D4Sh1 unique seq. allele alignment

The following alignment contains alleles recovered by PCR from different mice at a unique sequence downstream from MuERVC-C105 (locus = D4Sh1). Spretus strains are: SMZ, SPRET/Ei, SEG, outbred spretus Morocco (D3878 and D3879), outbred spretus Spain (D3889, D3890, and D3891) and STF^h and STF^f (two different sequences recovered from STf, which had been expected to be inbred). M. cervicolor is an outgroup. The M. spiciligus strain was PANCEVO. Classical inbred domesticus strains are C57BL/6j, C58/j, C57BL/KsJ, CBA, and SJL. C105 is from the sequenced lambdaphage clone lambda C105 corresponding to coordinates 6544..7055 in AF049340. Wild derived inbred domesticus are DMZ, WSB; M. molossinus and M. castaneus are wild derived inbred members of the musculus subspecies other than domesticus. "." is an alignment gap. "-" is missing data. Private variants are in lower case.
These sequences (sans primers) are being processed into GenBank with accession numbers AF068303-AF068317, and AF147461-AF147462.
               1                                                   50
cervicolor     TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTAA AGTTATTTCT
PANCEVO        TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTAA AGTTATTTCT
SMZ            TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTAA AGTTATTTCT
STFh           TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTGA AGTTATTTCT
STFf           TGGATATACC cGTTGAAGCA TCATCAGCTT CAATCTGTGA AGcTATTTCT
SPRET-Ei       TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTGA AGTTATTTCT
D3891 (sp-S)   TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTGA AGTTATTTCT
D3889 (sp-S)   TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTGA AGTTATTTCT
D3890-2 (sp-S) TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTGA AGTTATTTCT
D3890-1 (sp-S) TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTGA AGTTATTTCT
C57BL-6J       TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTGA AGTTATTTCT
C105           TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTGA AGTTATTTCT
C58-J          TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTGA AGTTATTTCT
SEG            TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTAA AGTTATTTCT
D3878 (sp-M)   TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTAA AGTTATTTCT
D3879 (sp-M)   TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTAA AGTTATTTCT
C57BL-KsJ      TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTAA AGTTATTTCT
molossinuS)    TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTAA AGTTATTTCT
castaneuS)     TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTAA AGTTATTTCT
DMZ            TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTAA AGTTATTTCT
WSB            TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTAA AGTTATTTCT
CBA            TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTAA AGTTATTTCT
SJL            TGGATATACC TGTTGAAGCA TCATCAGCTT CAATCTGTAA AGTTATTTCT
