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Celia A. May
The views expressed in this document are those of the document owner, Alec J. Jeffreys.
The sequence is taken from Beck et al. (1999) 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 L1 repeats plus 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 DMB 1 and DMB 2 are also shown.
To download a pdf version of this page, click here.
90759 TGCGATTATTCTCTCCAGTAATCTACGGAAATCTACTGGTTGTTCTGCAGAAAAAGAATT
90819 AAGAGAGACAAGGAGACCTGTTGTCTAAGACTAAGGCAGGATGACGTTTACCTAGTAACT
90879 GATGATGCTAGGCTGAGGCACTCAGTGATTTGTCTCTACATTTGTCCCTGCCTACCTAGC
HLA-DMB exon 1-->
90939 CAATCTGTCCCTGTTTGGGACACTGGACTCCCGTGAGCTGGAAGGAACAGATTTAATATC
90999 TAGGGGCTGGGTATCCCCACATCACTCATTTGGGGGGTCAAGGGACCCGGGCAATATAGT
91059 ATTCTGCTCAGTGTCTGGAGATCATCTACCCAGGCTGGGGCTTCTGGGACAGGCGAGGAC
91119 CCACGGACCCTGGAAGAGCTGGTCCAGGGGACTGAACTCCCGGCATCTTTACAGAGCAGA
ini
91179 GCATGATCACATTCCTGCCGCTGCTGCTGGGGCTCAGCCTGGGCTGCACAGGAGCAGGTA
91239 AGGACACTTCTTCTGGGGACTCTCCCTTCCCCTGCTCCTGTTTCAGGGTAAGGGTGTTCC
91299 GTTTTGTAATTGCATTTGACACCCCAGATAGTTTGTCTCCCTGGTATACATTCCTATAGC
<-------R67.0R------
91359 ACTTTGTACTTTGTAGCAATTTTAATGTAATTAATCTGTATAATTATCTGTGCAGTGTAT
91419 ATTCCCTGCTGGAATATAGGCAAGGACAATGTTCATCTTATTTATTGCTGCCTCCTCAGC
91479 TCCTAGCACAGTGCCTTGCATGCAGCAAGTGCTTCATAAATATGTGCGAAGTGAATATTT
91539 AATATTTCCAGCACAATACAAGGCTGACTCTTTCTCTTGACCCTTTTTCTCTCTCAATAA
91599 TTTGCCTTACTGAAGGTCTGTGTTCTGGGCAAATTGTCATGTTTAAACATGCAAATAATC
91659 TCGGGGGGCTACTCCTATCCCTGTGCTTAGTCTTGCATAAAGAGGAGACTGGATCTAAAA
-----R67.3F-------->
91719 ACTTATCTACTACTTCTACTGACTCCCTCAAATCAGACTTTCAGAAACTTCAGTGTATGA
91779 GCTTGGTCAGTAGATGTTCCCTGAGCAGGAAATCTGTGCCAGACTAGCTGGATGTCACCA
91839 AGGCTTAGGTTCTGAGCTGAATATAGGAAAAATCAACTTTTTTTCTTCTATATGCTCACA
<----R67.5R---------
91899 CTCAACACTTCTTTGACCAACTGTGTGAGGTTTTTTTTTTTTTTTTACTCATACCAACCA
<-------R67.6R------ ------R67.8F-
91959 ATTCTCCTATATTAGCTGGATATCCTATAATTCAATTCCATTGTGACATTAACTAGAGTT
------>
92019 AACATAGACACCAAAGGTTAAAGACTCAGTCCCATAAGACTGCCTCCATTTCAGACACCA
92079 ATCACAAGTAGTAGGTTCCCAAATTACCCACATCTTCTGTCCAACTTGCCTACAAATCAG
