Polymorphisms in the HLA-DNA region of the human MHC, spanning crossover hotspots DNA 1-3

The sequence is taken from Beck et al. (1999) and is orientated centromere to telomere. Coordinates are given relative to SNP DA1+/- located at position 3,260,370 of the current consensus MHC sequence. Exons are shown in blue, Alu repeats in red and microsatellites in green. The locations of PCR primers used for amplification of genomic DNA and for resequencing for SNP discovery are indicated below the sequence. Regions resequenced are underlined. The alternative allele at each SNP is shown below the sequence. The approximate positions of the centres of meiotic crossover hotspots DNA 1-3 are also shown.

 

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18319    GGTTTTGCGCTGGCCTAGGACTCCAGCTGGCCCTCCTTTCTCTTTACACACATGACACCA
                   ------- R-6.0F ---->

18379    ACACAGATGGCCACTAGTGGGTCAAAATAATACCTTTAGGGAGTGCCGACACCTCAAAAG
18439    AAAAACAGCAAACAGGACCATCTATGTCCTTGAAAGAAGTGGTAGAAAATATAGACCAGC
18499    CGCTTAAAATGAGCATTAAAAGTGCACTTTAAAAGTCAGAAGCTATTATAATATGAAAAA

                                 DD15A/C          DD19-/+
18559    ATAGAGAATATAGGGAAAACACCTAGAAGTTCTAGGTGTAAAAAATATATATAATAGTCA
                                    C               |+T

18619    AAGTAAAAGCCACATTAATGGGATAAATAGTGGGAGAGATGCAACTGAAAAACAAAACAG

18679    AAAGATGGAGGACTACACTGAGGAGCTAGTTCAGAACAAAAGAGGGAAGAATTGAGAAGT
18739    CATCAATAGAAAAGTCAGGGGAAAAGGAGGAGAGAATTATCCAAATATAGATTATATGAG

                            DD20-/+
18799    TTTCACAAAGACAAAAAATAGAGGAGAAAAATAGTTAAAGAAATAAAAAGATGAATTCCC
                               |+GAGA

18859    AGAATTAAAAGATAGAGAAGATCCATAATGTCTTACAGAGAGAAGGAAAAACCCACTCTA
18919    GACACACTAGCAAAATTTAAAAATATCAAAGACAATGAGAAAATTCTAGAAGATTCCAGC

                                               length polymorphic (A)n
18979    ATGAAAGACTGACATGGGATTTTCTAACTGTGACATTGGATGCAAAAAAAAAAATTTGGA
                                <---- R-5.3R -------           ------

                             DD21+/-  DD22T/C
19039    ATGATGTTATTTAGAATATTAAAGGGGAAAATACTTCAAATAGTATGTAATACACAGCTA
         -- R-5.3F --->           -     C

              DD23A/T DD16G/A DD17T/C
19099    AACTTTATTCAAAAGTGCTGGTATAATTTTAAAAAATTATCAAGCATACAAGACTTTAGA
                    T    A    C
                                   DD24G/T DD18T/C
19159    AGGTTTGCTATGCAAATTCCCACATCTGAAAGGTTTTGGAAGAAGAATTCTAATCAGAGA
                                         T C

19219    ACGCATTCTAGAAGGTGCCAAAAGATATGAAAAGTAATGTTGACCAAATAATTTGGTGAA

19279    GGAGAAAATATGTGAATAAATTTGAAAGCATGCTAAAGTTCTTATCCAGTCAGAGGGAAG
                                                                    <-
                                                      ---- R-5.0F ---

19339    ATGGAGAAGGTATCGGTAACACTTAAAAAAAAAAAAGGCAATGAAGATTAAAAAAGAAAA
         ------ R-5.0R -----
         --------->

            full length Alu --->
19399    CTTGGCCGGGTGTGATGGCTCACGCCTGTAATCCTAGCAGTTTGTGAGGCCGAGCCAGGC
19459    AGATTGCCTGAGCTCAGGAGGATAAGCCTGGGCAACACGGTGAAACCCCGTCTCTACTAA
19519    AATACAAAAAAAAAAAAAAAAAAATAGCCAAGCATGGTGGCATGCACCTGGAGTCCCAGC
19579    CACTCGGGAAGCTGAGGAGAATCGCTTGAACCCGGGAAGCAGAGGTTGCAGTGAGCCAGC
19639    CCAGATCATGCCACTACACTCCAGCCTGGCAACAGAGCGAGACTCCGTCTCAAAAACAAA
19699    CAAACAAACAAACAAAAAAACTTTAAAAAATAGAAATATTGAAATAAATAAGGTATTACA

                                                                DD9G/T
19759    AACAAGCCCAAGTGCATCAATATTCACAATAAACACAATCAGAATGCAGCAAAGACAGGG
                                                                   T

19819    CCATGTGCTCACCAAACCATTATATCTTCCTGCACACATAGGTAACGTACATTTTTCCAT
19879    CCCCGTGCGCCTATGTGGGGTCATTGTTTACTTCTTGCCAATGGAATGTGAGCAGAGATG
19939    GCAAATAGTTTCTGGTCCAAAACCATGGAAACAATGTGCCTTTCCCAGGTTCTCTCTCCT

                                  DD10C/G                 DD11T/C
19999    ACCTGCAAAGCTAGGAGTTCATGAAGTGCTTTTCAATAATAGAGATGCAAAGTGGAGCTT
                                     G                       C
                                                                 DD12C/G
20059    AGCCACCTTGAGGCATGTTTTGGAAAAGAGCTACAGAGTGCCCAACCTGCCTTGAACTAC
                                                                    G
       DD13C/T
20119    ACGTGGCTAAAAAATAAACCTGTGTTTTGTTAAACCACTGAGGCTTCAGTGTTTGTCTCT
          T
               DD14A/G
20179    TGCAGAAACAAGTTTGCTCACTTTGACTACCATATGAATTGAACATAGGTTAGAAGACAG
                  G

20239    AGATCGTCAGATTGAATCAGAAGCAAAAATCTATATTTATGACATTTCAAGGGCTACATC
20299    TAAAGCATAAGTACAAAGGAAGAGTAAAAACAAAAGAGTAGAAAAAGATACAGTGAACAA
20359    ATACCCAAAGACAGCTGTAGAACTTATTACTATCAGACAAGACAGAGTAGGACAGAAAGA
            ----- R-3.9F ------>

20419    TTCTCAGGACAAATTGGGAAAAGGCTCAGTTCACCAAGACTGTAATAATTCCCAAGAGTA
                               <----- R-3.9R ------

20479    AACACCTTAATAACCTAAATGCAGAGAGGGCAAAAGTTGATTTAAAAATTAGAAACAAGT

                                                        5' truncated Alu -->
20539    TGAAAAACCTACAGTCACAGTTAGAGATTTAAATATACCATTCATAGGCCAGGAATTGTG
                <----- R-3.8R ------
                                                      DE1C/G
20599    GGGCATGCCTATAGTCCCAGCTACTCTGGGAGGCTGAGGCAGGAGGATCGCTTAAGCCCA
                                                         G

