Single nucleotide and indel polymorphisms in the interval from upstream of the HLA-DNA gene to the TAP2 gene in the Class II region of the MHC

The location of each SNP (centromere to telomere) used in the linkage disequilibrium and sperm crossover studies is given relative to the position of SNP DA1+/-. DA1+/- is located at position 3,260,370 of the current consensus MHC sequence reported by Beck et al. (1999). SNPs T1G/T to T45C/T are described in Jeffreys, Ritchie & Neumann (2000). SNPs DS4-31 were identified from the Public SNP Database.

Allele frequencies were determined from genotypes of a panel of 50 unrelated UK Caucasian semen donors, established by hybridisation of appropriate 1-5 kb genomic PCR products with each of the indicated allele-specific oligonucleotides. The SNP or indel site in each ASO is indicated in red. Mixed bases shown in green correspond to definite or suspected nearby SNP sites. Alu repeat sequences are shown in blue.

 

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SNP  location,bp  allele  freq.   allele-specific oligonucleotide

DA1           1      +    0.73     5' GAAAATCAATCATATACT 3'
                     -    0.27     5' GAAAATCATATACTTAGA 3'

DA3         556      A    0.96     5' AAGGAACATTTCTCAACT 3'
                     G    0.04     5' AAGGAACGTTTCTCAACT 3'

DA5        1907      G    0.67     5' GWGTGCTGGAGACCGTGG 3'
                     A    0.33     5' GWGTGCTAGAGACCGTGG 3'

DA9        2292      +    0.63     5' AATATCAGGGGAAAGGAT 3'
                     -    0.37     5' AATATCAGGGAAAGGATT 3'

DB1        5402      A    0.71     5' ATAGCCTATAAACATCCT 3'
                     G    0.29     5' ATAGCCTGTAAACATCCT 3'

DB2        7201      C    0.67     5' AGGGAACCCTTGTACACT 3'
                     T    0.33     5' AGGGAACTCTTGTACACT 3'

DC1       11741      A    0.54     5' CTCCAGAAAGACTGGACT 3'
                     C    0.46     5' CTCCAGACAGACTGGACT 3'

DC3       11972      +    0.94     5' GCCTGACTCTCTGCCCAA 3'
                     -    0.06     5' GCCTGACTCTGCCCAAAC 3'

DC8       13807      A    0.68     5' CACAAAGATAAAGATTTG 3'
                     T    0.32     5' CACAAAGTTAAAGATTTG 3'

DC9       13964      A    0.56     5' AAGAAGAAAGATGAGGGT 3'
                     G    0.44     5' AAGAAGAGAGATGAGGGT 3'

DC10      13995      G    0.90     5' ATGAGAAGAGCATTAGGG 3'
                     C    0.10     5' ATGAGAACAGCATTAGGG 3'

DD1a      17276      C    0.75     5' TAAAAAGCAATAAGAAAC 3'
                                 + 5' TAAAAAGCATAAGAAACA 3'
                     G    0.25     5' TAAAAAGGAATAAGAAAC 3'
                                 + 5' TAAAAAGGATAAGAAACA 3'

DD1b      17278      +    0.90     5' TAAAAAGSAATAAGAAAC 3'
                     -    0.10     5' TAAAAAGSATAAGAAACA 3'

DD2a      17459      T    0.58     5' GGTGGCTTGYGGCTACTG 3'
                     G    0.42     5' GGTGGCTGGYGGCTACTG 3'

DD2b      17461      T    0.58     5' GGTGGCTKGTGGCTACTG 3'
                     C    0.42     5' GGTGGCTKGCGGCTACTG 3'

DD7       17951      T    0.94     5' ATACATATACATTCCAAG 3'
                     C    0.06     5' ATACATACACATTCCAAG 3'

DD15      18586      A    0.58     5' ACACCTAGAAGTTCTAGG 3'
                     C    0.42     5' ACACCTAGACGTTCTAGG 3'

DD19      18603      -    0.58     5' GTGTAAAAAATATATATA 3'
                     +    0.42     5' GTGTAAAAATATATATAT 3'

DD20      18821      -    0.58     5' AAAATAGAGGAGAAAAAT 3'
                     +    0.42     5' AAAATAGAGAGAGGAGAA 3'

DD21      19064      +    0.58     5' ATTAAAGGGGAAAAYACT 3'
                     -    0.42     5' ATTAAAGGGAAAAYACTT 3'

DD22      19070      T    0.58     5' GGGAAAATACTTCAAATA 3'
                     C    0.42     5' GGGAAAACACTTCAAATA 3'

DD23      19110      A    0.98     5' TTTATTCAAAAGTRCTGG 3'
                     T    0.02     5' TTTATTCATAAGTRCTGG 3'

DD16      19115      G    0.58     5' CAWAAGTGCTGGYATAAT 3'
                     A    0.42     5' CAWAAGTACTGGYATAAT 3'

DD17      19120      T    0.58     5' GTRCTGGTATAATTTTAA 3'
                     C    0.42     5' GTRCTGGCATAATTTTAA 3'

DD24      19191      G    0.82     5' CTGAAAGGTYTTGGAAGA 3'
                     T    0.18     5' CTGAAAGTTYTTGGAAGA 3'

DD18      19193      T    0.58     5' CTGAAAGKTTTTGGAAGA 3'
                     C    0.42     5' CTGAAAGKTCTTGGAAGA 3'

DD9       19817      T    0.72     5' AAGACAGTGCCATGTGCT 3'
                     G    0.28     5' AAGACAGGGCCATGTGCT 3'

DD10      20027      C    0.68     5' TGAAGTGCTTTTCAATAA 3'
                     G    0.32     5' TGAAGTGGTTTTCAATAA 3'

DD11      20051      T    0.58     5' TGCAAAGTGGAGCTTAGC 3'
                     C    0.42     5' TGCAAAGCGGAGCTTAGC 3'

DD12      20118      C    0.92     5' TGAACTACAYGTGGCTAA 3'
                     G    0.08     5' TGAACTAGAYGTGGCTAA 3'

DD13      20120      C    0.98     5' AACTASACGTGGCTAAAA 3'
                     T    0.02     5' AACTASATGTGGCTAAAA 3'

