3. Do an intrasubtype alignment and construct the consensus sequence of each subtype, after this step you should have two consensus sequences, one from HIV-1 subtype-B and the remaining sequence from HIV-1 subtype-E

intrasubtype B 

              1
Bu84793       -------AAAACCATGTGTAAAATTAACCCCACTCTGTATTACTTTAAATTGCACCAATTGGAAGAAGAATGATACTAAA
Bu84792       -------AAAACCATGTGTAAAATTAACCCCACTCTGTATTACTTTAAATTGCACCAATTGGAAGAAGAATGATACTACA
Bu84797       -------AAAGCCATGTGTAAAATTAACCCCACTCTGTGTTACTTTAAATTGCAGTGATTATA---GGAATGCTACTGAT
Bu84796       -------AAAGCCATGTGTAAAATTAACCCCACTCTGTGTTACTTTAAATTGCAGTGATTATA---GGAATGCTACTGAT
Bu84798       -------AAAGCCATGTGTAAAATTAACCCCACTCTGTGTTACTTTAAATTGCAGTGATTATA---GGAATGCTACTGAT
Bu84807       -------AAAGCCATGTGTAAAATTAACCCCACTCTGTGTTACTTTAAATTGCACTGATGATTTAGGGAATGCTACTAAT
Bu84810       -------AAAGCCATGTGTAAAATTAACCCCACTCTGTGTTACTTTAAATTGCACTGATGATTTAGGGAATGCTACTAAT
Bu848103      -------AAAGCCATGTGTAAAATTAACCCCACTCTGTGTTACGTTAAATTGCACTGACCCAA------ATGTTACTAA-
Bu84801       AAAGCCTAAAGCCATGTGTAAAGTTAAACTCACTCTGTGTTACTTTAAAGTGCA--------------------------
Bu84802       AAAGCCTAAAGCCATGTGTAAAGTTAACCTCACTCTGTGTTACTTTAAAGTGCA--------------------------

              81
Bu84793       ACTAGTA---------------------GTAGTAGTACTACAACTAATAGTAGTTGGGGAGAGATAAAGGAGGGAGAAAT
Bu84792       ACTAATAATAGTAGTGCTACAGCTAATAGTAGTAGTACTACAACTAATAGTAGTTGGGGAGAGATAAAGGAGGGAGAAAT
Bu84797       TATAAGA---------------------ATGCTACTGATACCACTAGTAGTAACGAGGGAAAGATGGAGAGAGGAGAAAT
Bu84796       TATAGGA---------------------ATGCTACTGATACCACTAGTAGTAACGAGGGAAAGATGGAGAGAGGAGAAAT
Bu84798       TATAAGA---------------------ATGCTACTGATACCACTAGTAGAAACGAGGGAAAGATGGAGAGAGGAGAAAT
Bu84807       ACCAATA---------------------GTAGTGCCACTACTAATAGTAGTAGTTGGGAAGAAATGAAG---GGGGAAAT
Bu84810       ACCAATA---------------------GTAGTGCCACTACCAATAGTAGTAGTTGGGAAGAAATGAAG---GGGGAAAT
Bu848103      --------------------------------------------------TAGCGAGAGAACAATAGAGGGGGGAGAAAT
Bu84801       --------------------------------------------------------------------A---GGATAAAT
Bu84802       --------------------------------------------------------------------A---GGATAAAT