20659    GCTGTTTGAGGCTGCAGCGAGCCATGATTACTTCACTGCCCTCCAGCCTGAGCAACAGAG
20719    CAAGGCCCTGTCTCTAAAAAATAAATAAATAAATGCACCACTCTTAGTTATGTATAGGCC

                           DE2G/A
20779    AGTCCAAAGATAAAGAAAACCGTAATAAATTAGAATGACAAAATCCACATGCTTGATCCA
                              A

20839    ATAAACATGTACATGTATAAAATTCTGCATCACATTTATTAGAGCCCATGTGAAATATTT
20899    ACAGAAGTTCACCACACTCCAAGCCATAGAGGATTATCATGTAATTAAATTATAAGTTAA
20959    TAACAAAAAACATACTTTAAAAAATCTATGTATGTTTTCAAATAAAAAAAAACACCCGAT
                                                            ---------

21019    ACTCGACTGTTATTAACCAAAGAAGCAACATTCTTTATCATGAGTTTTTCATGGCTTTCC
         - R-3.3F ->

21079    CGTCTTTCATCTCATGGCTCCAGCTCCCACCTCACTTGGGGGGAGGTGAAGGTGGCAAGG
21139    GTCCTAACCAGGGCAGGACCAAAGCAGTGAAGACACTGTTCATTCATGCGCAGGTGTCTC

                  DE3G/T                         DE4C/T
21199    CTAGGCGCCTATGATGTGCTAGGCATTACGTAGACACTGTGGACTAGAAACGAAAAAACT
                     T                              T

21259    AAGATTAGGGCTCCCCATAAACCGGGCCATGCAAATCAATTACTAGCTGTCATTTGATTA
21319    ATTTGAAGTCAGAAGCTGTGTCTGCCCCACTTAAAATAGGCATCCCTTATTCATTGAGGA
21379    AAGAGCATTGGAGCAGGTTTTACCAGTCCACAGACTACCCGAGAACCACCTGGGGAGCAT

                                     DE5G/T
21439    GCTGAAAACACAGGTTCCCTGGCCCTGCCTTGGAAAGGCTAATCTAACCCATTAAGTAAA
                                        T

21499    GAGGAAACTCAGGAACACGTATTATAACGAACCCCCCAGGTGATTCTCATTTGGAACCAG

                              DE6C/T
21559    AGACCCGCATGATTTCCTAGCTCCCTCCAAGTTGAAAATCATCGATTTCATGGTCTTTGA
                                 T
       DE7A/G
21619    CACATGGCCTAATTTGGTTAGATTTCTCTTTACACAGACGTTAGCTTTACGTTGTTGTTG
          G

21679    TTTTGTTTTGTTTTGTTTTTTAAATATATATACTGGACTAAATTCTCCCAGTGCCTCTTA
                                        ----- R-2.6F ------>

21739    TTAGCCGAGCCCAACCAGAAGCCAAAGGCAAGGGTGATGCCGTCCTCCAGCCTGTGTCAG
21799    CCTGGAGGAGGTGCCCGGGTCCTGGAGGGACCAACAGAGAGGACCAGCACCTCTGCCCTC
21859    CTCGGGGAGTCCACGGGAGCTCTTTACACTTTGCTTTAGACCAAACAACTCCAACAATTA

                                 DE8A/C
21919    CACATTTTTTCTTACACAATGAAATTAAATAATAATAAAAGAAAAATAAAATAACATTTT
                                    C

21979    TGAAAGTGATTTAAAGTTTTAAGAGGTTTTTATTCCATTGTGTAGCCAATGTTTTCCTTT
22039    TAAAGATTATTGGTAAAGTTTATTTTACTTTCTAACTCAAAATTTGTCCACGGAAACTTC
22099    TTGGGAAAGTAGGATTCCCTGCATCGCAGATGGACATAGAGAGAGGATTTGTTGGAGCTC
22159    AGCTGCGCGGTGCTCTGACGGCCTTTTCTCTCTCTTCAGGGGGTCCCTTCTTGGAGGACG

                                                  DE9T/C
22219    TGGTAATAGTTGGTCCAAGCCCCTCCCATCCTCCAAAACTTCCTTTGGCCTCTCCTGGGG
                                                     C

22279    GCCCAGTGAATCCTTCCACCTTCTCACCCCGGCTCTTTCCCTCTTTACCCAGCAACAGAT


APPROXIMATE CENTRE OF HLA-DNA HOTSPOT 1
            |
            |                                DE10A/C
22339    ACATTCACTCAGAGAATTTCTGTGATTGGCTGAAGACAGAAGGGGTCGCCCCCATCCTCG
                                                C  ---- R-1.9F ----->

                   HLA-DNA exon 1 -->                    DE11G/C
22399    AATCTGTTTTCTTCTTCTTTACCTCCGCCTTGTTCCTGTCCTCACCACACGGACTGAGAC
                                                            C
                           DE12T/C ini
22459    TGATTTGATTAAAGCACCAGAGTGTAATGGCCCTCAGAGCAGGGCTGGTCCTGGGGTTCC
                                 C

22519    ACACCCTGATGACCCTCCTGAGCCCGCAGGAGGCAGGGGCCACCAAGGGTGAGTGCGAGG
22579    GCGAGGAGGGTGCGGCGGGGAGCAGAGATTTACGGAGTTGGGTTACATGAGGAGGTGGCA
22639    TGGAGGATGCTTGTTCCTCTCGCTCTCTGGTTTATGGGCAACTTCCTTCACCAAGAGACA

                     DE13C/T                                 DE14C/T
22699    CCCAATCCCCCTCATCTCTGTCACATCCACTCTGGACCTAAATGAAGATGCAGCTCGGTC
                        T                                       T

22759    AGCTGCGCAGGTGCCCCAGTCAGCCTTTGCTGACGTTCAGATTTCTCCTCATTCCTTCCT
22819    CCTTCCTGAGACCCAAACCTCCACCCAACAGATGCCAGCAAGCACCCTGATTTCTCTACC

                DE15T/G
22879    ACCCCTGGCCTGGAATGTGCCCGATCAAGTCCAGTTCTGTTGCAGTATTTATGCCCATGC
                   G

22939    CGGTAGTTAACTATTTACCTGTCTTTGTTCTTCGGGAGACATGAGCTGGGGTGCGGGTCT

                                              DE16C/A
22999    ACAGATGGTTCATCTTTTTTTTCTTTTATTTCCCTGGCCCCCCATTGTGCTGGGTGCATG
                                                 A
                                                 C----- R-1.3F ----->

23059    CTAGTTCCTCAATAACTGTTGCTCAAACAACTTCATAGAGTTCTACAAGAATTAAAACTT

                               DE17C/T        SapI
23119    AATCCCTAACTTCCAGAAAACTAGACAACAGTTATGGAAGAGCCACACTCAGTCATAATG
                                  T