DD14      20188      A    0.58     5' CAGAAACAAGTTTGCTCA 3'
                     G    0.42     5' CAGAAACGAGTTTGCTCA 3'

DE1       20647      C    0.84     5' GGAGGATCGCTTAAGCCC 3'
                     G    0.16     5' GGAGGATGGCTTAAGCCC 3'

DE2       20800      G    0.88     5' GAAAACCGTAATAAATTA 3'
                     A    0.12     5' GAAAACCATAATAAATTA 3'

DE3       21211      G    0.94     5' CGCCTATGATGTGCTAGG 3'
                     T    0.06     5' CGCCTATTATGTGCTAGG 3'

DE4       21242      C    0.99     5' CTGTGGACTAGAAACGAA 3'
                     T    0.01     5' CTGTGGATTAGAAACGAA 3'

DE5       21470      G    0.97     5' CTGCCTTGGAAAGGCTAA 3'
                     T    0.03     5' CTGCCTTTGAAAGGCTAA 3'

DE6       21583      C    0.82     5' TAGCTCCCTCCAAGTTGA 3'
                     T    0.18     5' TAGCTCCTTCCAAGTTGA 3'

DE7       21620      A    0.82     5' CTTTGACACATGGCCTAA 3'
                     G    0.18     5' CTTTGACGCATGGCCTAA 3'

DE8       21946      A    0.99     5' GAAATTAAATAATAATAA 3'
                     C    0.01     5' GAAATTACATAATAATAA 3'

DE9       22263      C    0.50     5' ACTTCCTCTGGCCTCTCC 3'
                     T    0.50     5' ACTTCCTTTGGCCTCTCC 3'

DE10      22378      C    0.71     5' AAGACAGCAGGGGTCGCC 3'
                     A    0.29     5' AAGACAGAAGGGGTCGCC 3'

DE11      22450      G    0.99     5' CCACACGGACTGAGACTG 3'
                     C    0.01     5' CCACACGCACTGAGACTG 3'

DE12      22483      T    0.85     5' CAGAGTGTAATGGCCCTC 3'
                     C    0.15     5' CAGAGTGCAATGGCCCTC 3'

DE13      22714      C    0.99     5' CCCTCATCTCTGTCACAT 3'
                     T    0.01     5' CCCTCATTTCTGTCACAT 3'

DE14      22754      C    0.90     5' TGCAGCTCGGTCAGCTGC 3'
                     T    0.10     5' TGCAGCTTGGTCAGCTGC 3'

DE15      22889      G    0.53     5' CCTGGCCGGGAATGTGCC 3'
                     T    0.47     5' CCTGGCCTGGAATGTGCC 3'

DE16      23039      A    0.52     5' CTGGCCCACCATTGTGCT 3'
                     C    0.48     5' CTGGCCCCCCATTGTGCT 3'

DE17      23144      C    0.90     5' AACTAGACAACAGTTATG 3'
                     T    0.10     5' AACTAGATAACAGTTATG 3'

DE18      23614      C    0.97     5' CTCTCTCCCAGGGCCAGC 3'
                     T    0.03     5' CTCTCTCTCAGGGCCAGC 3'

DE19      23651      A    0.98     5' TGTCCCCACACAGAACCC 3'
                     T    0.02     5' TGTCCCCTCACAGAACCC 3'

DE20      23929      C    0.71     5' CGCAGGGCGGGCTGGCCG 3'
                     T    0.29     5' CGCAGGGTGGGCTGGCCG 3'

DE21      24078      C    0.71     5' TCCTAGGCTCCCATCACT 3'
                     T    0.29     5' TCCTAGGTTCCCATCACT 3'

DE22      24099      C    0.84     5' GGGCGCGCTCTCAGCGCC 3'
                     G    0.16     5' GGGCGCGGTCTCAGCGCC 3'

DE23      24220      A    0.85     5' CCCGCCCAGGGACCAGTC 3'
                     G    0.15     5' CCCGCCCGGGGACCAGTC 3'

DE24      24287      C    0.67     5' TCTGTTTCCCTCCTCTCC 3'
                     T    0.33     5' TCTGTTTTCCTCCTCTCC 3'

F1        24416      C    0.59     5' TCAGGGCCCGTTCYTCCT 3'
                     T    0.41     5' TCAGGGCCTGTTCYTCCT 3'

F2        24541      G    0.55     5' CCTGGCTGCGCAACGGCC 3'
                     A    0.45     5' CCTGGCTACGCAACGGCC 3'

F3        24784      A    0.55     5' TACCACCAACTCCTTCCT 3'
                     G    0.45     5' TACCACCGACTCCTTCCT 3'

F4        24864      C    0.75     5' CCCTGGGCCTGGCCATCG 3'
                     T    0.25     5' CCCTGGGTCTGGCCATCG 3'

F10       24955      G    0.85     5' AGGCCCCGGGAGTCTGGG 3'
                     A    0.15     5' AGGCCCCAGGAGTCTGGG 3'

F11       25247      C    0.90     5' GTGACAGCCCCTGCGTGC 3'
                     A    0.10     5' GTGACAGACCCTGCGTGC 3'

F5        25397      A    0.51     5' CATTCAACACAAACACAC 3'
                     C    0.49     5' CATTCAACACACACACAC 3'

F6        25455      G    0.94     5' TTTGGTGGTGTTTGCACT 3'
                     A    0.06     5' TTTGGTGGTATTTGCACT 3'

F7        25530      A    0.50     5' GGCAGCCATCCTGGGGCC 3'
                     G    0.50     5' GGCAGCCGTCCTGGGGCC 3'

F8        25717      G    0.53     5' TGGGACAGGACAGGCTCA 3'
                     A    0.47     5' TGGGACAAGACAGGCTCA 3'

F9        25810      +    0.53     5' TTTCTACTTTTCCCTAGA 3'
                     -    0.47     5' TTTCTACTTTCCCTAGAG 3'

FG1       25919      A    0.82     5' GGTCTGCAAGGTATCTCG 3'
                     G    0.18     5' GGTCTGCGAGGTATCTCG 3'

FG2       25956      C    0.81     5' AGACACACTCTAAATATG 3'
                     T    0.19     5' AGACACATTCTAAATATG 3'

FG14      26003      G    0.86     5' GTGAACAGAATTTAAAAC 3'
                     A    0.14     5' GTGAACAAAATTTAAAAC 3'

