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