23179    CTCTGAGATGGAGGAATTGGGACATGAACCTTGACTTCTGACTCCTCGTCCAGTGCTCTT
23239    TGTAATGCCTTGAGTTGCCTCTCCCTATCCCCTTGGTCTCTGGGTCACTAACCTTAATTC
23299    TTACCCCTGCCAGCCGTGGCCTGTTTCCCCTCACACCCACCTGCACTGCATCTCTGTGCA
23359    AAGCTCCATACTCTCCTGTCCTTAATCATTCCTCCTCATCCCACCCCCACAGTCCCACCA
23419    GCTCACAACACAGGGCCTGACAACACAGCCAGGGCAGATGACCACAGCCAAGATTTAAAT
23479    TCTGGAACCCCAAGCATGATTTTAGGCAGTCCCTCCTCTTCCCATCCTGATATGCCAGAC
23539    TGCACTGTCTCTGTGCCGACTGCAGTGTGCTGGGATGAGCCTCTTTCTTCCTGTTCTCTC

                    DE18C/T                               DE19A/T
23599    TCCCTTTCTCTCTCCCAGGGCCAGCCCAGTGTCAGAACAGGACTCTGTCCCCACACAGAA
                       T                                     T

23659    CCCAGGACGGGGCCCAGGCTCAGGGACTCAACAATCACATATTGTGGATGAGACAGACAC

                                                  HLA-DNA exon 2 -->
23719    ATTTTTTTCTCTCTCCTTGACCCTGAACTCGCCAAACACAGCTGACCACATGGGCTCCTA

23779    CGGACCCGCCTTCTACCAGTCTTACGGCGCCTCGGGCCAGTTCACCCATGAATTTGATGA
23839    GGAACAGCTGTTCTCTGTGGACCTGAAGAAAAGCGAGGCCGTGTGGCGTCTGCCTGAGTT

                                    DE20T/C
23899    TGGTGACTTTGCCCGCTTTGACCCGCAGGGTGGGCTGGCCGGCATCGCCGCAATCAAAGC
                                       C
                                                           KpnI
23959    CCATCTGGACATCCTGGTGGAGCGCTCCAACCGCAGCAGAGCCATCAACGGTACCGGCCC

                                                                 DE21T/C
24019    TCCCTCTGCCCACCCAGTCAGGCGGGAAGGTCCAGAGAAACTTCCTCCCAGTTCCTAGGT
                                                                    C
                          DE22C/G
24079    TCCCATCACTCTGGGGCGCGCTCTCAGCGCCCGCGCCTGTCATGCCCTGTTCCTTTCTTT
                             G

24139    CCCAGGAGGCTCCAGGTCTTCCCAGACCCCTTTGGCACCCCTCTCCTTGAGGAATGACAC

                           DE23A/G
24199    CTCTCACCCGGACTCCCGCCCAGGGACCAGTCAAATATAGGAGCTCCTGGCGTCCCCACT
                              G
                                  DE24C/T
24259    CCCTCCCCAGTCTCCTCTCCCTCTGTTTCCCTCCTCTCCTGCCCCAGTGGATACCCCAGA
                                     T

24319    GCATCCCCTGCCCACAGATGGCTACAAAGGGGGAACGTCCCTTAATCCCAGTCCTAGTAA
              ------- R0.0F ----->
                                             F1C/T         HLA-DNA exon 3->
24379    GGCCCTGGGGTGAGGGATGAGCCTGTGGACTCAGGGCCCGTTCCTCCTAGTGCCTCCACG
                        <----- R0.1R -------   T

24439    GGTGACCGTGCTCCCCAAGTCTCGGGTGGAGCTGGGCCAGCCCAACATCCTCATCTGCAT

                                                 F2A/G (L148L)
24499    CGTGGACAACATCTTCCCCCCTGTGATCAATATCACCTGGCTACGCAACGGCCAAACTGT
                                                   G

24559    CACTGAGGGAGTGGCCCAGACCAGCTTCTATTCCCAGCCTGACCATTTGTTCCGCAAGTT
24619    CCACTACCTGCCCTTCGTGCCCTCAGCCGAGGACGTCTATGACTGCCAGGTGGAGCACTG
24679    GGGCCTGGATGCGCCACTCCTCAGGCATTGGGGTACGGAGCCCCCTCCCCATGCACCCTC

                                                    F3G/A
24739    CTGGCCCCAGGTTTCCTTTACTCTAGAATCCTTTCATATACCACCGACTCCTTCCTTTCT
                                                      A
                HLA-DNA exon 4->
24799    CTCCTAGAGCTCCAGGTGCCTATTCCACCACCAGATGCCATGGAGACCCTGGTCTGTGCC
                                     ------ R0.5F ------>
            F4T/C (G224G)
24859    CTGGGTCTGGCCATCGGCCTGGTGGGCTTCCTCGTGGGCACCGTCCTCATCATCATGGGC
              C
                                           F10G/A
24919    ACATATGTGTCCAGTGTCCCCAGGTGCAGAGGCCCCGGGAGTCTGGGGGGTGGGGGAGGA
                                             A

24979    AAGTGGATGACTCTGAACAGGACGTGGGTGGAGAATCAGAGATTCTGTTGTGGGGAAAGA
25039    AGTCAGAAAAGAAATGGGCAGGGAGAAAAGAAGCAGAGGTGGGGTGAGAGAGTGAGGTTT
25099    TGGGGGAGGTGGGCACTCAGAGATAGGATCCCAGCATATTGAAATTGAGCAACCTCGATC

                             HLA-DNA exon 5->
                               ter
25159    GTATGTTTTCTGCTATTTTAGGTAATGATCCTTCTGAGAGAAATGACTTGTGGGAGACAC

                                   F11C/A
25219    CCTGCAGATCCTCATGGGTTTGTGACAGCCCCTGCGTGCTCAGTGCCCTTTAAGTGCATC
                                     A

25279    CCGCTGTGCTGACTTTGAGTGGGATCAACATCTGTCCTACGGGTCCCCTCTTTTTTGGCC

                                                                 F5A/C
25339    CCAGTATTCATGGCAGGGTTTGTTGGACACCTACTAGCTTCCCTTCCCATTCAACACAAA
                                                                   C

                                                               F6G/A
25399    CACACATTCTTGCTCTACCCAAAGCTCTGGCTGGCAGCACTAAATGCTTTGGTGGTGTTT
                                                                 A

25459    GCACTGTGTCCTTTCCAGGCCTTGGCCAGTTCTTCCAGGGGTGAGGCATGTGGTGCTGGG

                  F7G/A
25519    GATTGGCAGCCGTCCTGGGGCCCACACAGGTGTGTCTTGCTCCATTTGGCCCATTGTGTG
                    A

25579    TTACTTTGTGAATGAGCCATTTCACATGGACTTCATGAAATTTGCCTCCTGAGTTCAGGT
25639    TTACCCTGAAAGGGATGCAGATTATCCTGTTCCTCACGACCCCCTCAGCTAACAACAGTT