FG15      26054      A    0.83     5' TATGTCAAGACCAAAATG 3'
                     G    0.17     5' TATGTCAGGACCAAAATG 3'

FG3       26198      G    0.86     5' GGGACAGGACTGCTTGAG 3'
                     A    0.14     5' GGGACAGAACTGCTTGAG 3'

FG4       26284      C    0.50     5' TAACCAGCCATGGTGGCT 3'
                     G    0.50     5' TAACCAGGCATGGTGGCT 3'

FG11      26516      G    0.52     5' AACAGGGGGGCTGTCTTT 3'
                     A    0.48     5' AACAGGGAGGCTGTCTTT 3'

FG5       26534      A    0.54     5' TCTGAGAAGGGGTCTCAC 3'
                     T    0.46     5' TCTGAGATGGGGTCTCAC 3'

FG6       26894      C    0.87     5' CCAGTGACGTAATCAGGT 3'
                     T    0.13     5' CCAGTGATGTAATCAGGT 3'

FG7       26910      C    0.71     5' GTGCCATCGGGGGTCATG 3'
                     T    0.29     5' GTGCCATTGGGGGTCATG 3'

FG12      27107      A    0.88     5' TTAAGAGAGAATAAGTTG 3'
                     G    0.12     5' TTAAGAGGGAATAAGTTG 3'

FG13      27155      G    0.88     5' TGGAGGAGAATCATCTCA 3'
                     A    0.12     5' TGGAGGAAAATCATCTCA 3'

FG8       27393      A    0.95     5' GCATGTTAGCGGTGTTCT 3'
                     G    0.05     5' GCATGTTGGCGGTGTTCT 3'

FG9       27590      G    0.95     5' AGAGCAGGAATCAAGATC 3'
                     A    0.05     5' AGAGCAGAAATCAAGATC 3'

FG10      27634      C    0.95     5' TCAGCCCCGGGGCGAGGG 3'
                     T    0.05     5' TCAGCCCTGGGGCGAGGG 3'

G1        28089      C    0.77     5' AGGGTCACCCTACAAATC 3'
                     T    0.23     5' AGGGTCATCCTACAAATC 3'

G2        28251      -    0.95     5' CTCTTTCGGTTTTAATTT 3'
                     +    0.05     5' CTCTTTCGGGTTTTAATT 3'

G6        28647      A    0.92     5' GCAAACCATAGAGCAAGC 3'
                     G    0.08     5' GCAAACCGTAGAGCAAGC 3'

G7        28689      G    0.97     5' CGACTTCGTTTTCTCTGG 3'
                     A    0.03     5' CGACTTCATTTTCTCTGG 3'

G3        28926      A    0.93     5' CAGGATTTACCTATCCTC 3'
                     G    0.07     5' CAGGATTTACCTGTCCTC 3'

G4a       28932      C    0.97     5' TCCTCCGAGWTGGATCTT 3'
                     T    0.03     5' TCCTCTGAGWTGGATCTT 3'

G4b       28936      T    0.92     5' TCCTCYGAGTTGGATCTT 3'
                     A    0.08     5' TCCTCYGAGATGGATCTT 3'

G5        29080      C    0.93     5' ATTTATTCTACTCTCACA 3'
                     T    0.07     5' ATTTATTTTACTCTCACA 3'

GA1       29347      C    0.51     5' CTCAAACCGTCCTCAGGG 3'
                     T    0.49     5' CTCAAACTGTCCTCAGGG 3'

GA3       29436      T    0.95     5' AGTGCAGTGGTGCAATCT 3'
                     A    0.05     5' AGTGCAGAGGTGCAATCT 3'

GA4       29527      -    0.81     5' AGGCACCCCCCACCATGC 3'
                     +    0.19     5' AGGCACCCCCCCACCATG 3'

GA5       29598      C    0.95     5' CTGGTCTCGAACTTCTGA 3'
                     T    0.05     5' CTGGTCTTGAACTTCTGA 3'

GA6       30338      G    0.70     5' GTTTTAAGTTCAATCTGT 3'
                     A    0.30     5' GTTTTAAATTCAATCTGT 3'

GA7       30405      G    0.83     5' TGACACAGTGCTGAGGCC 3'
                     T    0.17     5' TGACACATTGCTGAGGCC 3'

GA8       30668      C    0.75     5' GCTCTTTCAGACCCACAG 3'
                     T    0.25     5' GCTCTTTTAGACCCACAG 3'

GA9       30866      A    0.75     5' GTGACAAACCTAAATACA 3'
                     C    0.25     5' GTGACAACCCTAAATACA 3'

GA10      30939      C    0.83     5' CTTATGACCAATCTGCAA 3'
                     T    0.17     5' CTTATGATCAATCTGCAA 3'

GA11      31102      G    0.75     5' AGCGAATGGAGACCAGCT 3'
                     A    0.25     5' AGCGAATAGAGACCAGCT 3'

GA12      31197      C    0.83     5' TTGGGAACAAACTTCTTC 3'
                     T    0.17     5' TTGGGAATAAACTTCTTC 3'

A1        31309      C    0.93     5' CAGTCGAAGCACTCCCCC 3'
                     T    0.07     5' CAGTTGAAGCACTCCCCC 3'

A2        31352      A    0.95     5' TAGTCTAAATTCCCTCCT 3'
                     G    0.05     5' TAGTCTAGATTCCCTCCT 3'

A3        31457      C    0.92     5' ACACTATCTTCCCCAGAA 3'
                     G    0.08     5' ACACTATGTTCCCCAGAA 3'

A4        31520      C    0.76     5' CGTGTGGCACCAATTCAG 3'
                     T    0.24     5' CGTGTGGTACCAATTCAG 3'

A5        31660      C    0.96     5' TTCCTTTCTCTCTGACTT 3'
                     T    0.04     5' TTCCTTTTTCTCTGACTT 3'

A6        31858      +    0.75     5' CTCCCCGGCACTTCCGTC 3'
                     -    0.25     5' ACTCCCCGCACTTCCGTC 3'

A7        31882      C    0.75     5' AAACGTTCTGCTGCCTCC 3'
                     G    0.25     5' AAACGTTGTGCTGCCTCC 3'

