A multiple-sequence alignment of the kit's HIV-1 subtype reference sequences is presented below in GDE format:

Note that half the HMA primers (near the bottom of this page) were reversed and complemented to match the strand orientation of the alignment.  These primers are indicated within their sequence names.  Subtypes are indicated after the hyphens

#sf170-A3

atgggaccagagtctaaagccatgtgtaaagttaacccctctctgcgttactttaaattgtagccat---aa catcaccacc---------------------------------cataacatcaccaccaacaaccccaatat caccaaatacatggaaggagaaataaagaactgctcttacaatatgaccacagaactaagggataagaaaca gaaagtgtattcacttttttataaacttgatgtagtaccaattgataaaaataatggtaataacaatataag gactcagtatagattaataaattgtaatacctcagccattacacaggcttgtccaaaagtatcctttgagcc aattcccatacattattgtgctccagctggttttgcgattctaaagtgtaatgatgcagagttcaatggaac agggccatgcaagaatgtcagcacagtacaatgcacacatggaatcaggccagta-atatcaacccaactgc tgttaaatggcagtctagcagaaggaagggtaaagattagatctgaaaatatcacaaacaatgccaaaacca taatagtacaacttaacaagactgtagaaattaattgtaccagacctaacaacaatacaagaaaaagtgtac gtataggaccaggacaagcattctatgcaacaggtgacataataggggatataagacaagcatattgtaatg tcagtagagcagactggaataaaactttacaaggggtagccaaccaattaaaaagttactttagtaacaaaa caataatctttgctagctcctcaggaggggatttagaaattacaacacatagttttaattgtggaggagaat ttttttattgtgatacatcaggcctgtttaatagcacatgggggggaaatagcactgacagcatacaggagt caaatagcacagagtcaaatgacactataattctcccatgcagaataaagcaaattataaatatgtggcaga gagtaggacaagcaatgtatgcccctcccatc---caaggagtaataaagtgtatatcaaatattacaggac ttctattaacaagagatggtgg---------gga------taataacagtgca------aatgaaaccttca gacctacaggaggaaatatgagggacaattggagaagtgaattatataagtataaagtagtaaaaattgaac cactaggagtagcacccaccccggcaaagagaagagtggtgcag---agagaaaaaagagcagttgga---a taggagctgtattcattgggttcttaggagcagccggaagcact

#br20-B1

atgggatcaaagcctaaagccttgtgtaaagttaaccccactctgtgttactttaaattgcattgatttgaa t------------------------------------aatagtactaacaacaataatagtagtggggtaaa aacagggatagacaagggagagataaaaaactgctctttcaataccaccacaagtgtaaaagataaggagaa gaaggaatatgctctcttctataatcttgatgtagtacaaat---------aggtaatgataa------tac tagc---tatagattgacaagttgtaatacctcagtcattacccaggcctgtccaaaggtaacctttgagcc aattcccatacattattgtaccccggctggttatgcgattctaaagtgtaatggtaagaagttcaatggaac aggaccctgtacaaatgtcagcacagtacaatgtacacatggaattaagccagta-gtgtccactcaactgc tgttaaatggcagtctagcagaagaagatatagtaattagatctgaaaatctcacaaacaatgctaaaacca taatagtgcagctaaaggaccctgtagacattaattgtacaagacccaacaacaatacaagaaagagtatac atataggaccagggagagcattttatgcaacaggagacataataggagatataagacaagcacattgtaacc ttagcagagcacaatggaatgacactttaagcaagatagttacaaaattaagagaacaatttgagaataaaa caataaagtttcagccaccctcaggaggggatccagaaattgtatttcacagttttaattgtggaggggaat ttttctactgtaatacaacacaactgtttaatagtacctggacaaataacac---tgaagggacaagtaaca ctacagggaatgacac---------aatcacactcccatgtagaataaaacaaattgtaaacatgtggcagg aagtaggaaaagcaatgtatgcccctcccatc---aagggaaaaattaaatgttcatcaaacattacagggc tactattgacaagggatggtgg---------taa------taatgagatgaac---acgaccgagatcttca gacctggaggaggagatatgagggacaattggaggagtgaattatataaatataaagtagtaagaattgaac cattaggaatagcacccaccagggcaaagagaagagtggtgcaa---agagaaaaaagagcagtgggaacat taggagctatgttccttgggttcttgggagcagcaggaagcact