                         F8A/G
25699    CTGAAGGGTGCTGGGACAAGACAGGCTCATGGGGACTCCACTCCTGCCTGGGTTTACTCT
                           G
                                                          F9-/+
25759    GTATGAAGAGGCCACTGGTATCCTGCCATGATGTTATCTCCTTTTTCTACTTTCCCTAGA
                                                            |+T

25819    GTCCCATGCATGATAAAGAGAGGCCCAAGGCTTGGATAAGGTGGCCACTTCCCTCAGTGG
                                                ------ R1.5F ------>

                                               FG1A/G
25879    AGTCAGTCATGTTAGGTAGGAGGTGGTAGAGTCGGTCTGCAAGGTATCTCGTAAGAGGGG
                                                 G                 <-
                        FG2C/T
25939    AGGTCCACCTAGACACACTCTAAATATGTGGCCTAGAAGATTTTGGTCTACTTTTCTGTG
                          T
         --- R1.6R -------C

          FG14G/A                                            FG15A/G
25999    AACAGAATTTAAAACATACAAAGAGATAAATCACCATACCACATAGTTTATGTCAAGACC
             A                                                  G

26059    AAAATGAGCAATACAGATTACGGTTTTCAAACCAGAATGCACATAAGAACTGCTTGGGAT

                           full length Alu--->
26119    CCTTTTAAAAGTACAGGCATTGGCCTGGTGCAGTGGCTCATTCCTGTAATCCCAGCACTT

                         FG3G/A
26179    TGGGAGGCCAAGGGGACAGGACTGCTTGAGGCCAAGAGGTGGAAACCATCTTGGGCTACA
                            A
                                                    FG4G/C
26239    TAGAGAGACCCCATCTCTACAAAGAAAGATTTAAAAATTAACCAGGCATGGTGGCTCGCA
                                                      C

                               APPROXIMATE CENTRE OF HLA-DNA HOTSPOT 2
                                                            |
                                                            |
26299    CCTGTATTCCCAGCCACTGGGGAGGCTGAGGCCGGAGGAGTGCTTGAGCCCAGGAGTTCA

26359    AGGCTGCAGTGAGCCAAGATTGCGCCACTGCACTCCAGCCTAGGTGACAGAGTGAGACCC

26419    TGTCTCTAAATAAATAAATAAATAAAATATAAAAATAACAGTCATCACCCAGACCTACTG

                                           FG11G/A           FG5A/T
26479    AATTAGAATCTCGGGAGTGCAGGGGGCAGCAACAGGGGGGCTGTCTTTTCTGAGAAGGGG
                                              A                 T

26539    TCTCACTCTGTCACCAGGCTGGAGTGCCATGGCATGATCTCAGCTCACTGCAACCTCCAC
26599    CTCCTGAGTTCAAGCCATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTACAGGTGTG
26659    CGCCACTACACTCAGCTAATTTTTGTATTTTAAGTAGAGACGGGGTTTCATCATGTTGGC

                                                             ScaI
26719    CAGGATGGCCTCCATCTCTTGACCTCGTGATCCACCCACCTTCCCTCCCAAAGTACTGGA

                    <---full length Alu
26779    ATTACAGGCATTAGCCACTGTGCCCAGCCGAGGCTGTCATTTTTAACCGGCTCTGGATGA

                                                             FG6C/T
26839    CTCTGATGCAGCCATCCTGGACCTTGGCTGTGGTCTGGTAACTGGAACCCAGTGACGTAA
                                                                T
                  FG7C/T
26899    TCAGGTGCCATCGGGGGTCATGGGAAAGGGGGATCCCCAAGGTCTGAGGTGGACTAGGAA
                    T

26959    GGCTTTCTGAAGAACCTGGGTCTGTTAGGGCATCAGCCAATCAAGGTACAAGTAAATAGA
27019    GGCAAAATGAGGGTTTGAACTGTGAGCAGTTGGTCCTGGAAAAGAAAGAAACCAAGAGAT

                                  FG12A/G
27079    TATGGGGACTCAATGGGCTTCTTAAGAGAGAATAAGTTGAAATCAATGACCAGAAGACCC
                                     G
                      FG13G/A
27139    TGATGGAAGTGGAGGAGAATCATCTCAGGCAAACTTTTTGTGTGCCAGTAACAGAAACCC
                         A

27199    TCTTTGTGTGATCACATGCAAAGTATAGGATATTTGCAATATAGCCATGGGGAGGAGTGC
                                            <----- R2.9R -------

27259    AGGGCCCAAGGGTAGATTTTAGCCAGGCCTCCCAGGAACAGAACTCGGATCCGAAAAGCC
27319    CAGAGAAGCTAGAGCTGCCCCTCCAACACTCTCGGATCCACATGGTCTGTGTTCTCTAGA

                    FG8A/G
27379    CCCCCCTGCATGTTAGCGGTGTTCTCTCTCTGTGGACTGACTGTCCTTCTCAGTGAACAT
                       G

27439    GTCCACCCGACAGCTCCTGAGTTTATATCATCTCAACCCTCACAACCCACAGAGGCTGTG
27499    TCTCCTAGTCACAGCTTTAAATTACTGGAAAAATAAATGACTGGCCAAACTTGGAGCAGG

                                      FG9G/A  BglII
27559    TGTCCATCCCAGCCCTGTGTAGTTAGAGCAGGAATCAAGATCTCAACACAAATGTGGCTG
                                        A
                     FG10C/T
27619    CCAAGCACTCAGCCCCGGGGCGAGGGGTCAAGTTCTTCTCAGAGAAAGAGGAATAAGTTG
                        T

27679    GTTCTCAGAAGACATCACAAGATACGTGTGTACCCAACAATCTCTGATCTCTGCTGATCT
27739    TTTGCTTAGACGTTAACTTGATGCATCATTGGAAAGGTGTTTCTCTCATCTCTGTCCTAA
27799    GGCTTGATAAAGTCATTAAAATTGTGTTCTTTTGACTAAAGAAATATGCTTTTTTTTTAC

27859    TGTTGCATATACTACCCTGAAGTCACTGGAACTTCTAGGAGTAATTCCAGAGCTTTTAGA
             --------- R3.5F ------->

27919    TTTATGCACCTGCGTGTATACTCACATTTGTTTCTAGTCTCAAGGTACGTAGTCTTTTAT
                                          <------ R3.6R -------

27979    TTTAAAAAACAAGTTGTCCTCCTGCATTCTTGATCTTTCACTCTCTTTTAGAACAGACAT

                                                         G1C/T
28039    CCAGTAGTCTCCTGTCCTTTGTATCCAAACTCTCCCTTTTTGCAGGGTCACCCTACAAAT
                                                           T