A11       32034      +    0.79     5' ACTCAATAAATGTTTAAA 3'
                     -    0.21     5' AACATGGTTAATGTTTAA 3'

A12       32055      C    0.75     5' CAGCTGACTAAAACAAAA 3'
                     G    0.25     5' CAGCTGAGTAAAACAAAA 3'

A13       32562      C    0.95     5' TACCGAGCAGCTGGGACT 3'
                     A    0.05     5' TACCGAGAAGCTGGGACT 3'

A9        33090      T    0.93     5' CATTGTATGCATGTAACA 3'
                     C    0.07     5' CATTGTACGCATGTAACA 3'

A10       33432      T    0.73     5' GACTCTGTCTCTACATAA 3'
                     C    0.27     5' GACTCTGCCTCTACATAA 3'

AB1       33850      C    0.75     5' GAATACACTTACTCTCTC 3'
                     T    0.25     5' GAATACATTTACTCTCTC 3'

AB2       34003      G    0.83     5' GTTTGTTGTTTGTTGTTT 3'
                     T    0.17     5' GTTTGTTGTTTTTTGTTT 3'

AB3       34044      T    0.95     5' CAGTAGCTGGGACTTCAG 3'
                     C    0.05     5' CAGTAGCCGGGACTTCAG 3'

AB4       34089      T    0.99     5' AAATACATGTTTTAAATA 3'
                     C    0.01     5' AAATACACGTTTTAAATA 3'

AB12      34407      C    0.85     5' ACCCCGTCTCYACTGAAA 3'
                     A    0.15     5' ACCCCGTATCYACTGAAA 3'

AB5       34410      T    0.83     5' CCGTMTCTACTGAAAACA 3'
                     C    0.17     5' CCGTMTCCACTGAAAACA 3'

AB13      34423      C    0.93     5' AAACACACAAAAAATCAG 3'
                     A    0.07     5' AAACACAAAAAAAATCAG 3'

AB14      34706      C    0.79     5' AATGATTCACTAACATAT 3'
                     T    0.21     5' AATGATTTACTAACATAT 3'

AB8       34729      T    0.85     5' CCTGCTCTAGCAAATGAA 3'
                     C    0.15     5' CCTGCTCCAGCAAATGAA 3'

AB9       34824      T    0.74     5' AAGGAAATAGAGCTTCTT 3'
                     C    0.26     5' AAGGAAACAGAGCTTCTT 3'

AB10      34855      G    0.99     5' GTTCCAGGCCTGAGTTAT 3'
                     C    0.01     5' GTTCCAGCCCTGAGTTAT 3'

AB11      34947      -    0.98     5' ATGTCAAAAAAACAGGTC 3'
                     +    0.02     5' ATGTCAAAAAAAACAGGT 3'

AB6       35095      T    0.60     5' TAAAAAGTAAGCAACAAC 3'
                     A    0.40     5' TAAAAAGAAAGCAACAAC 3'

B2        35522      G    0.77     5' AGCATATGCTTCCTAATA 3'
                     A    0.23     5' AGCATATACTTCCTAATA 3'

B3        35535      A    0.97     5' TAATAAGATGAAATGCAA 3'
                     G    0.03     5' TAATAAGGTGAAATGCAA 3'

B4        35594      -    0.64     5' TTCATCTAAATCTAGTCA 3'
                     +    0.36     5' TTCATCTAAAATCTAGTC 3'

B8        35843      C    0.93     5' TATAAAAGCACTTTTCAG 3'
                     A    0.07     5' TATAAAAGAACTTTTCAG 3'

B9        36007      G    0.75     5' TTACTTCGGAATGAATTC 3'
                     A    0.25     5' TTACTTCAGAATGAATTC 3'

B10       36501      -    0.77     5' ATGTTTTATATATAACAA 3'
                     +    0.23     5' ATGTTTTAATATATAACA 3'

B5        36968      C    0.62     5' ACAGAGTCTCGCTCTGTT 3'
                     T    0.38     5' ACAGAGTTTCGCTCTGTT 3'

B6        37003      G    0.52     5' ATGGTGCGATCTCAGCTC 3'
                     A    0.48     5' ATGGTGCAATCTCAGCTC 3'

B7        37366      T    0.52     5' AAATACATACATAAAATT 3'
                     G    0.48     5' AAATACAGACATAAAATT 3'

BC3       38020      C    0.55     5' GACTCCATCTCAWAWAAA 3'
                     T    0.45     5' GACTCCATTTCAWAWAAA 3'

BC4       38149      T    0.52     5' CCTACCCTTACCCCCAGC 3'
                     C    0.48     5' CCTACCCCTACCCCCAGC 3'

BC5       38383      T    0.59     5' TTACTTATATTTATGGAA 3'
                     C    0.41     5' TTACTTACATTTATGGAA 3'

BC6       38409      C    0.94     5' TTCGTTTCTTATTTGTGT 3'
                     T    0.06     5' TTCGTTTTTTATTTGTGT 3'

BC7       38666      G    0.80     5' CCTCTAAGCTTGAATCAG 3'
                     A    0.20     5' CCTCTAAACTTGAATCAG 3'

BC8       38940      C    0.98     5' GAATCCTCCCCAACTCAT 3'
                     T    0.02     5' GAATCCTTCCCAACTCAT 3'

BC9       39293      G    0.59     5' ATAGAAGGAACAAACCTC 3'
                     A    0.41     5' ATAGAAGAAACAAACCTC 3'

C1        39997      T    0.61     5' ACCAACCTGACAATCAAA 3'
                     A    0.39     5' ACCAACCAGACAATCAAA 3'

C2        40292      A    0.61     5' AAAATTCATATGGAACAA 3'
                     C    0.39     5' AAAATTCCTATGGAACAA 3'

C3        40306      C    0.56     5' ATGGAACAACAACAAAAA 3'
                     T    0.44     5' ATGGAACAACAATAAAAA 3'

C4        41868      A    0.52     5' ACTAAAAGTAGATCTACC 3'
                     T    0.48     5' ACTAAAAGTAGTTCTACC 3'

C5        41875      A    0.93     5' TCTACCATTTGATCTAGC 3'
                     G    0.07     5' TCTACCGTTTGATCTAGC 3'