Changes:       Primer---- ---------- >                  G    c

               51                                                 100
cervicolor     AAGCTAGTCA TCATCTTTAA AAAATATGAT TTTAGAATTA TCTTTTAAAT
PANCEVO        AAGCTAGTCA TCATCTTTAA AAAATATGAT TTTAGAATTA TCTTTTAAAT
SMZ            AAGCTAGTCA TCATCTTTAA AAAATATGAT TTTAGAATTA TCTTTTAAAT
STFh           AAGCTAGTCA TCATCTTTAA AAAATATGAT TTTAGAATTA TCTTTTAAAT
STFf           AAGCTAGTCA TCATCTTTAA AAAATATGAT TTTAGAATTA TCTTTTAAAT
SPRET-Ei       AAGCTAGTCA TCATCTTTAA AAAATATGAT TTTAGAATTA TCTTTTAAAT
D3891 (sp-S)   AAGCTAGTCA TCATCTTTAA AAAATATGAT TTTAGAATTA TCTTTTAAAT
D3889 (sp-S)   AAGCTAGTCA TCATCTTTAA AAAATATGAT TTTAGAATTA TCTTTTAAAT
D3890-2 (sp-S) AAGCTAGTCA TCATCTTTAA AAAATATGAT TTTAGAATTA TCTTTTAAAT
D3890-1 (sp-S) AAGCTAGTCA TCATCTTTAA AAAATATGAT TTTAGAATTA TCTTTTAAAT
C57BL-6J       AAGCTAGTCA TCATCTTTAA AAAATATGAT TTTAGAATTA TCTTTTAAAT
C105           AAGCTAGTCA TCATCTTTAA AAAATATGAT TTTAGAATTA TCTTTTAAAT
C58-J          AAGCTAGTCA TCATCTTTAA AAAATATGAT TTTAGAATTA TCTTTTAAAT
SEG            AAGCTAGTCA TCATCTTTTA AAAATATGAT TTTAGAATTA TCTTTTAAAT
D3878 (sp-M)   AAGCTAGTCA TCATCTTTTA AAAATATGAT TTTAGAATTA TCTTTTAAAT
D3879 (sp-M)   AAGCTAGTCA TCATCTTTTA AAAATATGAT TTTAGAATTA TCTTTTAAAT
C57BL-KsJ      AAGCTAGTCA TCATCTTTTA AAAATATGAT TTTAGAATTA TCTTTTAAAT
molossinuS)    AAGCTAGTCA TCATCTTTAA AAAATATGAT TTTAGAATTA TCTTTTAAAT
castaneuS)     AAGCTAGTCA TCATCTTTAA AAAATATGAT TTTAGAATTA TCTTTTAAAT
DMZ            AAGCTAGTCA TCATCTTTAA AAA.TATGAT TTTAGAATTA TCTTTTAAAT
WSB            AAGCTAGTCA TCATCTTTAA AAA.TATGAT TTTAGAATTA TCTTTTAAAT
CBA            AAGCTAGTCA TCATCTTTAA AAA.TATGAT TTTAGAATTA TCTTTTAAAT
SJL            AAGCTAGTCA TCATCTTTAA AAA.TATGAT TTTAGAATTA TCTTTTAAAT
Changes:                          T     X

               101                                                150
cervicolor     AAtTCAAGGT AGAAGCCCAT TGGAATTCTG AATATGAATC AATAGTAT..
PANCEVO        AAATCAAGGT AGAAGCCCAT TGGAATTCTG AATATGAATC AATAGTAT..
SMZ            AAATCAAGGT AGAAGCCCAT TGGAATTCTG AATATGAATC AATAGTAT..
STFh           AAATCAAGGT ATAAGCCCAT TGGAATTCTG AATATGAATC AATAGTAT..
STFf           AAATCAAGGT ATAAGCCCAT TGGAATTCTG AATATGAATC AATAGTAT..
SPRET-Ei       AAATCAAGGT ATAAGCCCAT TGGAATTCTG AATATGAATC AATAGTAT..
D3891 (sp-S)   AAATCAAGGT ATAAGCCCAT TGGAATTCTG AATATGAATC AATAGTAT..
D3889 (sp-S)   AAATCAAGGT ATAAGCCCAT TGGAATTCTG AATATGAATC AATAGTAT..
D3890-2 (sp-S) AAATCAAGGT ATAAGCCCAT TGGAATTCTG AATATGAATC AATAGTAT..
D3890-1 (sp-S) AAATCAAGGT ATAAGCCCAT TGGAATTCTG AATATGAATC AATAGTAT..
C57BL-6J       AAATCAAGGT AGAAGCCCAT TGGAATTCTG AATATGAATC AATAGTATCA
C105           AAATCAAGGT AGAAGCCCAT TGGAATTCTG AATATGAATC AATAGTATCA
C58-J          AAATCAAGGT AGAAGCCCAT TGGAATTCTG AATATGAATC AATAGTATCA
SEG            AAATCAAGGT AGAAGCCCAT TGGAATTCTG AATATGAATC AATTGTAT..
D3878 (sp-M)   AAATCAAGGT AGAAGCCCAT TGGAATTCTG AATATGAATC AATTGTAT..
D3879 (sp-M)   AAATCAAGGT AGAAGCCCAT TGGAATTCTG AATATGAATC AATTGTAT..