28099    CATAAGCATGTCATCTCTCCTATATAACAAGAACATCAAATCCTCTGTCTGTCCTTGACC
28159    CAGTCTCCCTTCCACCCAAGCTCCTGGTCACGCTCTCTGAGAGTGTCTACGTGGACTGCC

                                        G2-/+
28219    TCCAGATCCCCTCTTCCCATCCACTCTCTTTCGGTTTTAATTTTTAACCAAATTATGTTA
                                          |+G

28279    TAGTTTAAAGAGTCAAATATTTCTACAATATTTGCTACAGAAATACCAGTTTCCAGCCCC
28339    ATCTCCCACCATATCCTCACCCTTACAGAAAATAACTTTCAATTGTTCTAATATGTTTTG
28399    TTGGTATTAACCTCCCATCTCTAAATAACATGTTTGTGTTGCTACATCTAGATTTTTCAG
28459    CTTTAGGCTTTATCTCTTTACCTCCTGCTGTGGAAGAGGGGGATTTAGATTTTTTTCATC
28519    CTCAAAGAACATCATGCCCCCTTTCCCATGCCCTTTCTTTTAATGTGACTATATTGTAAT
28579    TTTTACAATATAGTAAAAGTTACTGTGTTTACTATGTTTCTATCAATATGACCATGTAAT

               G6A/G                                     G7G/A
28639    GGCAAACCATAGAGCAAGCCATGCTCACTCTTCCTTTTCTAGACGACTTCGTTTTCTCTG
                 G                                         A

28699    GAGTATATAGTTGTCCTGTTTTCCTTTGTGTGGCTGTATTTGTACTTATTATTAATGAAT
28759    CACAAAATTCCTCACAGTACAATCAAACACATCAGGTATTCTGTCAATTTTATCACCAGA
28819    TATAACTCTCCCAGAACCTTCTGTCTGCTCCATTCTTAACTCCTTGCCCTTGATGATACA

                                                             G4a G4b
                                                      G3A/G  C/T T/A
28879    GCGGTCACTCTGAGATCACTCTTCGCCATCCTCGTCAGGATTTACCTATCCTCCGAGTTG
                                                        G     T   A

28939    GATCTTCTGCTTCTTGTATCCAGTCATTGCCCTTTTGTGGTCTGCCTTATTTTAATGAGG
28999    CACCTCTTCTTTCCACTTCCTGAGAAACAGTGCATATGAGGAAAACTTTTTATGCTTCGT

                            G5C/T
29059    ATGTCGGAAAATATATTTATTCTACTCTCACACTTGAATAATAGCTTCCACGGTTATAAA
                              T

29119    ATTCAAGATTGGAAATCATTTCCATCAGAATTTTTAAGGCATTTCTCTATAATCCCTTAG
29179    CTTCCTGCGTTATTGTTGATAATCCAAAAGATATTGTGTCATGAAACTTTGTACGTAATC
29239    GTTGTTGTTTTTTTCTCTCAGAAGCTTATAGGATATCTGCTTTTTCCCTTCCTCCTTTAA
                         --------- R4.9F ------->
                                                       GA1C/T
29299    ATTCTTATAGGTGCTCCATTACCTACAAGATGAAGACCCTTCTCAAACCGTCCTCAGGGT
                  <-------- R5.0R -------                T

29359    ATTTCTTTTTCTTTTTTTCTTTTCTTTTTTTTTTTTTTGAGGTAGAGTCTCACTCTGTTA

                        GA3T/A
29419    CCCAAGCTGGAGTGCAGTGGTGCAATCTCAGCTCACTGCAACCTCTGTCTCCCAGGTTCA
                          A
                                                       GA4-/+
29479    AGCAATTCTCCTGCCTCACCCTCCTGAGTAGCTGGAATTACAGGCACCCCCCACCATGCC
                                                         |+C
                                                                 GA5C/T
29539    CGGCTAATTTTATTATTTTTAGTAGAGACCGGGTTTCACCATGTTGGCCAGGCTGGTCTC
                                                                    T

29599    GAACTTCTGACCTCAGGTGCTCCGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGC

          <--- full length Alu
29659    ATGAGCCACCGCACCTGGCCTATTTTAACCATATAATAGCTCCTCCTGAAAATGATCAAT

29719    GCTTAAGTCACAGAAAACTGTTGTCGCATGTTTACTCCTCCCTGCCTTTGCACAAACTAT
29779    TCTCTGTGCTGGACCTGCCTTCCTCCACCAACCAGTCAAAATTCTACCTGTCCTTCCAGG
29839    GTCCAGATTAAATGTCACCTCTTCTGTGAAGCATTTTCAATCCCAGCCCCCAATATGCTG
29899    GCCACCCTGTCCCTGCAGTGCATACCACATTCCGCCCTGTGTCAGTTGACTGTGTATGAA

29959    TTTGCCTTTGCCACTAACTGCTCCTCTAAAGCAAGAGAAGGCTGTGTCTTATAGTTCCAA
                          <------ R5.7R ------

30019    CACCCAGAACATAATGGGCATTGAAACACTGTAGAATTCTATTTAATTCAATTTTGTTTG
30079    CTTCAAATCCAGCCTGGTCCGACTGTCTGCAGCTGGTTTTAATAACATTGGCTACCGTTT
30139    ACCCAACACATGCAATGTGCCTGGCCTTAATGCTTTTCACGTGTAGTGGATTTGAATCTT
30199    GGTCCAAAAGATTAATAAGATAGTGCACAGAGTGCAAAAAATAGTAAATGTCTTTAAATA
30259    ATCGAAAATCTGATTCAAAACCTGCTCTTTAAAAAATCTTAAATCTGATTCAAAACCCCT

                          GA6G/A
30319    GCCATGAGGCTGGTTTTAAGTTCAATCTGTCTTTATTGGGGCTTCTGGTCTCTTACAGTT
                            A
                                GA7G/T
30379    GTTCCAAGGGTCTGCGCCCTGACACAGTGCTGAGGCCTTGGAGAAGCCCCTGTTGTCTTC
                                   T

                                  SphI
30439    TCCAGTCCAGACTGTTTACTCCAAGCATGCCTAGGGCTTAACCTGTATGCTCTTTTCCAA

30499    GTGGAAGCTCTGCTGCTTCTGCACTAGGCTTGGGGCAGGGGAATCTTTAGTGAGGAGTGA
30559    TCCCCAGTGCCTGGGAGCAGGACTGCAAAGATGCACCATACGGCCAACTTCCCCGTCCCT

                                                       GA8C/T
30619    GGGAGGCCTCCCCACCTGCCTTGGCTGCTGCAAGGAAGCAGGGCTCTTTCAGACCCACAG
                        <------ R6.3R ------              T