C6        41930      C    0.52     5' GTCATTACATCAAAAAGA 3'
                     T    0.48     5' GTCATTATATCAAAAAGA 3'

C7        42036      G    0.98     5' TGAAATCGTACTCATCCA 3'
                     A    0.02     5' TGAAATCATACTCATCCA 3'

D1        44495      +    0.95     5' CTAAACATACAAAAATTA 3'
                     -    0.05     5' CTAAACACAAAAATTATC 3'

D2        45139      T    0.61     5' TATTCACTTACTGTACAA 3'
                     G    0.39     5' TATTCACGTACTGTACAA 3'

E1        48876      G    0.93     5' CTATTTTGGAATAAAGTC 3'
                     T    0.07     5' CTATTTTTGAATAAAGTC 3'

E2        49185      +    0.59     5' GCAGTCAGACAAAATATT 3'
                     -    0.41     5' GCAGTCAAAATATTCTAT 3'

E3        49258      T    0.89     5' GTAATCCTTGACATAGAC 3'
                     C    0.11     5' GTAATCCCTGACATAGAC 3'

E4        49345      C    0.90     5' AACGCGTCTCTATTAAGT 3'
                     G    0.10     5' AACGCGTGTCTATTAAGT 3'

E5        49387      A    0.95     5' ATTCTCAAAAGGGAACCA 3'
                     G    0.05     5' ATTCTCAGAAGGGAACCA 3'

DS4       50965      A    0.90     5' GGCAGCTATGGCCTCAGG 3'
                     G    0.10     5' TGAATGGGGGCTCTGTGT 3'

DS6       52807      C    0.69     5' CTGTAATCCTGGCTACTT 3'
                     T    0.31     5' CTGTAATTCTGGCTACTT 3'

DS9       55021      C    0.62     5' TCACTGCCTGAGCATCCC 3'
                     T    0.38     5' TCACTGCTTGAGCATCCC 3'

DS14      57853      C    0.73     5' GATGGGGCTTAAGCAAAA 3'
                     A    0.27     5' GATGGGGATTAAGCAAAA 3'

DS17      59869      A    0.88     5' GCTTGAGATTTTCCCCAC 3'
                     C    0.12     5' GCTTGAGCTTTTCCCCAC 3'

DS20      63524      A    0.58     5' CGCGCGCATTTCGTGGGG 3'
                     T    0.42     5' CGCGCGCTTTTCGTGGGG 3'

DS21      64583      T    0.58     5' AATTCTTTGTCACATTCT 3'
                     G    0.42     5' AATTCTTGGTCACATTCT 3'

DS23      66353      A    0.94     5' GTTCTCAATAGCCACATG 3'
                     G    0.06     5' GTTCTCAGTAGCCACATG 3'

DS26      68233      A    0.65     5' GACAGAAAGACCATATTC 3'
                     G    0.35     5' GACAGAAGGACCATATTC 3'

H1        71802      G    0.90     5' TGGAAGAGAATAATACAA 3'
                     T    0.10     5' TGGAAGATAATAATACAA 3'

H5        72742      A    0.93     5' TGTTTAAAATACTCCAAA 3'
                     C    0.07     5' TGTTTAACATACTCCAAA 3'

H3        73191      G    0.99     5' TTCTCTAGGAATAGCTCT 3'
                     A    0.01     5' TTCTCTAAGAATAGCTCT 3'

DS31      75194      T    0.57     5' GAGGTTCTTCTTTGAAGG 3'
                     C    0.43     5' GAGGTTCCTCTTTGAAGG 3'

HA1       75717      G    0.89     5' ACTCTAGGTGGCTGTGTC 3'
                     A    0.11     5' ACTCTAGATGGCTGTGTC 3'

HA2       75929      C    0.93     5' GACACACACACATATATA 3'
                     T    0.07     5' GACACACATACATATATA 3'

HA3       77318      C    0.88     5' CTTCCCACTCCTTCTGCA 3'
                     T    0.12     5' CTTCCCATTCCTTCTGCA 3'

HA4       77699      C    0.65     5' ATCTCCTCCGCCTCCTCT 3'
                     T    0.35     5' ATCTCCTCTGCCTCCTCT 3'

HA5       77709      A    0.52     5' CTCCTCTAATTATGACTT 3'
                     T    0.48     5' CTCCTCTTATTATGACTT 3'

H6        78004      C    0.90     5' CCTTGCCCGAATTTGTAG 3'
                     A    0.10     5' CCTTGCCAGAATTTGTAG 3'

HB1       80100      C    0.90     5' ACCCAGGCTAGAGTGCAG 3'
                     G    0.10     5' ACCCAGGGTAGAGTGCAG 3'

HB2       80253      C    0.66     5' GTTTCATCATGTTTGCCA 3'
                     T    0.34     5' GTTTCATTATGTTTGCCA 3'

HB3       80281      T    0.98     5' AAACTCCTGACCTCAGGT 3'
                     C    0.02     5' AAACTCCCGACCTCAGGT 3'

HB4       80420      T    0.93     5' ACAATCATGGCTCACTGC 3'
                     C    0.07     5' ACAATCACGGCTCACTGC 3'

HB5       80542      +    0.66     5' GTAGAGACAGGGTCTCGC 3'
                     -    0.34     5' GTAGAGACGGTCTCGCTG 3'

H8        81796      C    0.93     5' CTGATGACGTGACTATGT 3'
                     T    0.07     5' CTGATGATGTGACTATGT 3'

H9        81919      C    0.90     5' GCTTCTACGTCTAGCTGC 3'
                     T    0.10     5' GCTTCTATGTCTAGCTGC 3'

H10       83221      C    0.93     5' GGATCTCCTCTTAGGGTA 3'
                     T    0.07     5' GGATCTCTTCTTAGGGTA 3'

H11       83358      C    0.93     5' TTCCCCCAACAAGGCAAT 3'
                     A    0.07     5' TTCCCCCCACAAGGCAAT 3'

HC1       83981      G    0.93     5' CTGTCCTGGGAAGATAAC 3'
                     A    0.07     5' CTGTCCTAGGAAGATAAC 3'

HC2       85056      C    0.93     5' CAGTATCCTCTCTAGTCT 3'
                     G    0.07     5' CAGTATCGTCTCTAGTCT 3'