              161
Bu84793       AAAGAACTGCTCTTTCAATATCACCACAAGCATAAGAGACAAGGTGAAGAAAGAATATGCACTTTTTTATAGCCTTGATG
Bu84792       AAAGAACTGCTCTTTCAATATCACCACAAGCATAAGAGACAAGGTGAAGAAAGAATATGCACTTTTTTATAGCCTTGATG
Bu84797       AAAAAACTGCTCTTTCAATATCACCACAAGCATAAAAAATAAGATGCAGAAAGAATATGCACTTTTCTATAAACTTGATA
Bu84796       AAAAAACTGCTCTTTCAATATCACCACAAGCATAAAAAATAAGATGCAGAAAGAATATACACTTTTCTATAAACTTGATA
Bu84798       AAAAAACTGCTCTTTCATTATCACCACAAGCATAAAAAATAAGATGCAGAAAGAATATGCACTTTTCTATAAACTTGATA
Bu84807       GAAAAGATGCTCTTTCAATATCACCACAAGCATAAGAGATAAGATTAAGAAAGAACATGCACTTTTCTATAGACTTGATG
Bu84810       GAAAAGATGCTCTTTCAATATCACCACAAGCATAAGAGATAAGATTAAGAAAGAACATGCACTTTTCTATAGACTTGAGG
Bu848103      AAAAAATCGCTCTTTCAATATCACCACAAACATAAGAGATAGGTTTCAGAAAGAATATGCACTTTTTTATAAACTTGATG
Bu84801       GACAAACTGCTCTTTCAACATCACCACAAGTATAAGAGATAAGGTGCAGAAAGAATATGCACTTTTGTATAAACTTGATG
Bu84802       GACAAACTGCTCTTTCAACATCACCACAAGTATAAGAGATAAGGTGCAGAAAGAATATGCACTTTTGTATAAACTTGATG

              241
Bu84793       TAGTACCAATAGAAAATGAT---AATACTAGCTATAGGTTGAGAAGTTGTAACACCTCAGTCATTACACAAGCCTGTCCA
Bu84792       TAGTACCAATAGAAAATGAT---AATACTAGCTATAGGTTGAGAAGTTGTAACACCTCAGTCATTACACAAGCCTGTCCA
Bu84797       TAGTACCAATAGATAAT---------ACAAGCTATACATTGATAAGTGGTAACACCTCAGTCATTACACAGGCCTGTCCA
Bu84796       TAGTACCAATAGATAAT---------ACAAGCTATACATTGATAAGTGGTAACACCTCAGTCATTACACAGGCCTGTCCA
Bu84798       TAGTACCAATAGATAAT---------ACAAGCTATACATTGATAAGTGGTAACAACTCAGTCATTACACAGGCCTGTCCA
Bu84807       TAGTACCAATAGATAATGAT---AATACCACATATAGGTTGATAAATTGTAATACCTCAGTCATTACACAGGCCTGTCCA
Bu84810       TAGTACCAATAGATAATGAT---AATACCACATATAGGTTGATGAATTGTAATACCTCAGTCATTACACAGGCCTGTCCA
Bu848103      TAATACCATTAGGTAATGAT---AATACTAGCTATAGGTTGATAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCA
Bu84801       TAGTACCAATAGAAGAAGATGACAATACTAGCTATAGATTGATAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCA
Bu84802       TAGTACCAATAGAAGAAGATGACAATACTAGCTATAGATTGATAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCA

              321
Bu84793       AAGGTAACTTTTGAGCCAATTCCCATACATTATTGTACCCCGGCTGGTTTTGCGATCCTGAAGTGTAAAGATAAAAAGTT
Bu84792       AAGGTAACTTTTGAGCCAATTCCCATACATTATTGTACCCCGGCTGGTTTTGCGCTTCTGAAGTGTAAAGATAAAAAGTT
Bu84797       AAGGTATCCTTTGAACCAATTCCCATACATTATTGTGTCCG---TGGTTTTGCGATTCTAAAGTGTAATGATAAGAAGTT
Bu84796       AAGGTATCCTTTGAACCAATTCCCATACATTATTGTGTCCG---TGGTTTTGCGATCCTAAAGTGTAATGATAAGAAGTT
Bu84798       AAGGTATCCTTTGAACCAATTCCCATACATTATTGTGTCGG---TGGTTTTGCGATTCTAAAGTGTAATGATAAGAAGTT
Bu84807       AAGGTATCATTAGAGCCAATTCCCATACATTTTTGTGCCCCGGCTGGTTTTGCGATTCTAAAGTGTAATAATAAGACGTT
Bu84810       AAGGTATCATTTGAGCCAATTCCCATACATTTTTGTGCCCCGGCTGGTTTTGCGATTCTAAAGTGTAATAATAAGACGTT
Bu848103      AAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGTTGGTTTGGCGATTCTAAAGTGTAAAGATAAGAAGTT
Bu84801       AAGGCATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAGTGTAATGATAAGAAGTT
Bu84802       AAGACATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAGTGTAATGATAAGAAGTT

              401
Bu84793       CAATGGAACAGGACCATGCAAAAACGTTAGCACAGTACAATGTACACATGGAATTAAGCCAGTAGTGTCAACTCAACTGC
Bu84792       CAATGGAACAGGACCATGCAAAAATGTTAGCACAGTACAATGTACACATGGAATTAAGCCAGTAGTGTCAACTCAACTGC
Bu84797       CAGTGGAAAAGGAGAATGTAAAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGC
Bu84796       CAATGGAAAAGGAGAATGTAAAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGC
Bu84798       CAATGGAAAAGGAGCATGTAAAAATGTCAGGACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGC
Bu84807       CGAGGGAAAAGGACCATGTAAAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTGTCAACTCAACTGC
Bu84810       CGAGGGAAAAGGACCATGTAAAAATGTCAGTACAGCCCAATGCACACATGGAATTAAGCCAGTAGTGTCAACTCAACTGC
Bu848103      CAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAAGCCAGTAGTATCAACTCAACTGT
Bu84801       CAATGGAACAGGACCATGTAAAAACGCCAGTACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGT
Bu84802       CAATGGAACAGGACCATGTAAAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGT

              481
Bu84793       TGTTAAATGGCAGCCTAGCAGAAGAAGAGGTAATAATTAGATCTGCCAATTTCTCAAACAATGCTAAAATCATAATAGTA
Bu84792       TGTTAAATGGCAGCCTAGCAGAAGAAGAGGTAATAATTAGATCTGCCAATTCCTCAAACAATGCTAAAATCATAATAGTA
Bu84797       TGTTAAATGGCAGTCTAGCAGAAGAAGAGGTGGTAATTAGATCTGACAATTTCACAGACAATACTAAAACCATAATAGTA
Bu84796       TGTTAAATGGCAGTCTAGCAGAAGAAGAGGTGGTAATTAGATCTGACAATTTCACAGACAATACTAAAACCATAATAGTA
Bu84798       TGTTAAATGGCAGTCTAGCAGAAGAAGAGGTGGTAATTAGATCTGACAATTTCACAGACAATACTAAAACCATAATAGTA
Bu84807       TGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAATAATTAGATCTGACAATATCACAGACAATACTAAAACCATTATAGTA
Bu84810       TGTTAAATGGCAGTCTAGCAGAAGAAGAGGCAATAATTAGATCTGACAATATCACAGACAATACTAAAACCATTATAGTA
Bu848103      TGTTATATGGCAGTCTAGCAGAAGAAGACATAGTAATTAGATCCGCCAATCTCACAGACAATGCTAAAAACATAATAGTA
Bu84801       TGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATCAGATCTGCCAATTTCACAGACAATGCTAAAACCATAATAGTA
Bu84802       TGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATCAGATCTGCCAATTTCACAGACAATGCTAAAACCATAATAGTA

              561
Bu84793       CAGTTGAGGGAACCTGTAGAAATTAATTGTACAAGACCCAGCAACAATACAATAAAAGGTATACACATAGGACCAGGGAG
Bu84792       CAGTTGAGGGAACCTGTAGAAATTAATTGTACAAGACCCAGCAACAATACAATAAAAGGTATACACATAGGACCAGGGAG
Bu84797       CAGCTGAAAGAATCTGTAGAAATTAATTGTATAAGACCCAACAATAATACAAGAAAAGGTATACATATAGGACCAGGGAG
Bu84796       CAGCTGAAAGAATCTGTAGAAATTAATTGTATAAGACCCAACAATAATACAAGAAAAGGTATACATATAGGACCAGGGAG
Bu84798       CAGCTGAAAGAATCTGTAGAAATTAATTGTATAAGACCCAACAATAATACAAGAAAAGGTATACATATTGGACCAGGGAG
Bu84807       CAGCTAAACGAATCTGTAGTAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGGAG
Bu84810       CAGCTAAACGAATCTGTAGTAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGCCCGGGGAG
Bu848103      CAGCTGAATGAATCTGTAACAATGAATTGTACAAGACCCAACAACAATACAATGAAAAGTATACATATAGGACCAGGCAG
Bu84801       CATCTAAATGAAACTGTAAAAATTAATTGTACAAGACTTGGCAACAATACAAGAAAAAGTATAAATATAGGACCAGGGAG
Bu84802       CATCTAAATGAAACTGTAAAAATTAATTGTACAAGACTTGGCAACAATACAAGAAAAAGTATAAATATAGGACCAGGGAG