30679    GCCACTGTGCCTTCCTCAGTTTGGGAGAACCTTCCCCCTTTGCCTGTCAAAGGCATTCCC
30739    CTCTCTCTCTCTGGCACAATGTCTGGGACACCTGGCATAATGTCAAGTGAGCTTCAGATT
30799    TTGGGAAATCCAAAGCCAGAAGAGGAAAGGCCTTGGCGGTGACATGTGCTATTGTCTTGT

             GA9A/C
30859    GTGACAAACCTAAATACAAACAAAGGAAAAAGAAAAGCATCATTCTGCCATACATGAATT
                C
                          GA10C/T
30919    ATTTCATTTCTTCCTTATGACCAATCTGCAAGTTAAGTATAATGATTTCATTTTATAAAG
                             T

30979    AAGGAAGCTAGGATTCAAATTACCTAACTTGCCCAAGGTCAAACAGCTAGGAGGTGGTTG

31039    GAAGGTCTGTGTGATGCTAGAGCCCATGTTCTTTCCACTGCACTGTCCTACTCAGCAGCG
                                                <------- R6.7R -----
         GA11G/A
31099    AATGGAGACCAGCTTGTGAGACATGAGGCAGGATGAACAGGGTCAGACATCAGCATTACT
            A
                                            GA12C/T
31159    AGGAAATGTGTAGGAGGAGGTATTCCCAACTTTGGGAACAAACTTCTTCTGAGGCTTCAG
                                               T

31219    CAGCAACAGGCTGCAGGGAATGAGGTGAGCTTGAAGAATGACTGGGGATGGAATTACTGA
                  ------- R6.9F ----->

           mismatch with EMBL seq |  A1C/T
31279    AGAGATTTTCTTCTCCCTCCTGGAT-CAGTCGAAGCACTCCCCCAGTTCAGACTTTCTTT
                                       T  <------ R7.0R ------
                    A2A/G
31339    CTTGCTTAGTCTAAATTCCCTCCTGGTCAACAAGACTCTATATGATCTGGCGCTGCATGT
                      G
                                                                 A3C/G
31399    GTCTTCATCTTTACTTCCCTCTACTCTTCCTTCTTTCATTAAGCAATAGCCACACTATCT
                                                                   G

31459    TCCCCAGAATTCTCCTTAACATTAATGCCTCCAATTCATCACCCATTCACAACTCGTGTG

        A4C/T
31519    GCACCAATTCAGAGAAGCTTCATTGACCAACTTTGCTAAATAAACCACCTATCTCCAATC
          T

31579    TCTCCCTATCATGTTACCCTATTTATCTCTACACACAGATGCCTTTCAATGAATGATGTC

                            A5C/T
31639    CCACTTCTCAGGCTTTCCTTTCTCTCTGACTTCAGAAAAGCTTCCAGACAAGTGATCGTG
                              T

31699    CACGCAGAGGAGCGACTTCACTTCCTCTCCTCTCCTCCTTGTGGTTTAGGAGGTTGCTAC
                                        -------- R7.4F ----->

31759    CTATGACTTGTAATTTGGCTCCATCTTGTGGTTTGCATCCACCCCACCTGGAGCCTCCAA

                                              A6+/-
31819    ATCTGAGTAAGCCTAAGGTCTCCCAAGGTGGACTCCCCGGCACTTCCGTCCACTGGAAAC
                                                -
          A7C/G
31879    GTTCTGCTGCCTCCTCCCTAGAGTCCCAACACCGCTCTTGAGACCTGGTCAGGTTCCCAG
            G                                ------- R7.6F ----->

31939    TTGCCCTTTATTCCTTTCCTCGGGCCTTCAGTATATGGATCTGCTTCAGGTACAAGTTCT

                                   A11+/-                     A12C/G
31999    TACTGTAATGCCTGAAACATGGTGGTTACTCAATAAATGTTTAAAGCCCCAGCTGACTAA
                                -----------T                     G

32059    AACAAAATGTAGTCACCCTGCTCTCAAATTCCCTGATGACATGTCCGCATAAAGAAAAAT
32119    AAATTAAAATTTGTTTTTCTGATATTAACAAGTATTGTTTTGTTAATACTATTATCTTTC
32179    ATAATAGTATTGACTATTATTATTGAGCACTTCCAATGTGCCAAACACTAGTCTAACCAA
32239    CTGATATTTGTCAAATCCAGTATCTCCACATTCACTAAGAAGCACACCAGATATTTCCTA

32299    AATTGTTGCATGAAACCGAAGTGTTTAGGAGAGTGTTAATAACCTAACCAAAAACAAATC
                        <-------- R8.0R --------

32359    AATAGAAGTAATATTTTTCTGTTAAAACATATTTTAATACATGTAAGGAAATGCCAAACT
32419    TAAATATGTATCTTTTTGTTTTTTGTTTTTTTTGAGACAGAGTCTTGCTCTGTTGCCCAG
32479    GCTGGAGTGCAGTGGTGCCATCTCAGCTCACTGCAACCTCCGCCTGCTGGGTTCAAGTGA

                             A13C/A
32539    TTCTCCTGCCTCAGCCTACCGAGCAGCTGGGACTACAGGCATTCACCACCGCACCCAGCT
                                A

32599    AATTTTTGTATTTTTAGTAGAGATAGGGTTTCACCATATTGGCCAGGCTGGTCTCGAACT

                    <---Alu repeat, 5' truncated
32659    CCTGACCTTGTGATCCGTCCGCCTTGGCCTCCCAAAGTGAAGTATGTATCTTTATTATAT

32719    AGTAATCTGCCTTTTAAAAATGATATGTCATTATTTGTAACAATTGAAAATTATTGGAAA

32779    CATGCCTAGTAAGAGTACAATAGTTGAAAAAATTATAGTACATCTGCACAATGGAGTAAT
                                              -------- R8.5F --------

32839    GCAAAGCTGTTAAAAAGAATGAGGAGATAGAAAAAATAAGTTCCAATGTTTGATAGCAGA
         ->

32899    CTGGGGTGACTGTAGTCAGCAACAATATATATATATATATATATATATATATATATATAT
             <------- R8.6R -----

32959    ATATATATATATATAGTATATTTCAAAGTAGCTAGAAGAGAGGACTTGAGATGTTGCCAA
                                    -------- R8.7F ------->

33019    CACATAGAAATGATAAATGCTCAAGGTGAAGGATACCCCAAATACCTGACTTGATCATTA

                  A9T/C
33079    GTCTCATTGTATGCATGTAACAGATACTCACATGTACCTCATAAATAAAATATGTAAAAT
                    C

33139    ATCATGTATCAATTAAAGGAAAAAGTCTAACGAAAAGGAATGAGAAAGATCTCTTTGAAC

33199    TAATACGGAGGAATCTCTAGGTTAGAGTGGAAAATTCACAGTGCAATACAATGATTAAAC
              <------ R8.9R --------

33259    TATGTACTGCCTTTGGGGTAAGAAAGAGGAAAGATACATATTTTTTCAAAAAGGTGGATT

         full length Alu---> 3
33319    GGGTCAGATGTGGTGGCTTGTGCCTATAATCCCCACACTTTGGGAGGATGAAGTGGGAGG

                                                           A10T/C
33379    ATCACTTGAGGTCAGGAATTTAACACCAGCCTGGCCAACATAGCAAGACTCTGTCTCTAC
                                                              C
                                       KpnI
33439    ATAAAATAAAAAAATTAGCCAGGCATGGTGGTACCCCCTGTAGTCCTAACTACTCAGGAC
33499    GCTGAAGCAAGAGGATCATTTGAGCCTAGGAGTTCGAGGCTATAGTGAGTTATGATGGTG