#th14-B2

atgggatcaaagcctaaagccatgtgtaaaattaaccccactctgtgttactttaaactgcactgatttgag g------------------------------------aatgctactaataccagtagtaca----------- -------atggagggaggagaaataaaaaactgctctttcaatatcaccacgagcataaaaactaaggta-- -aaagactatgcacttttttataaacttgatgtagtaccaat---------agataatgataa------tac cagc---tataggttgataaattgtaacacctcagtcattacacaagcttgtccaaaggtatcctttgagcc aattcccatacattattgtaccccggctggttttgcgattctacagtgtaacaataaaaagttcaatggaac aggaccatgtacaaatgtcagtacagtacaatgtacacatggaattaggccagta-gtatcaactcaactgc tgttaaatggcagtttagcagaagaagaggtagtaattagatctagcaatttcacggacaatgctagagtca taatagtacagctgaatgaatctgtagaaattaattgtacaagacccaacaacaatacaagaaaaagtatac atctaggaccagggcgagcatggtatacaacaggacaaataataggagatataagacaagcacattgtaacc ttagtagcacaaaatggaataacactttaagacagataactgaaaaattaagagaacaatttgggaacaaaa caatagtctttaatcaatcctcaggaggggacccagagattgtaatgcacagttttaattgtggaggggaat ttttctactgtaatacaacacaactgtttaatagtacttggaatgatactag---tacttgg---aataata atacaggaaatggcac---------tatcacgctcccttgcagaataaaacaaattgtaaacatgtggcagg aagtaggaaaagcaatgtatgcccctcccatc---agaggacaaattagatgttcatcaaatattacagggt tgctattaacaagagatggtgg---------taa------tagtgagaacaag---accaccgagaccttca gacctggaggaggagatatgagggacaattggagaagtgaattatataaatataaagtagtgaaaattgaac cattaggagtagcacccaccaagccaaagagaagagtggtgcag---agagaaaaaagagcagtgggaacga taggagctatgttccttgggttcttgggaacagcaggaagcact

#sf162-B3

atgggatcaaagtctaaagccatgtgtaaagttaaccccactctgtgttactctacattgcactaatttgaa g------------------------------------aatgctactaataccaagagtagtaat------tg gaaagagatggacagaggagaaataaaaaattgctctttcaaggtcaccacaagcataagaaataagatgca gaaagaatatgcacttttttataaacttgatgtagtaccaat---------agataatgataa------tac aagc---tataaattgataaattgtaacacctcagtcattacacaggcctgtccaaaggtatcctttgaacc aattcccatacattattgtgccccggctggttttgcgattctaaagtgtaatgataagaagttcaatggatc aggaccatgtacaaatgtcagcacagtacaatgtacacatggaattaggccagta-gtgtcaactcaattgc tgttaaatggcagtctagcagaagaaggggtagtaattagatctgaaaatttcacagacaatgctaaaacta taatagtacagctgaaggaatctgtagaaattaattgtacaagacctaacaataatacaagaaaaagtataa ctataggaccggggagagcattttatgcaacaggagacataataggagatataagacaagcacattgtaaca ttagtggagaaaaatggaataacactttaaaacagatagttacaaaattacaagcacaatttgggaataaaa caatagtctttaagcaatcctcaggaggggacccagaaattgtaatgcacagttttaattgtggaggggaat ttttctactgtaattcaacacagctttttaatagtacttgga---ataatac---tatagggccaaataaca ct------aatggaac---------tatcacactcccatgcagaataaaacaaattataaacaggtggcagg aagtaggaaaagcaatgtatgcccctcccatc---agaggacaaattagatgctcatcaaatattacaggac tgctattaacaagagatggtgg---------taa------agagatcagtaac---accaccgagatcttca gacctggaggtggagatatgagggacaattggagaagtgaattatataaatataaagtagtaaaaattgagc cattaggagtagcacccaccaaggcaaagagaagagtggtgcag---agagaaaaaagagcagtg---acgc taggagctatgttccttgggttcttgggagcagcaggaagcact