92139 AGGTTCCCATGACCCCCTCCTTGGGGTTGGTAATTTGCTAAAGTGGCTTATGGAACTCAG
92199 GAAAAGTTTACTTATTATTGTAGATTTTTTACAAAGGATATTTTAATTGATAATAATAAT
92259 TATAAATATTCATGGGGTGGATAATGATGTTTTAGTACATGTAATGTACAGTGATCAGAT
92319 CAGATCATCATCTCATTTATCATTTCTTTGTGTTGGAAACATTCCATATCCTTCTTCTAG
92379 CGATTTGAAATGATATAAAGTATTATTGTTAATGACAGTCATCCCACAGTGGTATAGAAC
92439 ACTAGATCATAATTTTGCATCCTTTAACAAAGGATATTTTAAAGCATACAAAGGAACATC
92499 CAGATGAAGAGATACCAGATCTGGAAGGGTCCCAATCACAGGAGCTCTGTCCCCACAGAA
92559 TTGGGGTACTTCACCTCCTGGCATGTGGATGTGTTTACCAACTGAGAAGTTCTCTGAACT
92619 CCATAGTTCCGGGATTTTTATGGAGGCTTCATCATGTAGGCATGACTGATTATTAACTCA
<------R68.3R-------
92679 ATCTCCAGCCCCTTCCCCTTCAGGGAGTATGGGGGATGGGACTAAAAGTTCCAGACTTCT
92739 AATCATGACTTGGTCTTTCTGGTGACCAGCCCCTCCTGCAGGAGCCCACCAAGAGTACCT
92799 CATTAGAACAAAAGACACTCCTGTTATCTAGGAAATTCTAAGCGATTAGGCACTCTATGT
92859 CAGGAACCAGGGTCAAAGACAAAGCTCTGTGCAGAGCTCCTAAATATACGTCTGTATGTT
92919 TTATATATTTATTATTTGTGTATATTTATTATTTATATATTTATTTATTTATTGCCAGGC
HLA-DMB exon 2 --->
92979 CAGTAGAAGACATTGACCTGTTCTCCCTTCCCTGGCTCCTCTAGGTGGCTTCGTGGCCCA
------ R68.7F ---->
93039 TGTGGAAAGCACCTGTCTGTTGGATGATGCTGGGACTCCAAAGGATTTCACATACTGCAT
<------R68.8R-------
93099 CTCCTTCAACAAGGATCTGCTGACCTGCTGGGATCCAGAGGAGAATAAGATGGCCCCTTG
93159 CGAATTTGGGGTGCTGAATAGCTTGGCGAATGTCCTCTCACAGCACCTCAACCAAAAAGA
93219 CACCCTGATGCAGCGCTTGCGCAATGGGCTTCAGAATTGTGCCACACACACCCAGCCCTT
93279 CTGGGGATCACTGACCAACAGGACACGTGAGGAGAGAGGGGTGCAGAGGGGCTACCAGGA
93339 AGTGCAGTTAGGAGGGCAGGCCAGGGAGGATCCCACAGTGGCCCAGGGGTTTGAGATTTG
-------R69.0F------>
JJ1G/A
93399 AGCAGCAAATAAGAGAAAATGTGTGGATCTGAAATGTAGAAAGACGGAGGATTGAACCTC
A
93459 AAGGGGAACAAGGTGGCTGACGTGAGTGGAACAGGAGTAAAGAAGGGGAGGTGAGGCTTG
93519 AACCGCGAGGTGCCATGTGGGGAGCTTATGCAGAGGCTGGGGCATCTCAGGATGCATACC
93579 CAAGATGTTCTTGCCTTGTTATCCCAGATTTTGATGTTCCAGATCTGATGTGGGCCCAGG
93639 CATGGGAATATTTGGAATCCCAGGGGATTCTGACACATGCTTTTTCTCACCCTTAAACTC
93699 TTGCATTGACAATGGCTTGAAGTTTGTGAAAGTAAACTTGAAGATCTCCACAGTACAGAA
93759 CAGTGTGTCTCAAGGGTGGTTTCTGAACCACCTTTCTCAGAATTGCCTGGAGGAGGTGCT
93819 TGTTAAAGATGCAAGCCCCTTAGTACCACTCCAGATCTGTTGAAAGAAAGTATCTGGGGA