C57BL-KsJ      AAATCAAGGT AGAAGCCCAT TGGAATTCTG AATATGAATC AATTGTAT..
molossinuS)    AAATCAAGGT AGAAGCCCAT TGGAATTCTG AATATGAATC AATTGTAT..
castaneuS)     AAATCAAGGT AGAAGCCCAT TGGAATTCTG AATATGAATC AATTGTAT..
DMZ            AAATCAAGGT AGAAGCCCAT TGGAATTCTG AATATGAATC AATTGTAT..
WSB            AAATCAAGGT AGAAGCCCAT TGGAATTCTG AATATGAATC AATTGTAT..
CBA            AAATCAAGGT AGAAGCCCAT TGGAATTCTG AATATGAATC AATTGTAT..
SJL            AAATCAAGGT AGAAGCCCAT TGGAATTCTG AATATGAATC AATTGTAT..
Changes:         t         T                                  T    XX

               151                                                200
cervicolor     .......GAT GTATCGACAT GTGTAC.... TTTAGATTAT TTTAATTTTC
PANCEVO        .......GAT GTATCGACAT GTGTACATAC TTTAGATTgT TTTAATTTTC
SMZ            .......GAT GTATCGACAT GTGTACATAC TTTAGATTAT TTTAATTTTC
STFh           .......GAT GTATTGACAT GTGTACATAC TTTAGATTAT TTTAATTTTC
STFf           .......GAT GTATTGACAT GTGTACATAC TTTAGATTAT TTTAATTTTC
SPRET-Ei       .......GAT GTATTGACAT GTGTACATAC TTTAGATTAT TTTAATTTTC
D3891 (sp-S)   .......GAT GTATTGACAT GTGTACATAC TTTAGATTAT TTTAATTTTC
D3889 (sp-S)   .......GAT GTATTGACAT GTGTACATAC TTTAGATTAT TTTAATTTTC
D3890-2 (sp-S) .......GAT GTATTGACAT GTGTACATAC TTTAGATTAT TTTAATTTTC
D3890-1 (sp-S) .......GAT GTATTGACAT GTGTACATAC TTTAGATTAT TTTAATTTTC
C57BL-6J       ATAGTATGAT GTATCGACAT GTGTACATAC TTTAGATTAT TTTAATTTTC
C105           ATAGTATGAT GTATCGACAT GTGTACATAC TTTAGATTAT TTTAATTTTC
C58-J          ATAGTATGAT GTATCGACAT GTGTACATAC TTTAGATTAT TTTAATTTTC
SEG            .......GAT GTATCAACAT GTGTACATAC TTTAGATTAT TTTAATTTTC
D3878 (sp-M)   .......GAT GTATCAACAT GTGTACATAC TTTAGATTAT TTTAATTTTC
D3879 (sp-M)   .......GAT GTATCAACAT GTGTACATAC TTTAGATTAT TTTAATTTTC
C57BL-KsJ      .......GAT GTATCAACAT GTGTACATAC TTTAGATTAT TTTAATTTTC
molossinuS)    .......GAT GTATCGACAT GTGTACATAC TTTAGATTAT TTTAATTTTC
castaneuS)     .......GAT GTATCGACAT GTGTACATAC TTTAGATTAT TTTAATTTTC
DMZ            .......GAT GTATCGACAT GTGTACATAC TTTAGATTAT TTTAATTTTC
WSB            .......GAT GTATCGACAT GTGTACATAC TTTAGATTAT TTTAATTTTC
CBA            .......GAT GTATCGACAT GTGTACATAC TTTAGATTAT TTTAATTTTC
SJL            .......GAT GTATCGACAT GTGTACATAC TTTAGATTAT TTTAATTTTC
Changes:       XXXXXXX        TA           xxxx         g

               201                                                250
cervicolor     CAAAAGAAAA CACATAAACT ATTGcATACC ATTGTTCTAA GATAGCATCA
PANCEVO        CAAAAGAAAA CACATAAACT ATTGTATACC ATTGTTCTAA GATAGCATCA
SMZ            CAAAAGAAAA CACATAAAtT AcTGTATACC ATTGTTCTAA GATAGCATCA
STFh           TAAAAGAAAA CACATAAACT ATTGTATACC ATTGTTCTAA GATAGCATCA
STFf           TAAAAGAAAA CACATAAACT ATTGTATACC ATTGTTCTAA GATAGCATCA
SPRET-Ei       TAAAAGAAAA CACATAAACT ATTGTATACC ATTGTTCTAA GATAGCATCA
D3891 (sp-S)   TAAAAGAAAA CACATAAACT ATTGTATACC ATTGTTCTAA GATAGCATCA