#ma959-C1

atgggatcaaagcctaaagccatgtgtaaagttgaccccactctgtgtcactttaaattgtagcaatgctaa c---------------------------------------------aacactgctaccaataatgtaactgc taccaataatgtaaccagtgacatgaaaaattgttctttcaatgcaaccacagaattaagagataagagaca gaaagtgtatgcacttttttataaacttgatatagtaccacttaatgagaaggataacagcag------ctc tggagaatatagattaataaattgcagtacctcaactgtaacacaagcctgtccaaaggtctcttttgaccc aattcctatacattattgtactccagctggttatgcgattctaaagtgtaataataagacattcaatgggac aggaccatgccataatgtcagcacagtacagtgtacacatggaattaagccagtg-gtatcaactcaactac tgttaaatggtagcctagcagaaggagaaataataattagatctgaaaatctgacaaacaatgtcaaaacaa taatagtgcaccttaatgaatctgtagaaattgtgtgtacaagacccaacaataatacaagaagaagtataa gaataggaccaggacaagtattctatgcaaataatgacataataggagacataagacaagcacattgcaaca ttagtaaggatgtctggaacagtactttacaaaaggtaggtaaaaaattaaaagaacacttccctaataaaa caataacatttgaaccacactcaggaggagatctagaaattacaacacatagttttaattgtagaggagaat ttttctattgcaatacatcagggctgtttaatagta---------actttaa---tgatacagaaggtaatt ca------actttaag---------cataaccctcccatgcagaataaaacaaattataaacatgtggcagg aggtaggacgagcaatgtatgcccctcccatt---gaaggaaacataacatgtaaatcaaatatcacaggac tactattgacacgtggtggagg---------tcc------a---actaacaca---aagacagagacattca ggcctggaggaggagatatgagggacaattggagaagtgaattatataagtataaagtggtagaaattaagc cattgggagtagcacccactaaggcaaaaaggagagtggtggag---agagaaaaaagagcagtggga---a taggagctgtgttccttgggttcttgggagcagcaggaagcact

#zm18-C2

atgggatcaaagcttaaagccatgtgtaaagttgaccccactctgtgtcactttagaatgtggaaatgttaa t---------------------------------------------------------------gttaccca tgagaatagcacgaagggggaaatgaaaaattgctctttcaatgcaaccacagaactaaaagataaaaaaca gagagtgtatgcacttttttataaacttgatatagtaccacttaatgagaataacaactctagtgaggactc tagtgagtatagattaataaattgtaatacctcagccataacacaagcctgtccaaaggtcactttggatcc aattcctatacattattgtgctccagctggatatgcgattctaaagtgtaataataagacattcaatgggac aggaccatgccataatgtcagcacagtacaatgtacacacggaatcaagccagtg-gtatcaactcaactac tgttaaatggtagcctagcagaagaagagataataattaggtctgaaaatctaacaaacaatgccaaaacaa taatagtacatcttaatgaatctgtagaaattgtgtgtacaagacccagcaataatacaagaaaaagtataa ggataggaccaggacaagcattctatgcaacaggtggcataataggaaacataagacaagcacattgtaaca ttagtaaagagaactggaataaaactttacaaaaggtaggaaaaaaattagcagagcacttccctaataaaa caataaaatttgaccaacactcaggaggggacctagaaattacaacacatagctttaattgtagaggagaat ttttctattgcaatacatcaaacctgtttaatagtacatata---agcctaa---tgatacaaatagtacat ataatcctaatgatac---------aatcacactcccatgcagaataaaacaaattataaacatgtggcagg gggtaggacaagcaatgtatgcccctcccatt---gcaggaaacataacatgtaaatcaaatatcacaggac tactattgacacgggatggagg---------gtc------aaatgataccaca---aacacagagacattca gacctggaggaggagatatgagggacaattggagaagtgaactatataaatataaagtggtagaaattaaac cattgggcatagcacccactgcggcaaaaaggagagtggtggagacgagagaaaaaagagcagtggga---a taggagctgtgttccttgggttcttgggagcagcaggaagcact

#in868-C3

atgggatccaagcctgaagccatgtgtaaagttgaccccactctgtgtcactttagaatgtagagaggttaa t---------------------------------------------gat------actagaaatggggttaa tgttaccaataatggggaagaaataaaaaattgctctttcaatgcaaccacagaaataagagataggaagca gacagtgtatgcacttttttatagacttgatatagtaccacttgataataagaagaagaaca---actctag tgagtattatagattaataaattgtaatacctcagccataacacaagcctgtccaaaggccacttttgatcc aattcctatacactattgtgctccagctggttttgcgattataaagtgtaataataagacattcaatgggac aggaccatgcagtaatgtcagcacagtacaatgtacacatggaattaagccagtg-gtatcaactcaactac tgttagatggtagcctagcagaagaagggataataattagatctgaaaatctgacaaacaatgccaaaataa taatagtacatcttgatcaacctgtagaaattgtgcgtacaagaccaaacaataatacaagaaaaagtataa ggataggaccaggacaaacattctatgcaacaggagacataataggagacataagacgagcatattgtaaca ttagtgaaaacaaatggaatgaaactttacaaagggtgagtaaaaaattagcagaatacttccctaataaaa caatacaatttgcatcatcctcaggaggggacctagaaattacaacacatagctttaattgtagaggagaat ttttctattgcaatacatcaaacctgtttaatggta------catacatgaa---tggtacaaaaagtaatt ca------agctcaac---------catcacaatcctatgcagaataaaacaagttgtaaacatgtggcagg aggtaggacgagcaatgtatgcccctcccatt---gaaggaaacataacatgtaaatcaaatatcacaggac tactattggcacgtgatggagg---------aac------a---gagtcaaat---catacagagatattca gacctggaggaggagatatgaggaacaattggagaagtgaattatataaatacaaagtggtagaaattaagc cattgggagtagtacccactacagcaaaaaggagagtggtggag---agagaaaaaagagcagtggga---a tgggagctgtgttccttgggttcttgggagcagcaggaaccact

