.simMouse.chr6 633907 40 + 636262 GGACTATACCATTAGACCCTCCTTAAGAGATAATTTATAA +s Anc0.Anc0refChr2 15986 40 + 17989 GCCTTACCCCATTAGACCTTCCTTAGGAGATAAATCGTAG +s Anc1.Anc1refChr1 67707 40 + 69767 GCCTTACCCCATTAGGCCTTCCTTCGGAGATAAATCGTAG +s Anc1.Anc1refChr2 123559 40 - 144309 GCTTTACCCCATTAGACCTTCCTTAGGAGATAAAGCATAG +s Anc2.Anc2refChr0 14516 38 - 56053 --CTTACCCCATTAGATCTTCCTTAGAAGACAAATCATAG +s Anc2.Anc2refChr1 140776 40 + 142988 GCCTTACCCCATTAGGCCTTCCTTTGGAGATAAATCGTAG +s mr.mrrefChr0 19961 40 + 130230 GCTTCTCCCCAGTATGCCTTCCTTAAGGGCTAAAGCATAG +s mr.mrrefChr3 179985 40 + 181027 GCACTACACCATTAGACCCTCCTTCAGAGATAAATTATAA +s simCow_chr6.simCow.chr6 599957 40 + 602619 ACCCTACCCCATTAGACCTTCCATAGAAGATAAATCATTT +s simCow_chr6.simCow.chr6 557453 26 - 602619 --CTTACCCCATTAGAACTTCCT------------CATAG +s simDog_chr6.simDog.chr6 591755 40 + 593897 GCCTTACTGCATGAAGCCTTCCTTTGGAGATAAATTGTAG +s simDog_chr6.simDog.chr6 554940 29 - 593897 -----------CTAGATCTTCCCTAGAAGACAAATCATAG +s simHuman_chr6.simHuman.chr6 562759 40 - 601863 GCTTTACCTCATTGAACCTTCCTCAGGAGATAAAGCATAG +s simHuman_chr6.simHuman.chr6 599808 40 + 601863 GCGTTACCCGATTAGGCCTTCCTTCGGAGATAAATCCTAG +s simMouse_chr6.simMouse.chr6 21650 39 + 636262 GCT-CTCCCCAGTATGCCTTCCTTAAGGGCTAAGGTATAG +s simRat_chr6.simRat.chr6 13586 40 + 647215 GCTTCTCCCAAGAATGTCTCCCTTAAGGGCTAAATCATAG +s simRat_chr6.simRat.chr6 645093 40 + 647215 GCACTACATCATTAGAGCCTCCTTCAGAGATAAATTATAA + +a +s simMouse_chr6.simMouse.chr6 633947 4 + 636262 GTAG +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 562799 4 - 601863 TGAG +s simHuman_chr6.simHuman.chr6 599848 4 + 601863 GGAG +s simMouse_chr6.simMouse.chr6 21689 4 + 636262 AGTA +s simRat_chr6.simRat.chr6 13626 4 + 647215 AGTG +s simRat_chr6.simRat.chr6 645136 4 + 647215 GTAG a s simMouse_chr6.simMouse.chr6 633951 88 + 636262 AAGTCTATCGATGGTGTGGGGTAATCACCTTTATTCACAGTGAAGTACAATGTGAGACTTTGGAGCGAGCGGCTGTCCTCGCCTTAAC @@ -238508,13 +255815,328 @@ 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 +s simMouse_chr6.simMouse.chr6 635259 12 + 636262 AAAAGCAAGAAG +s Anc1.Anc1refChr6 75607 9 - 197743 ATAAACGAG--- +s mr.mrrefChr3 156264 9 - 181027 ATAAACGAG--- +s mr.mrrefChr3 23675 9 - 181027 ATAAATGAG--- +s mr.mrrefChr5 198531 9 - 294540 ATAAACGAG--- +s simMouse_chr6.simMouse.chr6 167198 9 - 636262 ATAAACAGG--- +s simMouse_chr6.simMouse.chr6 26831 9 - 636262 ATAAATGAG--- +s simMouse_chr6.simMouse.chr6 393330 7 - 636262 ACTAACG----- +s simRat_chr6.simRat.chr6 168236 9 - 647215 ATAAACGAG--- +s simRat_chr6.simRat.chr6 563228 9 + 647215 ATAAATGAA--- +s