H12       85170      G    0.63     5' ATATCTGGTTTTGGTTTA 3'
                     A    0.37     5' ATATCTGATTTTGGTTTA 3'

H13       85418      C    0.97     5' TATAATTCAGGGATCATA 3'
                     G    0.03     5' TATAATTGAGGGATCATA 3'

H22       87154      A    0.97     5' AGAGGCAATAAAAGAAGG 3'
                     G    0.03     5' AGAGGCAGTAAAAGAAGG 3'

H23       87229      A    0.97     5' ATAATTAACAAATAAGTA 3'
                     G    0.03     5' ATAATTAGCAAATAAGTA 3'

HD2       88732      C    0.65     5' CAATCCTCTTTTGTTTAG 3'
                     G    0.35     5' CAATCCTGTTTTGTTTAG 3'

HD3       89298      A    0.68     5' TATGAAAAAATGTTCAAC 3'
                     C    0.32     5' TATGAAACAATGTTCAAC 3'

Jjh12     90621      G    0.92     5' CAGACAAGGGTTTTTGTA 3'
                     C    0.08     5' CAGACAACGGTTTTTGTA 3'

JJ1       93444      G    0.99     5' GAAAGACGGAGGATTGAA 3'
                     A    0.01     5' GAAAGACAGAGGATTGAA 3'

JJ3       94019      A    0.55     5' CAATCTCATTAGTTTGAC 3'
                     T    0.45     5' CAATCTCTTTAGTTTGAC 3'

JJ4       94225      T    0.97     5' CAGTTTATGTACTTGAAA 3'
                     C    0.03     5' CAGTTTACGTACTTGAAA 3'

JJ5       94679      C    0.96     5' AGCAGTGCGCACAAGACT 3'
                     A    0.04     5' AGCAGTGAGCACAAGACT 3'

JJ6       95104      T    0.51     5' GGTGTGGTTGATGTTGCT 3'
                     C    0.49     5' GGTGTGGCTGATGTTGCT 3'

JJ7       95164      A    0.61     5' AATGAGGATGTAAATTTG 3'
                     C    0.39     5' AATGAGGCTGTAAATTTG 3'

J8        95724      A    0.86     5' TCCCTTTAGWAATGGAGT 3'
                     G    0.14     5' TCCCTTTGGWAATGGAGT 3'

J1        95726      A    0.92     5' CCTTTRGAAATGGAGTGT 3'
                     T    0.08     5' CCTTTRGTAATGGAGTGT 3'

J2        95865      A    0.78     5' GATGTAGAAGGTACACAA 3'
                     G    0.22     5' GATGTAGGAGGTACACAA 3'

J3        96041      G    0.58     5' GGCTTTGGGGTAAAGGAA 3'
                     A    0.42     5' GGCTTTGAGGTAAAGGAA 3'

J4        96128      G    0.60     5' GAGATGGGTTCCCCAGGC 3'
                     A    0.40     5' GAGATGGATTCCCCAGGC 3'

J13       97182      C    0.83     5' TTAGCAACTTGGGGGACC 3'
                     T    0.17     5' TTAGCAATTTGGGGGACC 3'

J14       97651      G    0.93     5' GAACACCGCCAGGCACAT 3'
                     C    0.07     5' GAACACCCCCAGGCACAT 3'

Jjk1      97764      C    0.95     5' GCAGACCCCTCATACCCC 3'
                     T    0.05     5' GCAGACCTCTCATACCCC 3'

Jjk2      97831      C    0.83     5' ATTTCTTCCATACCCTGA 3'
                     T    0.17     5' ATTTCTTTCATACCCTGA 3'

Jjk13     98414      G    0.83     5' GTCAGTGGAAGGAACTTA 3'
                     A    0.17     5' GTCAGTGAAAGGAACTTA 3'

Jjk15     98757      T    0.80     5' ACCACCATGCCTGGCTAA 3'
                     C    0.20     5' ACCACCACGCCTGGCTAA 3'

Jjk16     98792      G    0.80     5' AGGGATGGGGTTTCACCA 3'
                     C    0.20     5' AGGGATGCGGTTTCACCA 3'

Jjk3      98977      G    0.81     5' CAAAGTGGCAGGATCCCA 3'
                     A    0.19     5' CAAAGTGACAGGATCCCA 3'

Jjk5      99046      C    0.63     5' AGAGATTCCCAKTGCAGG 3'
                     T    0.37     5' AGAGATTTCCAKTGCAGG 3'

Jjk9      99113      T    0.58     5' TCCCCTTTCAGGTAAGGA 3'
                     C    0.42     5' TCCCCTTCCAGGTAAGGA 3'

Jjk4      99122      G    0.88     5' AGGTAAGGAATAGGGAAA 3'
                     A    0.12     5' AGGTAAGAAATAGGGAAA 3'

Jjk18     99148      C    0.59     5' TAGGTCTCCTAGGATCCA 3'
                     G    0.41     5' TAGGTCTGCTAGGATCCA 3'

Jjk14     99163      A    0.59     5' CCAGAAAATCARAATACT 3'
                     G    0.41     5' CCAGAAAGTCARAATACT 3'

Jjk10     99336      C    0.83     5' AGGAGTGCGTGTGTGTGT 3'
                     T    0.17     5' AGGAGTGTGTGTGTGTGT 3'

Jjk11     99380      +    0.91     5' GTGAGAGAAAGAGAGGAA 3'
                     -    0.09     5' GTGAGAGAGAGAGGAAAA 3'

Jjk12     99397      +    0.96     5' AAAAGAGAAGGAGTGGAA 3'
                     -    0.04     5' AAAAGAGGAGTGGAAGAG 3'

Jjk6      99445      G    0.97     5' GAGAGGAGAGAAGTGGAG 3'
                     A    0.03     5' GAGAGGAAAGAAGTGGAG 3'

Jjk7      99627      G    0.99     5' TTTAAAGGTCATCTAGTC 3'
                     C    0.01     5' TTTAAAGCTCATCTAGTC 3'

Jjk8      99748      C    0.67     5' GCGTTGACCCCACATTTG 3'
                     G    0.33     5' GCGTTGAGCCCACATTTG 3'

J5       100281      C    0.67     5' AGGATTCCAAGAGGCCCC 3'
                     T    0.33     5' AGGATTCTAAGAGGCCCC 3'