D3889 (sp-S)   TAAAAGAAAA CACATAAACT ATTGTATACC ATTGTTCTAA GATAGCATCA
D3890-2 (sp-S) TAAAAGAAAA CACATAAACT ATTGTATACC ATTGTTCTAA GATAGCATCA
D3890-1 (sp-S) TAAAAGAAAA CACATAAACT ATTGTATACC ATTGTTCTAA GATAGCATCA
C57BL-6J       CAAAAGAAAA CACATAAACT ATTGTATACC ATTGTTCTAA GATAGCATTA
C105           CAAAAGAAAA CACATAAACT ATTGTATACC ATTGTTCTAA GATAGCATTA
C58-J          CAAAAGAAAA CACATAAACT ATTGTATACC ATTGTTCTAA GATAGCATTA
SEG            CAAAAGAAAA CACATAAACT ATTGTATACC ATTGTTCTAA GATAGCATCA
D3878 (sp-M)   CAAAAGAAAA CACATAAACT ATTGTATACC ATTGTTCTAA GATAGCATCA
D3879 (sp-M)   CAAAAGAAAA CACATAAACT ATTGTATACC ATTGTTCTAA GATAGCATCA
C57BL-KsJ      CAAAAGAAAA CACATAAACT ATTGTATACC ATTGTTCTAA GATAGCATCA
molossinuS)    CAAAAGAAAA CACATAAACT ATTGTATACC ATTGTTCTAA GATAGCATCA
castaneuS)     CAAAAGAAAA CACATAAACT ATTGTATACC ATTGTTCTAA GATAGCATCA
DMZ            CAAAAGAAAA CACATAAACT ATTGTATACC ATTGTTCTAA GATAGCATCA
WSB            CAAAAGAAAA CACATAAACT ATTGTATACC ATTGTTCTAA GATAGCATCA
CBA            CAAAAGAAAA CACATAAACT ATTGTATACC ATTGTTCTAA GATAGCATCA
SJL            CAAAAGAAAA CACATAAACT ATTGTATACC ATTGTTCTAA GATAGCATCA
Changes:       T                  t   c  c                         T

               251                                                300
cervicolor     TTAATTAaAA TCTGGATT.C TTAATTCAGA ATACTcCATC TCTATGCATT
PANCEVO        TTAATTAGAA TCTGGATT.C TTAATTCAGA ATACTGCATC TCTATGCATT
SMZ            TTAATTAGAA TCTGGATT.C TTAATTCAGA ATACTGCATC TCTATGCATT
STFh           TTAATTAGAA TCTGGACT.C TTAATTCAGA ATACTGCATC TCTATGCATT
STFf           TTAATTAGAA TCTGGACTTC TTAATTCAGA ATACTGCATC TCTATGCATT
SPRET-Ei       TTAATTAGAA TCTGGACT.C TTAATTCAGA ATACTGCATC TCTATGCATT
D3891 (sp-S)   TTAATTAGAA TCTGGACT.C TTAATTCAGA ATACTGCATC TCTATGCATT
D3889 (sp-S)   TTAATTAGAA TCTGGACT.C TTAATTCAGA ATACTGCATC TCTATGCATT
D3890-2 (sp-S) TTAATTAGAA TCTGGACT.C TTAATTCAGA ATACTGCATC TCTATGCATT
D3890-1 (sp-S) TTAATTAGAA TCTGGACT.C TTAATTCAGA ATACTGCATC TCTATGCATT
C57BL-6J       TTAATTAGAA TCTGGACT.C TTAATTCAGA ATACTGCATC TCTATGCATT
C105           TTAATTAGAA TCTGGACT.C TTAATTCAGA ATACTGCATC TCTATGCATT
C58-J          TTAATTAGAA TCTGGACT.C TTAATTCAGA ATACTGCATC TCTATGCATT
SEG            TTAATTAGAA TCTGGACT.C TTAATTCAGG ATACTGCATC TCTATGCATT
D3878 (sp-M)   TTAATTAGAA TCTGGACT.C TTAATTCAGG ATACTGCATC TCTATGCATT
D3879 (sp-M)   TTAATTAGAA TCTGGACT.C TTAATTCAGG ATACTGCATC TCTATGCATT
C57BL-KsJ      TTAATTAGAA TCTGGACT.C TTAATTCAGG ATACTGCATC TCTATGCATT
molossinuS)    TTAATTAGAA TCTGGACT.C TTAATTCAGG ATgCTGCATC TCTATGCATT
castaneuS)     TTAATTAGAA TCTGGACT.C TTAATTCAGG ATACTGCATC TCTATGCATT
DMZ            TTAATTAGAA TCTGGACT.C TTAATTCAGG ATACTGCATC TCTATGCATT
WSB            TTAATTAGAA TCTGGACT.C TTAATTCAGG ATACTGCATC TCTATGCATT
CBA            TTAATTAGAA TCTGGACT.C TTAATTCAGG ATACTGCATC TCTATGCATT
SJL            TTAATTAGAA TCTGGACT.C TTAATTCAGG ATACTGCATC TCTATGCATT