93879 TACAGCCTAGGAAATCTGCATTTTAACATAATTCCTTGGATTTTTATTTAAGATTGTGTT
93939 TGAAAAATGTCAAGATAGAGGCAAGCAAGAGGATCACCTAGGAGAGTAAATTAGTAAAAG
JJ3T/A
93999 ATGGCAGTATTAGCAATCTCTTTAGTTTGACTACATTCATTCCAAATTTAAGAGTGAGTC
A
94059 CTAAGTTAGGCTTGTTTCCTTGAACTATGTGAGGAGAAAAAGCTTTAACTAGCAAAAGAA
94119 CGTATTAAACAAGATTTGGAGAAAAATTCCTTTTCCACCTTAAAAAAACCCAATGTACAA
JJ4T/C
94179 CTCTGGATTACTCTTAGCTTCCTTATTTCAAATACTTTCCAGTTTATGTACTTGAAATAA
C
94239 ATACAACAACTTCTAGAACAGCTTGCAGTTCAGATCTGGCTTTTACTAATTGTAATCAAA
94299 CATAATTCTGGAGGAGGAAAGAAAGAAAGGGGCAATGAAGGAATGGGAGAGAAGAAAGAG
94359 TAATGCAGGAATACATTCTAACGGTTCCCCTTCAAGGGGCAGCATGGCAGAGGGGGCTGG
94419 GGTGGAAAGTGGGTTGCAAAATCTACGAAGAGTTGCGATAGGGAAGAAACCAGGTTGAGG
HLA-DMB exon 3 --->
94479 AAGCAGCCAGAATGTCACCCTCCTTCCTAAACATGTTTTTTTCTCCTATGCAGGGCCACC
<--------R70.2R------
94539 ATCTGTGCAAGTAGCCAAAACCACTCCTTTTAACACGAGGGAGCCTGTGATGCTGGCCTG
94599 CTATGTGTGGGGCTTCTATCCAGCAGAAGTGACTATCACGTGGAGGAAGAACGGGAAGCT
JJ5C/A Ala->Glu
94659 TGTCATGCCTCACAGCAGTGCGCACAAGACTGCCCAGCCCAATGGAGACTGGACATACCA
A
94719 GACCCTCTCCCATTTAGCCTTAACCCCCTCTTACGGGGACACTTACACCTGTGTGGTAGA
94779 GCACATTGGGGCTCCTGAGCCCATCCTTCGGGACTGGAGTAAGTGTATGGCAGATGGATG
-------R70.5F------>
94839 GAATTAGGGTCAAAGCAGAGAAAATGAGATGTGGATCGATACATGGTACATGGTAGACAG
94899 CGAAGTGCTGAAAATGGGGACTGAGTCTGGAGGAACTTACGGGGGGCTTAGGACCAGAAT
<---------R70.6R----
94959 GGGGAAATGGGATAAAGAAATGGAAATATTTAGGTTGGTGCAAAAGTAATTGCAGTTTTT
95019 GCCATTACTTTCAGTGGCAAAAACCGCAATTACTTTTGCACCAGTTTAATATTTAGTCTG
JJ6T/C
95079 TGCTATTGCTGCTCTGGTGGTGTGGTTGATGTTGCTGCGTCTATGTTTGAGGGTGAGAGG
C
JJ7A/C
95139 GGAGCGTGCTTGCTTTGAAATGAGGATGTAAATTTGGCAATCATATTTTCAGAACCCCAA
C
95199 ATTGTAATACACTATTCTAGCCTCCTTAGATTTCAACTATTCTGGTGCCAGAAGCAGATG
95259 GGAGCTGAAGGAATGATGAAGGTTGAAGAAGGGGGGCTTTTCTTGGTGTGGGGCAGTACT
95319 GCATTTGGCCTGCTCTACCAAGCATACGGGAGTAGTAAAGCCACGGCTGGCAGACCATTT
------RU71.1F----
------- R71.0F ---->
95379 GGCATGCATGCTCAGGGGCCAGTGGATAAAGAATTACTTACAGTTCAAACACTGTTTGAA
------>
<------ R71.1R -----
95439 CTCAGTGTCGGGAGTAGTTAAAGGTATCGTGAGAAGTTGCACACAGCTTTGGGGACTCTT
<------R71.2Rs------