simRat_chr6.simRat.chr6 294533 9 - 647215 ATAAACGAG--- +s simRat_chr6.simRat.chr6 580158 9 + 647215 ATAAACGAG--- + +a +s simMouse_chr6.simMouse.chr6 635271 1 + 636262 T +s Anc1.Anc1refChr6 75616 1 - 197743 C +s mr.mrrefChr3 156274 1 - 181027 C +s mr.mrrefChr3 23684 1 - 181027 C +s mr.mrrefChr5 198540 1 - 294540 T +s simMouse_chr6.simMouse.chr6 167208 1 - 636262 C +s simMouse_chr6.simMouse.chr6 26840 1 - 636262 C +s simMouse_chr6.simMouse.chr6 393337 1 - 636262 T +s simRat_chr6.simRat.chr6 168246 1 - 647215 C +s simRat_chr6.simRat.chr6 563237 1 + 647215 C + +a +s simMouse_chr6.simMouse.chr6 635272 1 + 636262 G +s Anc1.Anc1refChr6 75617 1 - 197743 A +s mr.mrrefChr3 156275 1 - 181027 A +s mr.mrrefChr3 23685 1 - 181027 A +s mr.mrrefChr5 198541 1 - 294540 G +s simMouse_chr6.simMouse.chr6 167209 1 - 636262 A +s simMouse_chr6.simMouse.chr6 26842 1 - 636262 A +s simMouse_chr6.simMouse.chr6 393338 1 - 636262 G +s simRat_chr6.simRat.chr6 168247 1 - 647215 A +s simRat_chr6.simRat.chr6 563238 1 + 647215 A + +a +s simMouse_chr6.simMouse.chr6 635273 18 + 636262 GCTTCTTAGAAACTTGTT +s Anc1.Anc1refChr6 75620 8 - 197743 GA----------GTGCTG +s mr.mrrefChr3 156278 8 - 181027 GA----------GTGCTG +s mr.mrrefChr3 23688 8 - 181027 GA----------GTGCTG +s mr.mrrefChr5 198542 8 - 294540 GC----------CTTGTG +s simMouse_chr6.simMouse.chr6 167212 8 - 636262 GA----------GTGCTG +s simMouse_chr6.simMouse.chr6 26845 8 - 636262 GA----------GTGCTG +s simMouse_chr6.simMouse.chr6 393339 8 - 636262 GC----------CTGGTG +s simRat_chr6.simRat.chr6 168250 8 - 647215 GA----------GTGCTG +s simRat_chr6.simRat.chr6 563241 8 + 647215 GA----------GTTGTG + +a +s simMouse_chr6.simMouse.chr6 635291 5 + 636262 TCTTG +s Anc1.Anc1refChr6 75628 5 - 197743 CATTG +s mr.mrrefChr3 156286 5 - 181027 TATAG +s mr.mrrefChr3 23696 5 - 181027 CAATG +s mr.mrrefChr5 198550 5 - 294540 CCTTG +s simMouse_chr6.simMouse.chr6 167220 5 - 636262 TATAG +s simMouse_chr6.simMouse.chr6 26853 5 - 636262 CAATG +s simMouse_chr6.simMouse.chr6 393347 5 - 636262 CTTTG +s simRat_chr6.simRat.chr6 563249 5 + 647215 CATTG + +a +s simMouse_chr6.simMouse.chr6 635296 2 + 636262 AT +s Anc1.Anc1refChr6 75633 2 - 197743 TG +s mr.mrrefChr3 156291 2 - 181027 TG +s mr.mrrefChr3 23701 2 - 181027 GA +s mr.mrrefChr5 198555 2 - 294540 TG +s simMouse_chr6.simMouse.chr6 167225 2 - 636262 TG +s simMouse_chr6.simMouse.chr6 26859 2 - 636262 GA +s simMouse_chr6.simMouse.chr6 393352 2 - 636262 TG +s simRat_chr6.simRat.chr6 563254 2 + 647215 GA + +a +s simMouse_chr6.simMouse.chr6 635298 105 + 