Changes:              a         T x           G   g  c

               301                                                350
cervicolor     ACCTTTCTAA TTCCTCAAAT CTTTGTGGAT TTTTCTCATC TGGAACTATA
PANCEVO        ACCTTTCTAA TTCCTCAAAT CTTTGTGGAT TTTTCTCATC TGGAACTATA
SMZ            ACCTTTCTAA TTCCTCAAAT CTTTGTGGAT TTTTCTCATC TGGAACTATA
STFh           ACCTTTCTAA TTCTTCAAAT CTTTGTGGAT TTTTCTCATC TGGAACTATA
STFf           ACCTTTCTAA TTCTTCAAAT CTTTGTGGAT TTTTCTCATC TGGAACTATA
SPRET-Ei       ACCTTTCTAA TTCTTCAAAT CTTTGTGGAT TTTTCTCATC TGGAACTATA
D3891 (sp-S)   ACCTTTCTAA TTCTTCAAAT CTTTGTGGAT TTTTCTCATC TGGAACTATA
D3889 (sp-S)   ACCTTTCTAA TTCTTCAAAT CTTTGTGGAT TTTTCTCATC TGGAACTATA
D3890-2 (sp-S) ACCTTTCTAA TTCTTCAAAT CTTTGTGGAT TTTTCTCATC TGGAACTATA
D3890-1 (sp-S) ACCTTTCTAA TTCTTCAAAT CTTTGTGGAT TTTTCTCATC TGGAACTATA
C57BL-6J       ACCTTTCTAA TTCCTCAAAT CTTTGTGGAT TTTTCTCATC TGGAACTATA
C105           ACCTTTCTAA TTCCTCAAAT CTTTGTGGAT TTTTCTCATC TGGAACTATA
C58-J          ACCTTTCTAA TTCCTCAAAT CTTTGTGGAT TTTTCTCATC TGGAACTATA
SEG            ACCTTTCTAA TTCCTCAAAT CTTTGGGGAT TTTTCTCATC TGGAACTATA
D3878 (sp-M)   ACCTTTCTAA TTCCTCAAAT CTTTGGGGAT TTTTCTCATC TGGAACTATA
D3879 (sp-M)   ACCTTTCTAA TTCCTCAAAT CTTTGGGGAT TTTTCTCATC TGGAACTATA
C57BL-KsJ      ACCTTTCTAA TTCCTCAAAT CTTTGGGGAT TTTTCTCATC TGGAACTATA
molossinuS)    ACCTTTCTAA TTCCTCAAAT CTTTGGGGAT TTTTCTCATC TGGAACTATA
castaneuS)     ACCTTTCTAA TTCCTCAAAT CTTTGGGGAT TTTTCTCATC TGGAACTATA
DMZ            ACCTTTCTAA TTCCTCAAAT CTTTGGGGAT TTTTCTCATC TGGAACTATA
WSB            ACCTTTCTAA TTCCTCAAAT CTTTGGGGAT TTTTCTCATC TGGAACTATA
CBA            ACCTTTCTAA TTCCTCAAAT CTTTGGGGAT TTTTCTCATC TGGAACTATA
SJL            ACCTTTCTAA TTCCTCAAAT CTTTGGGGAT TTTTCTCATC TGGAACTATA
Changes:                     T            G

               351                                                400
cervicolor     GGTTTCAGAT CaGATTCTTG TGAAGATTGT TTACTCTGAT TCAAAGAATc
PANCEVO        GGTTTCAGAT TGGATTCTTG TGAAGATTGT TTACTCTGAT TCAAAGAATA
SMZ            GGTTTCAGAT TGGATTCTTG TGAAGATTGT TTACTCTGAT TCAAAGAATA
STFh           GGTTTCAGAT TGAATTCTTG TGAAGATTGT TTACTCTGAT TCAAAGAATA
STFf           GGTTTCAGAT CGAATTCTTG TGAAGATTGT TTACTCTGAT TCAAAGAATA
SPRET-Ei       GGTTTCAGAT TGAATTCTTG TGAAGATTGT TTACTCTGAT TCAAAGAATA
D3891 (sp-S)   GGTTTCAGAT TGAATTCTTG TGAAGATTGT TTACTCTGAT TCAAAGAATA
D3889 (sp-S)   GGTTTCAGAT TGAATTCTTG TGAAGATTGT TTACTCTGAT TCAAAGAATA
D3890-2 (sp-S) GGTTTCAGAT TGAATTCTTG TGAAGATTGT TTACTCTGAT TCAAAGAATA
D3890-1 (sp-S) cGTTTCAGAT TGAATTCTTG TGAAGATTGT TTACTCTGAT TCAAAGAATA
C57BL-6J       GGTTTCAGAT TGAATTCTTG TGAAGACTGT TTACTCTGAT TCAAAGAATA
C105           GGTTTCAGAT TGAATTCTTG TGAAGACTGT TTACTCTGAT TCAAAGAATA
C58-J          GGTTTCAGAT TGAATTCTTG TGAAGACTGT TTACTCTGAT TCAAAGAATA
SEG            GGTTTCAGAT TGAATTCTTG TGAAGATTGT TTACTCTGAT TCAAAGAATA