#ug21-D1

atgggatcaaagcctaaaaccatgtgtaaaattacccccactctgtgtcactttaaactgcactgaatggaa g------------------------------------aatgccaccactaatgccactaatgagggcata-- -------------------ggaatgaaaaactgctctttc---------acagaagtaagagataagaagaa gcaagcatatgcacttttttataagcttgatgtggtacaaatgaatg---atgataatagtac------taa taccagttatagattaataaattgtaatgcctcaaccattacacaggcgtgtccaaagatatcctttgagcc aattcccatacattattgtgccccagctggatttgcaattctaaaatgtaatgataaaaagttcaatgggac aggtccatgtaaaaatgtcagcacagtacagtgtacacatgggattaagccagta-gtgtcaactcaactgt tgttgaatggcagtctagcagaagaagagataataattagatctgaaaatctcacaaataatgctaaaatta taatagtacatcttaatgagtctgtaccaattaattgcacaaggccctacgataaggtaagctacaggacac ctataggagtagggcgagcatcctatacaacaag---aataaaaggagatataagacaagcacattgtaaca ttagtggagaaaaatggaataaaactttacaacaggtagctgcgaaattaagagaccttcttaaccaaacag caataatttttaaaccatcctcgggaggggacccagaaattacaacacacagctttaattgtggaggggaat ttttctactgcaatacatcaggactgtttaacaatagtgtatggacatcaaa---tagt---acgatagggg ca------aatgggac---------aatcacactcccatgcagaataaaacaaattataaatatgtggcagg gagtaggaaaagcaatgtatacccctcccatt---gaaggacaaatcaactgttcatcaactattacaggac tattgttgacaagagatggtgg---------tgt------gaaaaataatagt---cagaacgagaccttca gacctggagggggagatatgagagacaactggagaaatgaattatacaaatataaagtagtaagaattgaac cactaggtctagcacccaccaaggcaaggagaagagtggtggaa---agagaaaaaagagcaatagga---c tgggagctttgttccttgggttcttgggagcagcaggaagcacg

#ug46-D3

------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ -----------------------------ataataattagatctgaaaatctcacaaataatgctaaaacca taatagtacagcttaatgagtctgtaccaattaattgctcaaggccctacgaaaataaaagacgacgtacac ctataggactagggcaagcgtactatacaacaaa---attaaaaggatatataagaccagcacattgtaata ttagtggagcagaatggaataaaactttacaacaggtagctaaaaaattaggagaccttttcaaccagacaa caataatttttcaacca------------------------------------------------------- ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ --------------------------------------------

#th22-E1

atgggatcaaagtctaaagccatgtgtaaagttaactcctctctgtgttactttaaattgtaccaatgctaa tttgatcaat---------------------------------gtcaataacataaccaatgtctctaacat aataggaaatataacagatgaagtaagaaactgtacttttaatatgaccacagaaataagagataaacagca gaaggtccatgcacttttttataggcttgatatagtacaaat---------gcataatgaaaa------tag tagtgagtataggttaataaattgtaatacttcagtcattaagcaggcttgtccaaagatatcctttgatcc aattcctatacattattgtactccagctggttatgcgattttaaagtgtaatgacaagaattttactgggac agggccatgtaaaaatgtcagctcagtacaatgcacacatggaattaagccagtg-gtatcaactcaattgc tgttaaatggcagtctagcagaagaagagataataatcagatctgaaaatctcacaaacaatgccaaaacca taatagtgcaccttaataaatctgtagaaatcaattgtaccagaccctccaacaatacaagaacaagtataa ctataggaccaggacaagtattctatagaacaggagacataataggagatataagaagagcatattgtgaga ttaatggaacaaaatggaataaagctttaaaacaggtaactgaaaaattaaaagagcactttaat---aaga caataatctttcaaccaccctcaggaggagatctagaaattacaatgcatcattttaattgtagaggggaat ttttctattgcaatacaacacgactgtttagtaatacttgcataaaaaatga---aaccatggcgggg---t gt------aacggcac---------tatcatacttccatgcaagataaagcaaattataaacatgtggcagg gagcaggacaagcaatgtatgctcctcccatt---aggggaagaattaattgtgtatcaaatattacaggaa tactattgacaagggatggtgg---------tgc------taataatgcg---------aacgagaccttca gacctggaggaggaaatataaaggacaattggagaagtgaattatataaatataaagtagtacaaattgaac cactaggaatagcacccaccagggcaaagagaagagtggtggag---agagaaaaaagagcagtggga---a taggagctatgatctttgggttcttaggagcagcaggaagcact