95499 GGAAAAGAAAGAGGAAGAAATGAGGAAGAGGAAGGGTGTCTACAAAGGGCCAGAGAACAG
95559 GATCTCAGATCAGCTGCTGTAACCAGGTTTCCCCTTGTGGGAAGTGTTGTTTCTTGCTGG
95619 GCAGTTGGGAAGGGAATGGAGAACAGAGAAGAGAGTGGAAATCACATGCTCACTTGAACT
J8A/G J1A/T
95679 TTCCTGGGGAACGTCTCCTCACAGCGTGCACAAGAGCCTCCCTTTAGAAATGGAGTGTTC
G T
95739 ATTTTATCATGGGAAAAGAATCTGAGTGGGACATGATTCAGAACAGGACCGGCCCAAGGA
---- R71.5F -
95799 AGTGCAGGGGCTGTGGAGTGGGATGGAGACAAGCTCTGAAAGGACACATGGGAGATCTAG
------>
J2A/G
95859 ATGTAGAAGGTACACAAGTAGTAGGATAACTCACAGGATGGATCCACTGGAGGTTAAGAC
G
95919 ATGTGGTAAGACAGTGTAATAGGAAGCTGCTCAGTTGGAGAAAGTAAGGAAGCAAACATT
95979 GTTACCGTGGGGGCAATGGAGAGGACAGTGAGGAGCCCTTTATCCTGATAAGGGTGGCTT
J3A/G
96039 TGAGGTAAAGGAAGGAAAGAGGATGCCTTGAGAGGCCCCACTGTATTAGAGAGGACCTGG
G
J4A/G
96099 AAGCCAGGATGCTAATTCTGGGGAGATGGATTCCCCAGGCTTACTCTAGGAGTAGAGGTC
G
96159 CATGGGACGAGGGTTTGATTTGAGAAAGATCATTTTCTTGGGAGTGGGTGGTGTGAGCTA
96219 GACCCTTGGAGCTGGGATAAAGGACCTTTTAACCCACTGAGAGGTGGCTGCAATAAATGG
HLA-DMB exon 4->
96279 AATTGCCCTGGGGGTGAGCAACAGAAACTGGGTCAAGTAAGTTTCTATTTTTTGCAGCAC
APPROXIMATE CENTRE OF HLA-DMB HOTSPOT 1
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96339 CTGGGCTGTCCCCCATGCAGACCCTGAAGGTTTCTGTGTCTGCAGTGACTCTGGGCCTGG
96399 GCCTCATCATCTTCTCTCTTGGTGTGATCAGCTGGCGGAGAGCTGGCCACTCTAGTGAGT
96459 GACTCGCTGAACTCCCATCCCCACTCTTGGTCCCACTCTCTGCTTACTTTCTGTTTGTGA
96519 TTAACTCTCTCCTTCCTACTGCATTTGCTATGAATACTGCTAGATATTTTCATCCACAAA
HLA-DMB exon 5 ->
96579 GACTGGTATAATCAAGTATCTTCCTCTCTTAGGTTACACTCCTCTTCCTGGGTCCAATTA
96639 TTCAGAAGGTAACATCTCTGTTGGTCTGTTTCCCTACTTGCCCTTTGGTAGGGGTGCGGG
96699 TTAGAGGGGTCAGTGTTGGGTTCAACTAATCTTGATTATTATATGGGTGAGCTTCCATGA
96759 GGATCTAGGCAAGGGCATGATTTAAGCTGCCATTGCTAGGATTAAGAGCAGGAAGGAGCA
96819 TCCTCCTCTTCTACCAAGTGGGATGTCTGTGGAGAGGAGGCTGAAGGTGCTTCCTTTGTA
96879 TTAGTTGTTGGTGCCCTGGAGTTTTCAGTATCACTGTATTAAGGCATGGGATGGTTACAG
96939 TGACAAACGATGGGGGCAAGTTGGGTTGAAGCCTCATTATCTCCCTTTTATTTATTCTGT
HLA-DMB exon 6-> ter
96999 AGGATGGCACATTTCCTAGAGGCAGAATCCTACAACTTCCACTCCAAGTGAGAAGGAGAT
<------ R72.7R -----
97059 TCAAACTCAATGATGCTACCATGCCTCTCCAACATCTTCAACCCCCTGACATTATCTTGG
97119 ATCCTATGGTTTCTCCATCCAATTCTTTGAATTTCCCAGTCTCCCCTATGTAAAACTTAG