J6       100470      G    0.51     5' AGAGGCCGGGGACAGAAG 3'
                     A    0.49     5' AGAGGCCAGGGACAGAAG 3'

J7       100629      T    0.82     5' CCCTCTTTCCTCTGCTCT 3'
                     C    0.18     5' CCCTCTTCCCTCTGCTCT 3'

JK4      103442      T    0.51     5' GGGACTATAGGCGCCCGC 3'
                     C    0.49     5' GGGACTACAGGCGCCCGC 3'

Kk3      110885      C    0.99     5' GATAAACCCTATTTGTTC 3'
                     G    0.01     5' GATAAACGCTATTTGTTC 3'

Kk4      110909      A    0.89     5' TAGTTACACATTTACTGT 3'
                     T    0.11     5' TAGTTACTCATTTACTGT 3'

Kk5      111204      C    0.52     5' GTATTCTCTTCCTCTTTA 3'
                     G    0.48     5' GTATTCTGTTCCTCTTTA 3'

K1       119361      G    0.99     5' TGTTATGGTGTGTTTCTT 3'
                     C    0.01     5' TGTTATGCTGTGTTTCTT 3'

K3       120299      T    0.91     5' AGGTGAGTGTCCACTATT 3'
                     C    0.09     5' AGGTGAGCGTCCACTATT 3'

K5       128910      G    0.99     5' TGTAGAAGCTGCATTGTT 3'
                     A    0.01     5' TGTAGAAACTGCATTGTT 3'

K7       130067      C    0.72     5' GAGTTCYCGTATGTCCCC 3'
                     T    0.28     5' GAGTTCYTGTATGTCCCC 3'

K8       130731      A    0.59     5' GATTCAGATATTTCCCTG 3'
                     G    0.41     5' GATTCAGGTATTTCCCTG 3'

L1       144388      G    0.66     5' AATCCTTGCTGAAATAGA 3'
                     C    0.34     5' AATCCTTCCTGAAATAGA 3'

L3       144554      T    0.91     5' CATCCAATAGGAGTCTTC 3'
                     C    0.09     5' CATCCAACAGGAGTCTTC 3'

L4       144647      G    0.91     5' ATGCCATGAGAAAAAAAT 3'
                     A    0.09     5' ATGCCATAAGAAAAAAAT 3'

L5       145031      C    0.87     5' GTGTTGCCCATTAGTCAC 3'
                     T    0.13     5' GTGTTGCTCATTAGTCAC 3'

M1       164994      G    0.79     5' GTGGAGTGGCTGCCGTGA 3'
                     A    0.21     5' GTGGAGTAGCTGCCGTGA 3'

M2       165497      T    0.58     5' AATCCCCTATTGTCCCAG 3'
                     C    0.42     5' AATCCCCCATTGTCCCAG 3'

M5       166360      G    0.63     5' AGACTGAGGTCCTCCAAG 3'
                     T    0.37     5' AGACTGATGTCCTCCAAG 3'

T1       190501      G    0.57     5' CCAGCCTGGCCAACATGG 3'
                     T    0.43     5' CCAGCCTTGCCAACATGG 3'

T2       190648      C    0.56     5' AAGATGGCGCCACTGCAT 3'
                     T    0.44     5' AAGATGGTGCCACTGCAT 3'

T3       191492      C    0.56     5' CTGTGTGCTCCATTGTTA 3'
                     T    0.44     5' CTGTGTGTTCCATTGTTA 3'

T4       192204      T    0.59     5' CTCTGGGTCAGGAAGGAT 3'
                     A    0.41     5' CTCTGGGACAGGAAGGAT 3'

T5       192234      G    0.91     5' AATTACTGTTCTAAACAG 3'
                     A    0.09     5' AATTACTATTCTAAACAG 3'

T6       192271      C    0.52     5' AGAACCAAAGCCCAGTAC 3'
                     T    0.48     5' AGAACCAAAGCTCAGTAC 3'

T7       192278      C    0.52     5' CAGTACCGGGCATTTCCC 3'
                     G    0.48     5' CAGTACGGGGCATTTCCC 3'

T8       192774      G    0.59     5' CCGCCTCGGCCTCCCAAA 3'
                     A    0.41     5' CCGCCTCAGCCTCCCAAA 3'

T9       192937      A    0.59     5' ACAGATAAAGTTGCCCTT 3'
                     C    0.41     5' ACAGATACAGTTGCCCTT 3'

T10      193139      C    0.55     5' AAGGCCTTGGCTGGGGAA 3'
                     T    0.45     5' AAGGCCTTGGTTGGGGAA 3'

T11      193147      G    0.59     5' TGGGGAAGCGAAAGCGAA 3'
                     A    0.41     5' TGGGGAAACGAAAGCGAA 3'

T12      193262      T    0.51     5' GCAGAAGTCCCCGGAGCT 3'
                     C    0.49     5' GCAGAAGCCCCCGGAGCT 3'

T13      193332      G    0.55     5' CAACAGGGACGCAGCCCA 3'
                     A    0.45     5' CAACAGGAACGCAGCCCA 3'

T14      193604      A    0.51     5' ATAGGATAAAATGAGAAG 3'
                     G    0.49     5' ATAGGATGAAATGAGAAG 3'

T15      194255      G    0.60     5' GGGCCTGGGCACCAGCAC 3'
                     C    0.40     5' GGGCCTGCGCACCAGCAC 3'

T16      194418      G    0.71     5' GGTAGGTGGTGGGCAGCT 3'
                     A    0.29     5' GGTAGGTAGTGGGCAGCT 3'

T17      194676      A    0.61     5' GTCTCAGATGGAATGTCT 3'
                     G    0.39     5' GTCTCAGGTGGAATGTCT 3'

T18      194791      T    0.51     5' GTCACTCTCTCAGGATGG 3'
                     C    0.49     5' GTCACTCCCTCAGGATGG 3'

T19      194816      C    0.60     5' TCTCCCTCTCACTCTTCT 3'
                     T    0.40     5' TCTCCCTTTCACTCTTCT 3'

T20A     194844      T    0.58     5' ATCTTGCTARTCCCTGAA 3'
                     C    0.42     5' ATCTTGCCARTCCCTGAA 3'