#th06-E2

atgggatcaaagtctaaagccatgtgtaaagttaactcctctctgcgttactttaaattgtaccaatgctaa agtgaccaat---------------------------------gtcagtaatacaatcaatgcccctgacat a---ggaaatataacagatgaagtaagaaactgttcttttaatatgaccacagaactaagagataagaagca gaaggtccatgcacttttttataagcttgatatagtacaa------------------gttaa------tag tagtgagtacaggttaataaattgtaatacttcagtcattaagcaggcttgtccaaagatatcctttgatcc aattcctatacattattgtgctccagctggttatgcgattttaaagtgtaatgataaaaacttcaatgggac agggccatgtaaaaatgtcagctcagtacaatgcacacatggaattaagccagtg-gtatcaactcaattgc tgttaaatggcagtctagcagaagaagagataataatcagatctgaaaatctcacaaacaatgccaaaacca taatagtgtaccttaataaatctgtagaaatcaattgtaccagaccctccaacaatacaagaacaagtataa ctataggaccaggacaagtattctatagaacaggagacataataggagatataagacaagcatattgtgaga ttaatgaaacaaaatggaatgaaactttaaaacaggtaactaaaaaattaaaagagcactttaataataaga caataatctttcacccaccctcaggaggagatctagaaattataacgcatcattttaattgtagaggggaat ttttctattgcaatacaccaaaattgtttaatggaaccatggaggggcctaa---taacacggaggggccta at------aacactac---------tatcatacttccatgcaagataaagcaaattgtaaacatgtggcagg gagcaggacaagcaatgtatgctcctcccatc---agtggaagaattaattgtgtatcaaatattacaggaa tactattaacaagagatggtgg---------tgc------taataatacgac------taacgagaccttca gacctggaggaggaaatataaaggacaattggagaagtgaattatataaatataaagtagtacaaattgaac cactaggaatagcacccaccagggcaaagagaagagtggtggag---agagaaaaaagagcagtggga---a taggagctatgatctttgggttcttaggagcagcaggaagcact

#bz162-F1

atgggatcaaagcctaaagccatgtgtgaagttaaccccactctgtgttactttaaattgtactgatgccat c------------------------------------aatagcact------aaaaacagcacc-------- -ctgatggaagagtcaggggcaatacaaaactgttctttcaatatgaccacagaagtaagagataagcagaa gagagtacatgcacttttttataaacttgatatagtaccaat---------caatggcagtag------aac atca---tacaggctaataaattgtaatacctcaaccattacacaggcttgtccaaaggtatcttgggatcc tattcccatacattattgtgctccagctggttatacgattctaaagtgtaaggataaaaagttcaatgggac agggccatgcgagaatgtcagcacagtacaatgtacacatggaattaaaccagtg-gtatcaactcaattgt tgttaaatggcagcctagcagaagaaagtatagtaatcagatctcaaaatatctcagataatgcaaaaatca taatagtacaccttaatgaatctgtacaaattaattgtacaagacccaacaacaatacaagaaaaagtatac atataggaccaggacgggcactttatgcaacaggagacataataggagacatcagaaaggcacattgtaacg ttagtagaacacaatggaataagaagttagaccaggtaaaggcagagttaaagtctcatttccctaatgcaa caatacaatttaactcatcctcaggaggggacctagaagttacaatgcatcattttatttgtaaaggagaat ttttctactgcgatacatcaagactgttcagtaacac---------------------agaatccaatggca cagaatccaatggcac---------tatcactctcccatgtcgaataaaacaaatggtaaacatgtggcagg aagtaggacgaacaatgtatgccgctcccatc---gcaggaaacattacctgtaactcaaatattacaggtc tactattgacaagagacggtgggttagatgatggtaggaatactagtcagactaatcggactgagatcttca gacctgggggaggaaatatgaaagacaattggagaagtgaattatataaatataaagtagtagaaattgaac cactaggagtagcacccaccaaggcaaaaagacaagtggtgaag---agagaaaaaagagcagtggga---a taggagctatgttccttgggttcttgggagcagcaggaagctct