J13C/T
97179 CAACTTGGGGGACCTCATTCCTGGGACTATGCTGTAACCAAATTATTGTCCAAGGCTATA
T
97239 TTTCTGGGATGAATATAATCTGAGGAAGGGAGTTAAAGACCCTCCTGGGGCTCTCAGTGT
polyA signal
97299 GCCATAGAGGACAGCAACTGGTGATTGTTTCAGAGAAATAAACTTTGGTGGAAATATTGT
97359 TTTTCCATGTCTTCTTCCTGGGGCCCTGGGGAAGGAATATGGGCAAAGCAGGGACTGAGG
97419 TTAATTCTCTTCTGCTTGAGTAGGGGAGAAATCAATGCCTTCTTCCATTTTCCCACTTAG
97479 ACATGACAGAATTTGGGGCCGTTTTCTGATTTATAATTCATAAGGAGAAATTCAACTGTG
97539 GTGGGTTGGAGTCACAGAGTATGGGCAAGGAAGGGAATTAACAGCTTACTCACCTCATAC
<------ R73.2R -----
J14G/C
97599 AGGATCTTATGAGGATTAAATGAGTTCATACTTGTAAATGGCTAAGAACACCGCCAGGCA
C -----
97659 CATAGCCAGCCTGCAATAGTGACGTTAGCTATATTCGATTATTCAACTTTCTGGCCAGGC
--R73.3F------>
Jjk1C/T
97719 ATTGTACCAGGTGCTTTGATCCTCATCACAACCGTAAGGCAGACCCCTCATACCCCTCAG
T
Jjk2C/T
97779 GATTCAGGGGACAGAGCTTAACTCCAGATTGAGTTCTAGACAGTTATTTCTTCCATACCC
<------R73.5R------- T
97839 TGAATGCAGAAGGGAACATAGCTTGAGTGATTATTATGTCTTAGGCACTGGTCTCAGACC
97899 TTTATATTTGTAGCTCATTCTCTTCTCACAATAACCACACAAGGGACAGATTGTTTCCCT
97959 CTATGTTACAGACAAAAGATGTGAGGCTCAGAGACATTTAAGTGACTTGTCCAAGGTCAA
98019 AGAACAGATTTCTGTAGGATGTTTGTCTACCTGAGCTGGAAGTAGCAGATTACTTTATTC
-
98079 TGAAGACCCTCATGCTGGTGAGCACACATCTCTTCAGAGCCACCGTTCCATTCCCTTCTA
------R73.8F------>
98139 CCCCAAGACCAAGGAGAGCCCTTTGGGGGAATGGACTCCACCCTAAGGAAGAGAGGATGC
98199 TGGCTGGTGGTTTGTTGTCCCACGAAGGGCGACACCTGCTGGACACAGAAACCTAGGGTG
98259 TGGAATTGTTTTTGGAATTAGAGCTAGATACTAGAATATGGGTAAGAAAAAGAAACCAAG
98319 AAATGAGTTGATTTGGAACACCTCCATAATTTCTTCAGAAGCATCCTTGGAATTAGAGCA
Jjk13G/A
98379 TCTCTTCTGGAAGGGGTTAACAGAAGAAGTCAGTGGAAGGAACTTAATCTCTACATTTTA
-------R74.1F------> A
98439 CCATTTTTATGTTTCATTTTCATTTTTTCTATTCACTGTTTTTGTTTTTATTTTTGTTTG
98499 TTTGACAAAGCAAATTCCTTTTGAAATTCTAGTTTAGTCTAGGAATGGGGGGCTTTGGGC
98559 CTTGTCTATATCTGGGCAGTTTTATTTATTATTTTTATTTTATTTATTTATTTTTTTTCG
98619 AGACAGAGTTTTGCTCTTGTTGCCCAGGCTGGAGTGCAATGGCGTGATCTCGGCTTATTG
98679 CAACTTCTGCCTCCCATGTTCAAGCGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGAGAT
----
Jjk15T/C Jjk16G/C
98739 TACAGGCGTGCACCACCATGCCTGGCTAATTTTGTATTTTCTTAGTAGGGATGGGGTTTC
----R74.4F-----> C C