636262 TGGAGACTTGTGTGTGTCATCTCTCTGTCATGTACATGGCTGCTTGCCTTTTATTGGAGCTTTGCACGAGACACTATGTGAAATCTAAACAACATAAAGCTAAAA +s Anc1.Anc1refChr6 75635 8 - 197743 TGGGTA-------------------------------------------------------------------------------------------------AA +s mr.mrrefChr3 156294 8 - 181027 TCAGTA-------------------------------------------------------------------------------------------------AA +s mr.mrrefChr3 23703 8 - 181027 TGGGTA-------------------------------------------------------------------------------------------------AA +s mr.mrrefChr5 198557 8 - 294540 TGGGGA-------------------------------------------------------------------------------------------------AA +s simMouse_chr6.simMouse.chr6 167228 8 - 636262 TCAGTA-------------------------------------------------------------------------------------------------AA +s simMouse_chr6.simMouse.chr6 26861 8 - 636262 TGGGTA-------------------------------------------------------------------------------------------------AA +s simMouse_chr6.simMouse.chr6 393354 8 - 636262 TGGGGA-------------------------------------------------------------------------------------------------AA +s simRat_chr6.simRat.chr6 563256 8 + 647215 TGGGTA-------------------------------------------------------------------------------------------------AA + +a +s simMouse_chr6.simMouse.chr6 635403 6 + 636262 TCTAAA +s Anc1.Anc1refChr6 75643 6 - 197743 TCCACA +s mr.mrrefChr3 156302 6 - 181027 TCCACA +s mr.mrrefChr3 23711 6 - 181027 TCCGCA +s mr.mrrefChr5 198565 6 - 294540 TATAAA +s simMouse_chr6.simMouse.chr6 167236 6 - 636262 TCCACA +s simMouse_chr6.simMouse.chr6 26869 6 - 636262 TCCGCA +s simMouse_chr6.simMouse.chr6 393362 6 - 636262 TACAAA +s simRat_chr6.simRat.chr6 168258 6 - 647215 TCCACA +s simRat_chr6.simRat.chr6 563264 6 + 647215 TCTGCA + +a +s simMouse_chr6.simMouse.chr6 635409 1 + 636262 A +s Anc1.Anc1refChr6 75649 1 - 197743 G +s mr.mrrefChr3 156308 1 - 181027 G +s mr.mrrefChr3 23717 1 - 181027 G +s mr.mrrefChr5 198571 1 - 294540 A +s simMouse_chr6.simMouse.chr6 26875 1 - 636262 G +s simMouse_chr6.simMouse.chr6 393368 1 - 636262 C +s simRat_chr6.simRat.chr6 168264 1 - 647215 G +s simRat_chr6.simRat.chr6 563270 1 + 647215 G + +a +s simMouse_chr6.simMouse.chr6 635410 12 + 636262 TTCTTTGCAAAT +s Anc1.Anc1refChr6 75650 12 - 197743 TTCGTTGGTAAC +s mr.mrrefChr3 156309 12 - 181027 TTTGTTGGTAAT +s mr.mrrefChr3 23718 12 - 181027 TTCGTTGGTAAC +s mr.mrrefChr5 198572 12 - 294540 TTCTTTGGAAAC +s simMouse_chr6.simMouse.chr6 167242 12 - 636262 TTCATTGGTAAT +s simMouse_chr6.simMouse.chr6 