T20B     194846      A    0.58     5' ATCTTGCYAATCCCTGAA 3'
                     G    0.42     5' ATCTTGCYAGTCCCTGAA 3'

T21      194927      C    0.72     5' CCTTTCTCTTTCTAGACA 3'
                     T    0.28     5' CCTTTCTTTTTCTAGACA 3'

T22      195038      A    0.92     5' TTACCCAAATCCCAGCCG 3'
                     G    0.08     5' TTACCCAGATCCCAGCCG 3'

T23      195155      C    0.65     5' CTACAGTCGTGCACTGCA 3'
                     T    0.35     5' CTACAGTTGTGCACTGCA 3'

T24      195172      T    0.59     5' ATAACGATGTTTAGGTCA 3'
                     A    0.41     5' ATAACGAAGTTTAGGTCA 3'

T25      195311      C    0.70     5' GTGCAGTCATATGTTGTA 3'
                     T    0.30     5' GTGCAGTTATATGTTGTA 3'

T26      195344      T    0.98     5' GGAGCAATAGGCTAAACT 3'
                     A    0.02     5' GGAGCAAAAGGCTAAACT 3'

T27      195426      A    0.50     5' ATACAACAATGAAACCAT 3'
                     G    0.50     5' ATACAACGATGAAACCAT 3'

T28      195441      T    0.50     5' CATCTAATGACACATTTC 3'
                     C    0.50     5' CATCTAACGACACATTTC 3'

T29a     195506      C    0.57     5' TCTGACTCTYCCAAACGC 3'
                     A    0.43     5' TCTGACTATYCCAAACGC 3'

T29b     195508      C    0.57     5' TCTGACTMTCCCAAACGC 3'
                     T    0.43     5' TCTGACTMTTCCAAACGC 3'

T30      195655      A    0.90     5' AGGATGAAAGATGGGAAT 3'
                     C    0.10     5' AGGATGACAGATGGGAAT 3'

T31      195885      C    0.58     5' TTGTAGTCTTCTATTGTG 3'
                     T    0.42     5' TTGTAGTTTTCTATTGTG 3'

T32      196317      A    0.93     5' GGCCTGGAGTCCAGGTCT 3'
                     T    0.07     5' GGCCTGGTGTCCAGGTCT 3'

T33      196905      G    0.56     5' CTCAGCCGTTAGGGGAGA 3'
                     A    0.44     5' CTCAGCCATTAGGGGAGA 3'

T34      196918      G    0.84     5' GGAGAAGGTATATTGTAG 3'
                     A    0.16     5' GGAGAAGATATATTGTAG 3'

T35      197010      +    0.91     5' CTGTAAACAAAAATGTAA 3'
                     -    0.09     5' AACTGTAAAAAATGTAAA 3'

T36a     197372      G    0.98     5' TTGGGTARCCATCATCAC 3'
                     T    0.02     5' TTGGTTARCCATCATCAC 3'

T36b     197374      A    0.92     5' TTGGKTAACCATCATCAC 3'
                     G    0.08     5' TTGGKTAGCCATCATCAC 3'

T37      197522      A    0.54     5' TGACTCCAGGTGCGGTAC 3'
                     C    0.46     5' TGACTCCCGGTGCGGTAC 3'

T38      197716      G    0.88     5' CATTTGCGTTGTTTCCAC 3'
                     A    0.12     5' CATTTGCATTGTTTCCAC 3'

T39      197887      +    0.54     5' GACCTCACAATCATGGCG 3'
                     -    0.46     5' AGACCTCAAATCATGGCG 3'

T40      198854      G    0.89     5' CTTTCCTGATTCAGACAC 3'
                     A    0.11     5' CTTTCCTAATTCAGACAC 3'

T41      199313      G    0.89     5' CCTGCTCGTAAGGAGGGT 3'
                     A    0.11     5' CCTGCTCATAAGGAGGGT 3'

T42      199501      G    0.82     5' ACTTGGGGGTGCAGATGC 3'
                     T    0.18     5' ACTTGGGTGTGCAGATGC 3'

T43      199802      A    0.85     5' CACATGTATACATCCTGT 3'
                     G    0.15     5' CACATGTGTACATCCTGT 3'

T44      199880      A    0.91     5' CCCACCCATATTATTCTG 3'
                     C    0.09     5' CCCACCCCTATTATTCTG 3'

T45      200052      C    0.81     5' ATTTCCACTTGTGGTATC 3'
                     T    0.19     5' ATTTCCATTTGTGGTATC 3'

T46      200568      T    0.93     5' TTCTTCATGTATTAGCTG 3'
                     C    0.07     5' TTCTTCACGTATTAGCTG 3'

T47      200936      G    0.81     5' AKGGACTGTATATCCTTT 3'
                     A    0.19     5' AKGGACTATATATCCTTT 3'

T49      201375      T    0.86     5' CTGCTGCTAATGCATAAT 3'
                     G    0.14     5' CTGCTGCGAATGCATAAT 3'

T51      201849      T    0.54     5' CTGTCCCTGCTGCACAGG 3'
                     C    0.46     5' CTGTCCCCGCTGCACAGG 3'

U1       210241      T    0.73     5' ATTGAGATGTACGTTTTA 3'
                     C    0.27     5' ATTGAGACGTACGTTTTA 3'

U2       210333      C    0.91     5' TGCCACCCTCAAAAAACA 3'
                     T    0.09     5' TGCCACCTTCAAAAAACA 3'

U4       213653      T    0.91     5' TCCTTTCTACAGATACCT 3'
                     C    0.09     5' TCCTTTCCACAGATACCT 3'

U5       213817      C    0.55     5' GGTAACTCCTAACGTACT 3'
                     A    0.45     5' GGTAACTACTAACGTACT 3'

U6       214007      A    0.76     5' TATATATATCACATACTA 3'
                     G    0.24     5' TATATATGTCACATACTA 3'

U7       215332      C    0.99     5' TTAGGATCCTTATTGTGT 3'
                     T    0.01     5' TTAGGATTCTTATTGTGT 3'

U8       215648      C    0.67     5' TACTTGTCACTGTTATTT 3'
                     A    0.33     5' TACTTGTAACTGTTATTT 3'

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Last updated: 8 September, 2005
Celia A. May
The views expressed in this document are those of the document owner, Alec J. Jeffreys.