98799 ACCATGTTGGTCAGGCTGGTCTCGATCTCCTGACCTCAAGTGATCCACCTGCCTCAGCCT
<---- full length Alu element
98859 CCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCACTAGGCCTATCTGGACAGTTTTAA
Jjk3G/A
98919 AGGAGAAGCTGCAGATCTGAAGGGTCTAGTTCTAGTCACAGCAGTGGGAATCAAAGTGGC
A
98979 AGGATCCCAGAGAAAGGAAGTAGAGAGTTAGCTAATGGGACGGCTTCCAGTTCCTTTTCT
<----- R74.7R -----
Jjk5T/C
99039 AGAGATTTCCAGTGCAGGCTTTTCTCTGCCCTAACTTTGTAGGTTTTTTGTTTTATAGGA
C
Jjk9C/T Jjk4G/A Jjk18G/C
99099 AAGGCTGTCCCCTTCCAGGTAAGGAATAGGGAAAAGTATATGTAGGTCTGCTAGGATCCA
T A C
<-------S--R74.8R--
Jjk14G/A
99159 GAAAGTCAGAATACTATAGGTAGAAAGGGGAGTTCTTACACAGGGGAATGAGTGGTACTT
A
-
99219 GAAAGGAAGGTGGAAGAAGGGTGATGGTGCACCAATTGTAGGAGGATGAGGAGAAGAGAA
Jjk10C/T
99279 TGGATGCTGCATGAGGAGAATGGAATGTAAACATAATGGATTGCCAAAAAAGGAGTGCGT
-------R74.9F------> T
Jjk11+/- Jjk12+/-
99339 GTGTGTGTGTGTGTGTGTGTGCACTTGAGCACATGTGAGAGAAAGAGAGGAAAAAAAGAG
-- --
<-----R75.0R--------
Jjk6G/A
99399 AAGGAGTGGAAGAGAGTAAGAGAGAGGGAGCAAAAGGGTGAGAGGAGAGAAGTGGAGTGG
- A
99459 GAGAAAGAAGGAGAGGGACATAGAGAGAGGGAGGGAGGGGAGCGGGGGAAGAGAGAGAGA
99519 GCTGGACTTTCGGGTTATACATAATCCAAGCTGCACAAAGAATTGTTTTCGCCCTTCAAT
APPROXIMATE CENTRE OF HLA-DMB HOTSPOT 2
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| Jjk7G/C
99579 GTCTTGTTGTTTTAAAAGCTGAACTTGGAGCTAGAATTGGTTTTAAAGGTCATCTAGTCC
C
99639 ACCTCCCCTCCCATGAAAGAACTGGGCCTGTGTTAACAAGGGCACACACAGTGCAGGGAG
---
Jjk8C/G
99699 TTCCTTCAACACTTGGGGCAGATAACAATATTTTAGAGAAACGCGTTGACCCCACATTTG
----R75.4F------> G
99759 AGCTTCTTCTTTTGACCATTAAAGACAATGAGAATAAATCTCAAATACACCACGGGAGGT
<------
99819 GGTATCCTTGGCATTTTTTTTTTCCCTGAGGGAGAGCATGTTCCTAGGTTCCAGGTTCTC
---R75.5R---- --------R75.5Fs---->
99879 TTTGCCTCCCTACCCACGAACACATGCATGTGAAAGAAACAGACAAGATTGACATTTAAT
99939 CCCAATGTCTATTTATGAAAATTATCTTTAGGCCATTTTCTCAAGTTTTTCTCTTTCCAA
99999 AGTAAAATTGGGCAAATCAGATGAAAAACGAGGGTGGAGTTCAACCCCATCCTCAAATCC
100059 TTTTTTTTTTTTGGCTTGAGTGTCTGTCATTCCCAAGAGCCCTCCAACTGCCTTGAAGCA
100119 AGGCATGGGGGATTTCTCCGTGGTGCTTCCTGCCACTACTTGGCCAGACCAGTCTCCAGG
--------75.8F------>
100179 GGTTTCAGAGAGTGGAGAGGCCCCAAACCTATAGAGACTACTCCCAGATGGGGGGCTCCT
<---------RU75.9R------