26876 12 - 636262 TTCGTTGGTAAC +s simMouse_chr6.simMouse.chr6 393369 12 - 636262 TTCGTTGGTAAC +s simRat_chr6.simRat.chr6 168265 12 - 647215 TTTGTTGGTAAC +s simRat_chr6.simRat.chr6 563271 12 + 647215 TTTGTTGGTAAC + +a +s simMouse_chr6.simMouse.chr6 635422 2 + 636262 AG +s Anc1.Anc1refChr6 75662 2 - 197743 CA +s mr.mrrefChr3 156321 2 - 181027 CA +s mr.mrrefChr3 23745 2 - 181027 TC +s mr.mrrefChr5 198584 2 - 294540 CA +s simMouse_chr6.simMouse.chr6 167254 2 - 636262 CA +s simMouse_chr6.simMouse.chr6 26903 2 - 636262 TC +s simMouse_chr6.simMouse.chr6 393381 2 - 636262 CA +s simRat_chr6.simRat.chr6 168277 2 - 647215 CA +s simRat_chr6.simRat.chr6 563303 2 + 647215 TC + +a +s simMouse_chr6.simMouse.chr6 635424 2 + 636262 TG +s Anc1.Anc1refChr6 75664 2 - 197743 TG +s mr.mrrefChr3 156323 2 - 181027 GG +s mr.mrrefChr3 23747 2 - 181027 TG +s mr.mrrefChr5 198586 2 - 294540 TG +s simMouse_chr6.simMouse.chr6 167257 2 - 636262 GG +s simMouse_chr6.simMouse.chr6 26905 2 - 636262 TG +s simMouse_chr6.simMouse.chr6 393383 2 - 636262 TG +s simRat_chr6.simRat.chr6 168279 2 - 647215 AT +s simRat_chr6.simRat.chr6 563305 2 + 647215 CC + +a +s simMouse_chr6.simMouse.chr6 635426 7 + 636262 GGCACGA +s Anc1.Anc1refChr6 75666 7 - 197743 GGTATGA +s mr.mrrefChr3 156325 7 - 181027 GGTGTGA +s mr.mrrefChr3 23749 7 - 181027 GGTATGT +s mr.mrrefChr5 198588 7 - 294540 GGCACGA +s simMouse_chr6.simMouse.chr6 167259 7 - 636262 GGTGTGA +s simMouse_chr6.simMouse.chr6 26907 7 - 636262 GGTATGT +s simMouse_chr6.simMouse.chr6 393405 7 - 636262 GGCACGA +s simRat_chr6.simRat.chr6 168281 7 - 647215 AGTGTGA +s simRat_chr6.simRat.chr6 563307 7 + 647215 GGTATGT + +a +s simMouse_chr6.simMouse.chr6 635433 5 + 636262 AAGTC +s Anc1.Anc1refChr6 75673 5 - 197743 AAGTC +s mr.mrrefChr3 156344 5 - 181027 AAGTC +s mr.mrrefChr3 23756 5 - 181027 GAGTG +s mr.mrrefChr5 198595 5 - 294540 AAGTC +s simMouse_chr6.simMouse.chr6 167286 5 - 636262 AAGTC +s simMouse_chr6.simMouse.chr6 26914 5 - 636262 GAGTG +s simMouse_chr6.simMouse.chr6 393412 5 - 636262 AAGTC +s simRat_chr6.simRat.chr6 168300 5 - 647215 AAGTC +s simRat_chr6.simRat.chr6 563314 5 + 647215 GAGCA + +a +s simMouse_chr6.simMouse.chr6 635438 3 + 636262 GTT +s Anc1.Anc1refChr6 75678 3 - 197743 TTA +s mr.mrrefChr3 156349 3 - 181027 GTT +s mr.mrrefChr3 23761 3 - 181027 TTA +s mr.mrrefChr5 198600 3 - 294540 TTA +s simMouse_chr6.simMouse.chr6 167291 3 - 636262 GTT +s simMouse_chr6.simMouse.chr6 26920 3 - 636262 TTA +s simMouse_chr6.simMouse.chr6 393417 3 - 636262 TTA +s simRat_chr6.simRat.chr6 