#bz163-F2

atgggatcaaagcctaaagccatgtgtgaagttaaccccactctgtgttactttaaattgtactaatgccat t------------------------------------aatgccactgccattcaagacggggac-------- -ctgaaggaaggaccaggggcaatacaaaactgttctttcaatgtgaccatggaagtaagagataagcagca gaaagtacatgcactgttt-atagacttgatatagtaccaattagcaatggaagaaatggcag------tgg agactactacaggctaataaattgcaatacctcaaccattacacaggcttgtccaaaagtatcttggggtcc aattcccatacattattgtgctccagctggttatgcgattttaaagtgtaatgataaaaagttcaatgggac agggccatgcaagaatgtcgc-acagtacagtgtacacatggaattaaaccagtg-gtatcaactcaattgt tgttaaatggcagcctagcagaagaagatataataatcagatctcaaaatatctcagataatgcaaaaacca taatagtacactttaatgaatctgtacagattaattgtacaagacccaacaacaatacaagaaaaggtatac atataggaccaggacgagcattttatgcaacaggagacataataggagacatcagaaaggcccattgtaatg ttagtggaacacaatggaataaaacattagaacaagtaagggcaaagttaaagtctcattttcctaatgcaa caataaaatttaattcatcctcaggaggggacctagaaattacaatgcatagttttaattgtagaggagaat ttttctactgcaatacatcaggactgtt------------------------------------taacgaca caggatccaatggcac---------tatcactctcctatgtcgaataaaacaaatggtaaacatgtggcagg aagtgggacgagcaatgtatgccgctcccatc---tcagaaaacattacctgtaactcgaatattacaggtc tactattgacaagagatggtgg---------tca------gaataataatcag------actgagaccttca gacctgggggtggtgatatgaaagactattggagaagtgtattatataagtataaagtagtagaaattgaac cactaggagtagcacccaccagggcaaaaagacaagtggtgagg---agagaaaaaagagcagtggga---a tgggagctttgttccttgggttcttgagcgcggcaggaagcact

#ru131-G1

atgggatgaaagcctaaagccatgtgtaaagttaacccctctctgtgttactttaaactgtagaaatgtaag ctgtactaattgtactaagggaaac---------------------------------------aacaatag aactgtggaaggcaaggacgaaatgaaaaactgctctttcaatgtaactacagaaataagagataagaaaaa gacagaatacgcgcttttctataaacttgatgtagtaccaatta------atgatgaaagtag------taa tagtacttataggctaataaattgtaatgtctcaaccattaaacaggcttgtccaaaggtgaattttgaccc aattcccatacattattgtgctccagctggttttgcgattttaaagtgtagggataagaatttcactggaac aggaccatgtaaaaatgtcagtacagtacaatgtacacatggaattaagccagtg-gtatcaactcaattat tgctgaatggcagcttagcagaagaagaaataatagttagatctgaaaacttcacagacaatgccaaagtca taatagtgcagcttaataaatctgtagaaattacatgtaccagacctaataacaatacaagaaaaagtataa cttttgcaccaggacaagcgctctatgcaacaggtgaaataataggagatataagacaagcacattgtaatg ttagtagaaaagattggaatgagatgttgcagaatgtgactacaaaactaaaaggaatctttaacaacacaa acataacatataactcagctgcaggaggagatctagaaattacaacacatagttttaattgtagaggagaat ttttctattgcaatacatcaggactgtttaataatag---------tgagaa---taactccactatcgaga at------aactccac---------tatcacactcccatgtaggataaaacaaattataataatgtggcaga gagtggggcaagcaatgtatgcccctcccatc---gcaggaaacatcacatgtatttcaaacattacaggac tactattaacaagagatggtgg---------gaa------caataataacagcacaaataatgagaccttca gacctggaggaggagatatgagggacaattggagaagtgaattatataagtataaagtagtaagaattaaac cactaggagtagcacccaccagg------------------------------------------------- --------------------------------------------

#lbv21-G2

atgggatgaaagcctaaagccatgtgtaaagttaacccctctctgtgttaccttaaactgtactaat----- -------------gcaatcgctaatgtaaccaacagcaataagactagtaacaacagcagccttgggaatag cactgtgagtagcatagaagaaatgaaaaactgctctttcaatataaccacagaagtaagagataagagtaa gaaagaatacgctcttttctatagacttgatgtggtaccaattaatggtaatgaaaatagtag------tac aactgattataggctaataaattgtaatgcctcaaccattaaacaagcttgtccaaaggtgacttttgaccc aattcccatacattattgcgctccagctgggtttgcgattctaacatgtagggataagaagttcaatggaac aggaccgtgtaaaaatgtcagtacagtgcaatgtacacatggaattaagccagtg-gtatcaactcaattac tgctgaatggcagtttagcagaagaagaaataatgattagatctgaaaacttcacaaacaatgccaaaaaca taatagtgcaatttaataaatctatagatattgtgtgtaccagacccaacaacaatacaagaaaaagtatac acataggacctggacaagcattatatgcaacaggcgccataataggcgatataagacaagcacattgtaatg ttagtgaaacagactggagagacatgttacagaaggtaaaagcacaactacaaggaatctacaacaaaagc- --ataacctttaactcatcctcaggaggggacctagaaattacagcacatagttttaattgtagaggagaat ttttctattgtaatacatcaggactgtttaatagtagtatattatctaacaa---taatgcaccatctaata gc------agtaagaa---------tatcacactcccatgtagaataaaacaaattgtaagaatgtggcaga gggtgggacaagcaatgtatgcccctcccatt---gcaggaaacattacatgtaaatcaaacattacaggac taatattaacaagagatggtgg---------gaa------tagtaccaatgga------aatgagaccttca gacctgcaggaggagacatgagggacaattggagaagtgaattatataagtataaagtaataaaaattaaac cactaggagtagcacccaccaaggcaaggagaagagtggtgggg---agagaaaaaagagcaattact---- --ggagctgtcttccttgggttcttaggagcagctgggagcact