<-----R75.9R--------
J5C/T
100239 TGTTTCTCCAGACCCTTCCTCTTCCATTTCATATGAGGCTTCCAAGAGGCCCCTGGCCGT
T
100299 GCTGGTCTGGGGCAGGGAATAAAGAAATGGCTTTTATTGTATCAGAGTCTCAACAGAAAA
<------RU76.0R----------
100359 CAGATGGCATACTCGAAATAGGACATTTCAAGGAAAGTTTATTTATTAGCAAAGTATTTA
J6G/A
100419 CAAAGAACTGGGTGGAGGATAGCTGTTACTACCCCAAGGTCCAAAGAGGCCGGGGACAGA
A
100479 AGGGGTTATCAGGACTCAGAAGGACAGCAAGCCCTGTACAGTCACCACCTTGCCAAGGGC
100539 AGTGCCCTTCAGTCAAGGGACACAACAGCTTAAGGTGACCTTGTAGGGAGGAAGCCAAGG
---
J7C/T
100599 GATTAGAAACACTGACCTCACTCCCCTCTTCCCTCTGCTCTTAGGCTGATGCTGGAAGCA
---R76.3F-------> T
100659 AGAAGAAGCCAGGGAGCATGGGAGCCATTCAATGTCATGCAGGTCAGCACCTGAGGCAGA
100719 CCCCAGGTGCAGAAGTATTGAGAGTGGGTCCAGAAGGACAGATGGAGGACAGGAAGTACA
100779 TTCACAACAAGAAGGAAAAACGTCAATGTTGTGGGGTGGAGAGAGAGGTGCAAAATCTGG
100839 GCTTCTTTTGGCCTTGGACAATGACAAGCGCATAGTAGCAACAGAAACTAAGTTTGTAGT
100899 TTCCTACTGGGGAGTTTGGGAGGACACTCACTTCTAGTTCTGTCTTCCCCACTTGAATTT
100959 TGATTGTGGTTATACTGAATTTATAGAAATTTGGGGTTAACTGACTTGTTTTTATTACTA
101019 AATCATACCATGCAAAAACAGGATGTTTTCTCATTTATTGAAATCATTTTGTTTGCTCTT
101079 TATTATGGTTTTTAAACTTTACTTTTTCATAGTAGTCCTGAGTATGCTCAGTTAATTCTT
101139 AGGCATGTTGTAGCTTTTGCTGCTATTGTGATTGGTATCTTATTGCAATTCTACTTTTGA
101199 ATCAGTAATTTCTGATGTAGAAGAATGTATCTAATTTAAAAAATTGTGGTTAAAAAAATA
diverged L1 element
101259 ACATTTACCGTCTTAACCACTTTGAAGTGTACAGCTCAGCAGTGTTAAGTATATTCACAT
101319 TTTTGTGCAACCAATCTCCAGAACTCCTTTTCACCTTGCAAAACCAGAACTCTACACCCA
----R77.0F2-------->
-------R77.0F------>
101379 TTAAACAACAACTCCTCATTTCTCTCTTCCTCTAGCCCCTGGCTACTATCACTCTACATT
<-----R77.1R-------
101439 CTGTTTCTATGAATCTGACTACTTCAGATACCCTGTACAAGTGCAATCATGGAGTTTTTG
101499 TCTTTTGGCGATTGGCTTATTTCACTTAGCTTAATGTCCTTAAAATTCATACTTGTTGCA
101559 GCATGTAAGAGTGCTTTCTTCCTTTTTAGGCTGAATAATAAGCTACTGTATGTATATGCC
101619 ATATTTTGTTTGCCCATTCATCTGTCTATGGTCATCTTTGTTGCTTCCACCTCTTGGCTA
101679 TCGAGAATAGTGCTGCTATGAATATGGGGGAAAATATCTGCTTAAGTCCCTGCTTTCAAT
101739 TCTTTTGCATTTATACCCAGAAGTGGACTCTTGGGTCATATAGTAGTTTTACTACTGATT
101799 TTTTGAGGAACTGCCGTACTGTTTCCCATAGCAGTTACACATTTTACAATCCCACGAACA
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