D3878 (sp-M)   GGTTTCAGAT TGAATTCTTG TGAAGATTGT TTACTCTGAT TCAAAGAATA
D3879 (sp-M)   GGTTTCAGAT TGAATTCTTG TGAAGATTGT TTACTCTGAT TCAAAGAATA
C57BL-KsJ      GGTTTCAGAT TGAATTCTTG TGAAGATTGT TTACTCTGAT TCAAAGAATA
molossinuS)    GGTTTCAGAT TGAATTCTTG TGAAGATTAT TTACTCTGAT TCAAAGAATA
castaneuS)     GGTTTCAGAT TGAATTCTTG TGAAGATTAT TTACTCTGAT TCAAAGAATA
DMZ            GGTTTCAGAT TGAATTCTTG TGAAGATTAT TTACTCTGAT TCAAAGAATA
WSB            GGTTTCAGAT TGAATTCTTG TGAAGATTAT TTACTCTGAT TCAAAGAATA
CBA            GGTTTCAGAT TGAATTCTTG TGAAGATTAT TTACTCTGAT TCAAAGAGTA
SJL            GGTTTCAGAT TGAATTCTTG TGAAGATTAT TTACTCTGAT TCAAAGAGTA
Changes:       c          CaG              C A                    G c

               401                                                450
cervicolor     TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCGT CTTTCACTCC
PANCEVO        TagTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCcT CTTTCACTCC
SMZ            TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCcT CTTTCACTCC
STFh           TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCGT CTTTCACTCC
STFf           TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCGT CTTTCACTCC
SPRET-Ei       TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCGT CTTTCACTCC
D3891 (sp-S)   TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCGT CTTTCACTCC
D3889 (sp-S)   TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCGT CTTTCACTCC
D3890-2 (sp-S) TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCGT CTTTCACTCC
D3890-1 (sp-S) TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCGT CTTTCACTCC
C57BL-6J       TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCGT CTTTCACTCC
C105           TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCGT CTTTCACTCC
C58-J          TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCGT CTTTCACTCC
SEG            TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCGT CTTTCACTCC
D3878 (sp-M)   TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCGT CTTTCACTCC
D3879 (sp-M)   TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCGT CTTTCACTCC
C57BL-KsJ      TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCGT CTTTCACTCC
molossinuS)    TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCaT CTTTCACTCC
castaneuS)     TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCGT CTTTCACTCC
DMZ            TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCGT CTTTCACTCC
WSB            TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCGT CTTTCACTCC
CBA            TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCGT CTTTCACTCC
SJL            TTCTAATCTT TGTTCTATGA CCTCTAATTT AGCATCTCGT CTTTCACTCC
Changes:        ag                                      C
                                                        a