33559    CCACTGCACTCCAGCTTGGGCAACAGAGTGAGACCATGTCTCCAAAGGGGGAAAAAAGCT
                                     ------ R9.3F ------>

33619    GCATTGGAAGGATAAACAAGAAATTAATAAAAATGGCTACTTTTAGGAAGGAAGGGAGAA
                                           <------- R9.3R -------

33679    TAGAAGTGAGAAGTGAATATTGACCTTTGAAACGTATAAATAATTTACAATGTTAATAAA
33739    AAATTGACAAAAACCTCTAAAATTTAAAACAAATAGAACTGAACCACACAGAAAAAATAA

                                                         AB1C/T
33799    GTATCCCAAGTGATATTAAAAGATACTACTGTATGTTCTTGGTGGAATACACTTACTCTC
                              <------- R9.5R ---------      T

                                                   AB2G/T
33859    TCTCTTCTCTCTCTATTTTTTGTTGTTGTTGTTGTTTGTTGTTTGTTGTTTTTTTAGACA
                                                     T

33919    GGGTCTTGCTCTGTTGCCAGCCAAGGCTGGAGTGCTGGAGTGCGCTGGTGTGATTATAGC
33979    TCAGTGCACCCTCAAATTCCTGGGCTCACGTGATCCTCCCACCTCGGTCTCCCAAGTACA

                               <---5' truncated Alu, heavily diverged
            AB3T/C                                       AB4T/C
34039    GTAGCTGGGACTTCAGGAACATGCCACCATACCCAGTTAATTAAAATACATGTTTTAAAT
              C      ------ R9.7F ------>                  C

34099    AGAAATGGGGTCTCATTATGTTGCCCCAGCTGACTTAATAGAATATATTCTAAGGACAAA

                                                          SspI
34159    AAGAACTATCAGAACTTTGAACATCATTCAGTTGTTTTATGGTTAAGTAATATTTGTATC
34219    CTTATTTGAAACTATACTATATATAAAATAAAGCAAATCAGTGATTATGTTAATATAATT


                           APPROXIMATE CENTRE OF HLA-DNA HOTSPOT 3
                                                    |
                  full length Alu repeat---> 5      |
34279    AAGAACTAAGATTTTTAGGCCGGGGGCAGTGGCTCATCCCTGTAATCCCAACATTTTGGG

34339    AGGCCAAGGCGGGCGGATCACAAGGTCAGGCATTCAAGACCAGCCTGGCCAACACAGTGA

           AB12C/A  AB5T/C    AB13C/A
34399    AACCCCGTCTCTACTGAAAACACACAAAAAATCAGCTGGGTGTGGTGGCGGGCGCCTGTT
                 A  C            A

34459    ATCCCAGGTACTCGGGCGGCTGAGGCAGGAGAATTGTTTGAACCTGGGAGGCAGAGGTTG
34519    AGGTCAGCGGAGATTGCACCATTGCACTCCAGCCTGGGCAACAGGGAGAGACTCCATCTC
34579    AAAGAAAAAAAAAAAAAAAAAAAGAACTAAGATTTTCATGTATAAAAAGCAAGTAAAAGT

                           SspI        SspI
34639    AGCTGAATTAAAATAATAATATTAGAAAAAATATTTGAACTAGAACTGTCAATTTTAACT

             AB14C/T                AB8T/C
34699    AATGATTCACTAACATATATGTCCCTGCTCTAGCAAATGAAAGAGCCTAATAGTAGCCCT
                T                      C

34759    GTAGCAATGAGCATCCTCAATGCACAGATTGTAGTGTGTAAATATCATTTCCCACTCAAA

           AB9T/C                         AB10G/C
34819    GGAAATAGAGCTTCTTGGAGAAGTGACCAGTTCCAGGCCTGAGTTATGGAAAATACAAAG
              C                              C

34879    CAAGTGTGAGTATCTCATTGTTTTCATAAAACAAGGCACTGTTCAAAGACTAATAGAGTC

               AB11-/+
34939    ATGTCAAAAAAACAGGTCAGCCAGTTTGAAGGAGCTTCCATTGGCCAAAACTGGAACAAC
                 |+A

34999    TCAGACATCAAAAAGATGACTATAATATAATTAAACACATTGAGTATATAAAAATCCATG
                                                                 <---
                                           AB6A/T
35059    GGTTCCTATTAATAGTCGAATACAGATTTTAAAAAGAAAGCAACAACAACCCATTGATAT
         ----- R10.7R -----                  T

35119    TACCACTGGATGTGATCTTCCAATTCATAACACAGGAAATTGGTGCTTAAAGAAAACAAG
35179    TATATATCCTGACATTTCACAAGGAAATGTTCCACTGATGAAAAAAGGTCTACCCTTCAG
35239    AGTACCAGTGAATAAATGTTGGGAAAAATAACAGAATTAGAAAACCAGCATTTTGTAAGC
35299    CTAATGTGATCATTGATTCAGGGAAGGCATCATATATGTTAAAACCATTAGGAGAATAGA

35359    CAGTGAGGAACAAGAGAGTCACATCATGCCAAAGTATCATGGTCATAGATTATTTGCTAT
                -------- R11.1F ------>

35419    TGTCAAATGGGAGAAATACCTTTACAGAGGTGATGGCTGTCATCACCTCGACTGAGTGAT
                                               <------ R11.1R -----

                                                  B2G/A        B3A/G
35479    CAAGTTTAGCCTCACCAATAATAGGACAAGACATTAAGCATATGCTTCCTAATAAGATGA
                                                    A            G

                                                               B4-/+
35539    AATGCAAAGTACACAGCAATACCTATGAAGAATTATTGTCAAAAATCTTTCATCTAAATC
                                                                 |+A

35599    TAGTCAAGCCTTTGTTTCAAAAAGTTCTAGTCTATAAAAAAAATACATTGGATAGAGGAA
35659    TAAGTCAAATGAAACCACAAAGAACCAATCACACAAATTCAAAATGTGAGAGATTCTACT
35719    GGCCTTGTCTCTCTAAAAAGATGCTGTTTAAAAAATGGGTGGAATAGTGGGAATTAAGAG
35779    ACATTACAATCAAATTTAGTGAATGATTCTTGGCAATATCTTTGAGGAAAAACAGATATA