168305 3 - 647215 GTT +s simRat_chr6.simRat.chr6 563319 3 + 647215 CTA + +a +s simMouse_chr6.simMouse.chr6 635441 1 + 636262 A +s Anc1.Anc1refChr6 75681 1 - 197743 A +s mr.mrrefChr3 156352 1 - 181027 A +s mr.mrrefChr5 198603 1 - 294540 A +s simMouse_chr6.simMouse.chr6 167294 1 - 636262 A +s simMouse_chr6.simMouse.chr6 393420 1 - 636262 A +s simRat_chr6.simRat.chr6 168308 1 - 647215 A + +a +s simMouse_chr6.simMouse.chr6 635442 3 + 636262 TAA +s Anc1.Anc1refChr6 75682 3 - 197743 TAA +s mr.mrrefChr3 156353 3 - 181027 TAA +s mr.mrrefChr3 23764 3 - 181027 TAA +s mr.mrrefChr5 198604 3 - 294540 TAA +s simMouse_chr6.simMouse.chr6 167295 3 - 636262 TAA +s simMouse_chr6.simMouse.chr6 26923 3 - 636262 TAA +s simMouse_chr6.simMouse.chr6 393421 3 - 636262 TAA +s simRat_chr6.simRat.chr6 168309 3 - 647215 TAA +s simRat_chr6.simRat.chr6 563322 3 + 647215 TAA + +a +s simMouse_chr6.simMouse.chr6 635445 12 + 636262 CCAGTGAGTGCT +s Anc1.Anc1refChr6 75685 12 - 197743 CCAGTGAGTGCT +s mr.mrrefChr3 156356 12 - 181027 CCAATGAATTCT +s mr.mrrefChr3 23767 12 - 181027 CCAGTGAGTGCT +s mr.mrrefChr5 198607 12 - 294540 CCAGTGAGTGCT +s simMouse_chr6.simMouse.chr6 167298 12 - 636262 CCAATGAATTCT +s simMouse_chr6.simMouse.chr6 26926 12 - 636262 CCAGTGAGTGCT +s simMouse_chr6.simMouse.chr6 393424 12 - 636262 CCAGTGAGTGCT +s simRat_chr6.simRat.chr6 168312 12 - 647215 CCAGTCAGTGCT +s simRat_chr6.simRat.chr6 563325 12 + 647215 CCAGTGAGTCCT +s simRat_chr6.simRat.chr6 580167 12 + 647215 CTAATGAGTGCT + +a +s simMouse_chr6.simMouse.chr6 635457 4 + 636262 ACAT +s Anc1.Anc1refChr6 75697 4 - 197743 ACAT +s mr.mrrefChr3 156368 4 - 181027 ACAA +s mr.mrrefChr3 23779 4 - 181027 ACAT +s mr.mrrefChr5 198619 4 - 294540 ACAT +s simMouse_chr6.simMouse.chr6 167310 4 - 636262 ACAA +s simMouse_chr6.simMouse.chr6 26938 4 - 636262 ACAT +s simMouse_chr6.simMouse.chr6 393436 4 - 636262 ACAT +s simRat_chr6.simRat.chr6 168324 4 - 647215 ACAT +s simRat_chr6.simRat.chr6 563337 4 + 647215 AAAT +s simRat_chr6.simRat.chr6 580229 4 + 647215 ACAT + +a +s simMouse_chr6.simMouse.chr6 635461 2 + 636262 CG +s Anc1.Anc1refChr6 75701 2 - 197743 CG +s mr.mrrefChr3 156372 2 - 181027 CA +s mr.mrrefChr5 198623 2 - 294540 CG +s simMouse_chr6.simMouse.chr6 167314 2 - 636262 CA +s simMouse_chr6.simMouse.chr6 393440 2 - 636262 TA +s simRat_chr6.simRat.chr6 168328 2 - 647215 CA +s simRat_chr6.simRat.chr6 580233 2 + 647215 CG + +a +s simMouse_chr6.simMouse.chr6 635463 13 + 636262 TACTGTCTGGGCC +s Anc1.Anc1refChr6 75703 13 - 197743 TAATGTGTGGGCC +s mr.mrrefChr3 156374 13 - 