#vi525-G3

atgggatgaaagcttaaagccatgtgtagagctaacccctctctgtgttactttaaactgtactaaggtaac ctacaatagcactgcagccaacaatagatcatccactgtcaccacccctactagtactgtaaccaacaatag cactgtgagtggcaaagaagaaatgacaaactgctctttcaatgtaaccacagaactaagagataagcagaa ggcagaatacgcgcttttctataaacttgatgtagtaccaat---------tgataataatag------aaa tgatagttataggctaatacattgtaatgtctcaaccattaaacaggcttgtcccaaggtatcttttgaacc aattcccatacattattgtgctccagctggttttgcaattttaaagtgtagggagaagaatttcactggaac aggactatgtaaaaatgtcagtacagtacaatgtacacatggaattaagccagtg-gtatcaactcaactac tgctgaatggcagtttagcagaaaaagaaattataattagatctgaaaacttcacaaacaatgccaaagtca taatagtgcagcttaatgaaactgtagaaattaattgtaccagacccaacaacaatacaagaaaaagtataa aattcggaacaggacgagtgttatatgcaacaggtgccataataggaaatataagacaagcacattgtaatg ttagtacagaaaaatggggtaagatgttacagaatgtagctgcaaaactacaaaaagaatttaataaa---a acataacctttaactcatcctcaggaggggacctagaaattacaacacatagttttaattgtagaggagaat ttttttattgtaagacatcagagctgtttaatagtacttggttgtttaatagtactg---ggctggttaata gtacttggaatgatacacgaaaagatattacactgcaatgcaaaataaaacaaattgtgagaatgtggcaga gagtgggacaagcaatgtatgcccctcccatcgcagcaggaaacattgaatgtagatcaagcattacaggac taatattaacaagagatggtgg---------gaa------taataataatacc------aatgagaccttca gacctggaggaggagacatgaggggcaattggagaagtgaattatataagtataaagtagtaaaaatcaaat cactaggagtagcacccaccagggcaaggagaagagtggtggag---agagaaaaaagagcaattgga---c tgggagctgtcttccttgggttcttaggagcagcaggaagcact

#vi557-H2

------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ -----------------------aaccatgtaataattagatctaaaaatatcacagacaataccaaaaaca taatagtacagcttaaaagtcctgtaccaattaactgtaccagacccaacaataatacgagaaaaagtataa gtatagggccaggacaagcattctatgcaacaggtgacatcataggagatataagaaaagcatattgtaata ttactagggaagattggaaaaggactttacatgaggtagttcagcaattaagagaacactttaataatcaaa caataattttcgaaccatcctcaggaggggacatggaaattacaatgcatacttttaattgtagaggagaat ttttctattgcaatacatcaaaattgtttaacagtacttggg---ttaacag---tacatcaaatgatatct caaatggcacaacaat---------aattgaactgccatgcagaataaaacaaattataaacatgtggcaga gagtaggacaagcaatgtatgcccctcccatc---aaaggaaaaattacatgtgaatcaaatattacagggc taatattgacaagtgatcatg---------------------ttaattctgcagaaagtaatgttaccttca gacctggaggaggagatatgagggacaattggagaagtgaattatataaatataaagtagtaagagtcgaac cactaggattagcacccaccagggcaaggagaagagtggtggaa---agagaaaaaagagctgtggga---c tggaagctgttttccttgggttcttgggagcagcagggagcact