           B8C/A
35839    AAAGCACTTTTCAGACAAATGGGGAAATTTGAATATGAACTGGTAATCGATGATATTAGA
             A

35899    GAGCTGTTTTCAGTTTTGTTTAGTATGATTACAGTACCACGGTTATGTATCAAGTCATCT

                                                       B9G/A
35959    TTATGCTAAAGTATTTAGGGATGAAATGCTAGATCTCTAATTTACTTCGGAATGAATTCA
                                                         A

36019    GAATACACACACAGTTCAAACAAACACAGCAAAATCTTGACAGTTGTTGAATCTATATGA

36079    TGGGTATTTGTCTTAGTCCATTTTGTGTTGCCATAACAGAATACCACAGACTAGGTAATT
                                                     <---- R11.8R ---

36139    TACCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAGAAAGAAATTTGTTTCTCAC
         -------                                        ---- R11.9F -

36199    AGTTCTGGAGGCTGGGAAGCCTAATGTCAGGTGCCAACATCTGGCAAGGGCTTTCTTGCT
         ------->

36259    GTGATGAAGAAAAAAGGCAGAAGAAAAAAGGAGGAGAGAAAGGATGAAGGAGAGGAAAGG
36319    AGTCAAACTCATCCTTTCATCAGGAATTCACTCCTGAGATGAGATAACTAATCCACTCTA
36379    GAGATGATGGCATTAAGCCCTTTATGAGGGCTCTGCCCATCTCTTTAAGAGATGACCTAA
36439    TCGTATTTTAAAGGTCCCACTTCTCAACGTTGTTGCATTGGGGATTAAGTTTCCAATGTT

         B10-/+
36499    TTATATATAACAACTTTATGTTATGTATAAAATAAAGCAAATCAGTGATTATGTTCATGT
            |+A

36559    AATTCAGAACTGAGATTTTTAATGTATGAAAAGCAAGTAAACGTAGTTGAATTAAAACAA
36619    TAATATTAAATTTGAACTAGAAAAATATTTTGAACTAGAAATGTCAGTTTTAACTAATGA
36679    TTTACTAATATATATGTCCTAGCTCTAGCAAAAGGAAGAGCCTAGTAACTTTGGGAGACA
36739    CATTCAAACCATAGCAGCTTTCAAGTATTATTTTATTTTTCCCAAGTTTTCTGCAGGTTT
36799    GGAAATTTTCACAATTAAAGAGGTGTGTGTGTGTGTGTGTGTGTGTGTGTAATGCTTTAT
36859    TATACTTGAAAATAGCAGGAAATTAAAGGAGAGAGCACTAGATTCCTGAACTCACAAGTT

                                                        B5T/C
36919    GATGTATGTCACCAATTGAATAACTTTTTTTTTTTTTTTGAGACAGAGTTTCGCTCTGTT
                                                          C
                               B6G/A
36979    GCCCAGGCTGGAGTGCAATGGTGCGATCTCAGCTCACTGCACCCTCCACCTCCTGGGTTC
                                 A

37039    AGGTGATTCTCCTGCCTCAGTCTCCCGAGTAGCTGGGATTACAGGCGCCCACGACCACGC
37099    CCAACTAATTTTTGTATTTTTAGTAGAGGCAGGGTTTCACCAGGTTGGCCAGGCTGGTCT
37159    CGATCTCCTGACCTCAGGTGATCCACCCACCTCAGCCTCCTAAAGTGCTGGGATTACAGG

                                     <--- full length Alu
37219    CATGAGCCACCGCTCCCAGCCTGTTCTGTAATATTTTATAATTTAAATAAATAATGTAAA

37279    TGGGTTGTTCTTTTGTTTTAATTAAAATAAAATAAACATGATGTAATGCCTTTAAATTTT

                                  B7T/G
37339    TGTTCCACTACATGGCTATTAAATACATACATAAAATTTGACCATTTCCCCAGCAGATTT
          <---- R13.0R -------      G        ------ R13.0F ----->

37399    CTCATCCATAGGCTCAAAACCAACTCATTTTATTTTGGGAGCCCTACAATTACTTTATCA
         ------ R13.1F ------>

37459    ATATTATATCATTTGAAAAAAATGATCTGTAGTCAAAAGTTACTGTAACATTGTCTATAG

37519    ACATCCCAGGAACACCAAGAATAAGTTCACCTAGAAAAATGTCATATAATTTTGTTTTTA
          <--------- R13.2R ------

37579    TAAGACATTAAAATGTTATATAAAAAATTATAAAACATTAAAATGTTATATAAAATTATA
37639    AAACATAAAAATGTTATGTAAAAAATTATTTTCCCCATATTTGAGATTTTATTGCCAATC

                                                   full length Alu-->
37699    CCAATCAGAAAACAGAAAAGAGGAATAAAAAATAGTAAAAATGGGCCGGGCGCAGTGGTT

37759    CACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGAT
37819    CGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTATTAAAAATACAAAAAATTAGC
37879    CGGGCGTGGTGGCGGGCGCCTGTAGTCTCAGCTACTCGGGAGGCTGAGGCAGGAGAATGG
37939    CGTGAACCCGAGAGGCGGAGCTTGCAGTGAGCTGAGATCCCGCCACTGCACTCCAGCCTG

                           BC3C/T
37999    GGCGACAAAGCGAGACTCCATCTCAAAAAAAAAAAAAAAAAAAAAAGTAAAAATGAAGAA
                              T   T T                        --------

38059    GGTACTAAGTTTCCAAAATCTTAAAAAGTCTTTATAGTTTTTAAATCTCCTTCTTATGTA
         -- R13.7F --->
                                    BC4C/T
38119    GTCAACGCAAGCCCAGACGCACGCCTACCCCTACCCCCAGCTTTCCTCTCACCATCCATC
                                       T

38179    TCCTACAATCCAGTTCCCTCAGGCCTCTCTTCCTTCACAAAGGTCCCAGTGTCTAAGCCA
38239    AGCCTGAAGGTATGGTTAGGATGAATGGTAGGTATGAATAGTTACCATTTAGAAATTACG
38299    CAGTCTAAAGCGAATATTAATAGTTCAACTTAGCCTGGTTTCTCTTCGTGCAGCAAAAGC

                              BC5C/T                    BC6C/T
38359    CATCACTGGAATTTCCTTTACTTACATTTATGGAATGAAGTCGTTCGTTTCTTATTTGTG
                                 T                         T

38419    TCTTCACACTTCTTAATAGTTCTCCAGCTAAGCTAAATTAATTGGGCTTGGTGAAAAAAA
38479    TAAAATTTTCTACAGTATGCAGGAATCTTGTGTAGAAGCTGCATTTAAGAACATAGAAGA
38539    AAATGGAGACATTACAACTGACACTATAGAAATACAAAAGATCATCTAAGAATACTATAA

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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.