181027 TAACGTGTGGGCC +s mr.mrrefChr3 23783 13 - 181027 TAATGTGTGGGCC +s mr.mrrefChr5 198625 13 - 294540 TACTGTCTGGGCC +s simMouse_chr6.simMouse.chr6 167316 13 - 636262 TAACGTGTGGGCC +s simMouse_chr6.simMouse.chr6 26942 13 - 636262 TAATGTGTGGGCC +s simMouse_chr6.simMouse.chr6 393442 13 - 636262 TACTGTCTGGGCC +s simRat_chr6.simRat.chr6 168330 13 - 647215 TAACGGGTGGGCC +s simRat_chr6.simRat.chr6 563343 13 + 647215 TAATGTGTGGGCC +s simRat_chr6.simRat.chr6 580235 13 + 647215 AATTGTGTGGCCC + +a +s simMouse_chr6.simMouse.chr6 635476 61 + 636262 CACGGTCATGATTCGCTCAAGACGATTTGCTAACTGAGCGCTCTGGTATGCGACCGCCTTG +s Anc1.Anc1refChr6 75716 61 - 197743 CACAGTCATTATTAGCTCAAGACTATTTGCCATTTGAGGGCTCTGGTATGCAATTGCCTTG +s mr.mrrefChr3 156387 61 - 181027 CACAATCATTGTTGGCTTGGGACTAATTGCCATTTGAGGGCTCCGGTATGCAATTGACTTG +s mr.mrrefChr3 23796 61 - 181027 CACAGTCATTATTAACTCAAGACTATTTGCCATTTGAGTGCTCTAGTATGCAATTGCCTTG +s mr.mrrefChr5 198638 61 - 294540 CACGGTCATGATTCGCTCAAGACGATTTGCTAACTGAGCACTCTGGTATGCGACTGCCTTG +s simMouse_chr6.simMouse.chr6 167329 61 - 636262 CACAATCATTGTTGGCTTGGGACTAATTGCCATTTGAGGGCTCCGGTATGCAATTGACTTG +s simMouse_chr6.simMouse.chr6 26955 61 - 636262 CACAGTCATTATTAACTCAAGACTATTTGCCATTTGAGTGCTCTAGTATGCAATTGCCTTG +s simMouse_chr6.simMouse.chr6 393455 61 - 636262 CACGGTCATGACTCGCTCGAGACGATTTGCTAACTGAACACTCTTGTATACGACTGCCTCG +s simRat_chr6.simRat.chr6 168343 61 - 647215 CACAGTCATTATTGGCTTGGGGCTATCTGCCATTTGAGTGCTCCAGTATGCAATTGCTTTG +s simRat_chr6.simRat.chr6 563356 61 + 647215 CACAGTCATTAATCACTCAGGAATATTAGCCATTTAAGCATCCTGGTATTCGGTTGCCTTG +s simRat_chr6.simRat.chr6 294542 61 - 647215 CACAGCCATTATTGGCTCGGGATTATCCACCATTTGAGTCCTCTGGTCTGCTATAGCCTTG +s simRat_chr6.simRat.chr6 580248 61 + 647215 CACAGTCATTATTAGCTCAGGACTATCTGCCACTTGAGCACTCTGGTATGCTATGGCCTCC + +a +s simMouse_chr6.simMouse.chr6 635537 4 + 636262 CGTA +s Anc1.Anc1refChr6 75777 4 - 197743 CGTA +s mr.mrrefChr3 156448 4 - 181027 CGTA +s mr.mrrefChr3 23857 4 - 181027 CGTA +s mr.mrrefChr5 198699 4 - 294540 CGTA +s simMouse_chr6.simMouse.chr6 167390 4 - 636262 CGTA +s simMouse_chr6.simMouse.chr6 27016 4 - 636262 CGTA +s simMouse_chr6.simMouse.chr6 393516 4 - 636262 TGTA +s simRat_chr6.simRat.chr6 168404 4 - 647215 TGTA +s simRat_chr6.simRat.chr6 563417 4 + 647215 TGTA +s simRat_chr6.simRat.chr6 580309 4 + 647215 CATA + +a +s simMouse_chr6.simMouse.chr6 635541 18 + 636262 CGCTTTGTTCACGACTTC +s Anc1.Anc1refChr6 75781 18 - 197743 TGCTTTGTTTGCGACTTT +s mr.mrrefChr3 156452 18 - 181027 TGCTCTGTTTGCAACTTT +s mr.mrrefChr3 23861 18 - 181027 TGCTTTGTTTGCGGCTTC +s