#se9173-J1

atgggatgaaagcttaaagccatgtgtaaagataacccctctctgtgtcactttaaattgtagcgac----- -------------------------gtcaatagtaacaatagtacagatagtaatagtagtgcaagcaacaa tagtcct---------gaaatcatgaaaaactgctctttcaatgtaactacagaaataagaaataaaaggaa gcaagaatacgcgcttttctatagacaagatgtagtaccaat---------taatagtgacaa------taa aagt---tatattctaataaactgtaatacctcagttattaaacaggcttgtccaaaggtgtcttttcaacc aattcccatacattattgtgctccagctggttttgcgattctaaaatgtaataataagactttcaatggaac aggaccatgcaaaaatgtcagtacagtacaatgtacacacggaattaagccagtg-gtatcaactcaactac tgctaaatggcagtgtagcagaaggagacataataattagatctgaaaatatctcagacaatgctaaaaaca taatagtacaacttaatgacactgtagaaattgtgtgtaccagacctaataacaatacaagaaaaggtatac acatgggaccaggacaagtgctctacgcaacaggggaaataataggagatataaggaaagcatattgtaaca ttagtagaaaagattggaataacactttacgtagagtagctaaaaaactaagagaacactttaataaaaca- --atagactttacatcaccctcaggaggggacatagaaattacaacacatagttttaattgtggaggagaat ttttctattgtaatacatcaacactgttcaatagtagttgggatgagaataacattaaggacacaaatagta caaatgacaacacaac---------tatcacaataccatgtaaaataaaacaaattgtgagaatgtggcaaa gaacaggacaagcaatatatgcccctcccatc---gcaggaaacattacatgcaaatcaaatattacaggat tattattgacacgtgatggagg---------aaaca---ggaatggcagtgagaatggcactgagaccttca gacctacaggaggaaatatgaaagataattggagaagtgaattatataaatataaagtagtagagcttgagc cactaggagtagcacccaccaaggcaaaaagaagagtggtggag---agagaaaaaagagcagtggga---a taggagctgtgttccttgggttcttgggaacagcaggaagcact

#se9280-J2

atgggatgaaagcttaaagccatgtgtaaagataacccctctatgtgtcactttaaattgtagtaac----- -------------------------atcactagtaacagtaatacaactagtaacagtagtgtaagt----- -agtcct---------gatatcatgacaaactgctctttcaatataactacagaaataagaaataaaaggaa gcaagagtacgcgcttttctatagacaagatgtagtaccaat---------tgatagtaacaa------taa aaat---tatattctaataaactgtaatacctcagtcattaaacaagcttgtccaaaggtgtcttttcaacc aattcccatacattattgtgccccagctggttttgcgattctaaaatgtaatgataagaatttcaatggaac aggatcatgcaaaaatgtcagtacagtacaatgtacacacggaattaagccagtg-gtatcaactcaactac tgctaaatggcagtatagcagaaggagacataataattagatctgaaaacatctcagacaatgccaaaaaca taatagtacaacttaataaaactgtagaaattgtgtgttacagacctaataacaatacaaggaaaggtatac acatgggaccaggacaagtgctctacgcaacaggagaaataataggaaatataagagaaacacattgtaaca ttagtgaaagagattggagtaacactttacgtagagtagctacaaaactaagagaacactttaataaaaca- --ataaactttacatcaccctcaggaggggatatagaaattgtgacacatagttttaattgtggaggagaat ttttatattgtaatacatcaaaactgttcaatagtagttgggataagaatagcattgaagctacaaatgaca caagt---nacgcaac---------tatcacaataccatgtaaaataaaacaaattgtgagaatgtggcaaa ggacaggacaagcaatctatgcccctcccatt---gcaggaaacattacgtgcacatcaaatattacaggat tactattgacacgtgatggagg---------aaacagggggaatggcagtgagaatggcactgagaccttca gacctacaggaggaaatatgaaggacaattggagaagtgaattatataaatataaagtagtagagattgagc cactaggagtagcacccaccaaggcaaaaagaagagtggtggag---agagaaaaaagagcagtggga---a taggagctgtgttccttgggttcttgggaacagcaggaagtact

#primer_ed5

atgggatcaaagcctaaagccatgtg---------------------------------------------- ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ --------------------------------------------

#primer_ed31

------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ -----------------------------cctcagccattacacaggcctgtccaaag-------------- ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ --------------------------------------------

#primer_es7

------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ -----------------------------------------------------tgtaaaacgacggccagtc tgttaaatggcagtctagc----------------------------------------------------- ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ --------------------------------------------

#primer_ed33_reverse_complement

------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ---------------------------------------------------------------gaggggaat ttttctactgtaa----------------------------------------------------------- ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ --------------------------------------------

#primer_es8_reverse_complement

------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------tgagggacaattggagaagtgggtcatagctgtttcctg--------------- ------------------------------------------------------------------------ --------------------------------------------

#primer_ed12_reverse_complement

------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ ------------------------------------------------------------------------ --------------cttgggttcttgggagcagcaggaagcact