               451                                                500
cervicolor     TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTcaTACA GAGGATATAC
PANCEVO        TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTATTACA GAGGATATAC
SMZ            TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTATTACA GAGGATATAC
STFh           TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTATTACA GAGGATATAC
STFf           TCTCCTTATC TGAGCTTGTT TTA------- ---------- ----------
SPRET-Ei       TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTATTACA GAGGATATAC
D3891 (sp-S)   TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTATTACA GAGGATATAC
D3889 (sp-S)   TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTATTACA GAGGATATAC
D3890-2 (sp-S) TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTATTACA GAGGATATAC
D3890-1 (sp-S) TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTATTACA GAGGATATAC
C57BL-6J       TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTATTACA GAGGATATAC
C105           TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTATTACA GAGGATATAC
C58-J          TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTATTACA GAGGATATAC
SEG            TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTATTACA GAGGATATAC
D3878 (sp-M)   TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTATTACA GAGGATATAC
D3879 (sp-M)   TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTATTACA GAGGATATAC
C57BL-KsJ      TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTATTACA GAGGATATAC
molossinuS)    TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTATTACA GAGGATATAC
castaneuS)     TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTATTACA GAGGATATAC
DMZ            TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTATTACA GAGGATATAC
WSB            TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTATTACA GAGGATATAC
CBA            TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTATTACA GAGGATATAC
SJL            TCTCCTTATC TGAGCTTGTT TTATTCTGAC CTTTATTACA GAGGATATAC
Changes:                                            ca <-- --- primer

               501        513
cervicolor     AAAATTGTAA CCG
PANCEVO        AAAATTGTAA CCG
SMZ            AAAATTGTAA CCG
STFh           AAAATTGTAA CCG
STFf           ---------- ---
SPRET-Ei       AAAATTGTAA CCG
D3891 (sp-S)   AAAATTGTAA CCG
D3889 (sp-S)   AAAATTGTAA CCG
D3890-2 (sp-S) AAAATTGTAA CCG
D3890-1 (sp-S) AAAATTGTAA CCG
C57BL-6J       AAAATTGTAA CCG
C105           AAAATTGTAA CCG
C58-J          AAAATTGTAA CCG
SEG            AAAATTGTAA CCG
D3878 (sp-M)   AAAATTGTAA CCG
D3879 (sp-M)   AAAATTGTAA CCG
C57BL-KsJ      AAAATTGTAA CCG
molossinuS)    AAAATTGTAA CCG
castaneuS)     AAAATTGTAA CCG
DMZ            AAAATTGTAA CCG
WSB            AAAATTGTAA CCG
CBA            AAAATTGTAA CCG
SJL            AAAATTGTAA CCG
Changes:       ---------- ---