mr.mrrefChr5 198703 18 - 294540 CGCTTTGTTTGCGACTTT +s simMouse_chr6.simMouse.chr6 167394 18 - 636262 TGCTCTGTTTGCAACTTT +s simMouse_chr6.simMouse.chr6 27020 18 - 636262 TGCTTTGTTTGCGGCTTC +s simMouse_chr6.simMouse.chr6 393520 18 - 636262 CGCTTTGTTTGTGAATTT +s simRat_chr6.simRat.chr6 168408 18 - 647215 TACTTTGCTTGCAACTTT +s simRat_chr6.simRat.chr6 563421 18 + 647215 TGCCTTGTTTGTGACTTC +s simRat_chr6.simRat.chr6 294603 18 - 647215 TACATTGTTTGCGACTTA +s simRat_chr6.simRat.chr6 580313 17 + 647215 TGCTTCGTTTGCGACTT- + +a +s simMouse_chr6.simMouse.chr6 635559 4 + 636262 GAAG +s Anc1.Anc1refChr6 75799 4 - 197743 GAAG +s mr.mrrefChr3 156470 4 - 181027 GAAG +s mr.mrrefChr5 198721 4 - 294540 GAAG +s simMouse_chr6.simMouse.chr6 167412 4 - 636262 GAAG +s simMouse_chr6.simMouse.chr6 393538 4 - 636262 GAAG +s simRat_chr6.simRat.chr6 168426 4 - 647215 GAAG +s simRat_chr6.simRat.chr6 294621 4 - 647215 GAAG + +a +s simMouse_chr6.simMouse.chr6 635563 2 + 636262 TC +s Anc1.Anc1refChr6 75803 2 - 197743 CC +s mr.mrrefChr3 156474 2 - 181027 CC +s mr.mrrefChr5 198725 2 - 294540 TC +s simMouse_chr6.simMouse.chr6 167417 2 - 636262 CC +s simMouse_chr6.simMouse.chr6 393542 2 - 636262 TC +s simRat_chr6.simRat.chr6 168430 2 - 647215 CC +s simRat_chr6.simRat.chr6 294625 2 - 647215 CC +s simRat_chr6.simRat.chr6 580330 2 + 647215 CC + +a +s simMouse_chr6.simMouse.chr6 635565 2 + 636262 TC +s Anc0.Anc0refChr3 133326 1 - 222631 -C +s Anc1.Anc1refChr6 75805 2 - 197743 CC +s Anc2.Anc2refChr1 142501 1 - 142988 -C +s mr.mrrefChr3 156476 2 - 181027 CC +s mr.mrrefChr5 198727 2 - 294540 TC +s simCow_chr6.simCow.chr6 148730 1 - 602619 -C +s simDog_chr6.simDog.chr6 448535 1 + 593897 -C +s simMouse_chr6.simMouse.chr6 167419 2 - 636262 CC +s simRat_chr6.simRat.chr6 168432 2 - 647215 CT +s simRat_chr6.simRat.chr6 294630 2 - 647215 AC +s simRat_chr6.simRat.chr6 580332 1 + 647215 T- a s simMouse_chr6.simMouse.chr6 635567 2 + 636262 TG @@ -238522,27 +256144,16 @@ 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 +s simMouse_chr6.simMouse.chr6 635569 4 + 636262 GATT +s Anc0.Anc0refChr5 25915 4 - 87904 GCCA +s Anc1.Anc1refChr7 27595 4 + 47259 GCCA +s Anc2.Anc2refChr15 27830 4 - 86568 GCCA +s mr.mrrefChr5 198731 4 - 294540 gaTT +s simCow_chr6.simCow.chr6 363177 4 - 602619 GACA +s simDog_chr6.simDog.chr6 362358 4 - 593897 TCCA +s simHuman_chr6.simHuman.chr6 280430 4 + 601863 GCCA +s simRat_chr6.simRat.chr6 294634 4 - 647215 gtgg +s simRat_chr6.simRat.chr6 580333 2 + 647215 --TT a s simMouse_chr6.simMouse.chr6 635573 5 + 636262 TACTA