              641
Bu84793       AGCATTTTATGCAACAGGAGACATACGAGGAGATATAAGACAAGCACATTGTAACATTAGTGGAGCAAAATGGAATAACA
Bu84792       AGCATTTTATGCAACAGGAGACATACGAGGAGATATAAGACAAGCACATTGTAACATTAGTGGAGCAAAATGGAATGACA
Bu84797       AGCATGGTATGCAACAGGAGAAATAGTAGGAGATATAAGACAGGCATATTGTAACATTAGTAGAACAAAATGGAATAACA
Bu84796       AGCATGGTATGCAACAGGAGAAATAGTAGGAGATATAAGACAGGCATATTGTAACATTAGTAGAACAAAATGGAATAACA
Bu84798       AGCATGGTATGCAACAGGAGAAATAGTAGGAGATATAAGACAGGCATATTGTAACATTAGTAGAACAAAATGGAATAACA
Bu84807       TGCATTTTTTGCAACAGGAGAAATAATAGGAGATATAAGACAAGCACACTGTAACCTTAGTAGAACACAATGGAATAACA
Bu84810       TGCATTTTTTGCAACAGGAGAAATAATAGGAGATATGAGACAAGCACACTGTAACCTTAGTAGAACACAATGGAATAACA
Bu848103      AGCAATTTATGCAACAGGAAACATAATAGGAGATATAAGACAAGCACATTGTAACATTAGTGGGACAAAATGGAATGACA
Bu84801       AGTACTCTATGCAACAGGAGAAATAATAGGAGACATAAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACA
Bu84802       AGTACTCTATGCAACAGGAGAAATAATAGGAGACATAAGACAAGCACATTGTAACATTAGTAGAGCAAAATCGAATAACA

              721
Bu84793       CTTTAAAGAAGGTAGTTATAAAATTAAAAGAACAATTTCCAA------------ATAAAACAATAGTCTTTAACCATTCC
Bu84792       CTTTAAAGAAGGTAGTTATAAAATTAAAAGAACAATTTCCAA------------ATAAAACAATAGTCTTTAACCATTCC
Bu84797       CTTTAATACAGATAGCTAACAAATTAAAAGAACAATATA---------------ATACAACAATAAGCTTTAATCGATCC
Bu84796       CTTTAATACAGATAGCTAACAAATTAAAAGAACAATATA---------------ATACAACAATAAGCTTTAATCGATCC
Bu84798       CTTTAATACAGATAGCTAACAAATTAAAAGAACAATATA---------------ATACAACAATAAGCTTTAATCGATCC
Bu84807       CTTTAGGAAAGATAGTCATAAAATTAAGAGAACAATTTAGAAAACAATTTGGAGAAAAAACAATAGTCTTTAATCGATCC
Bu84810       CTTTAGGAAAGATAGTCATAAAATTAAGAGAACAATTTAGAAAACAATTTGGAGAAAAAACAATAGTCTTTAATCGATCC
Bu848103      CTTTGAACAAGATAGCTATAAAATTAAGAGAACAATTTA---------------ATGAGGCAATAGTCTTTAATCAATCC
Bu84801       CTTTAAAACAGATAGTTAGAAAATTAAGAGAACAATTTGGGA------------ATAAAACAATAGTCTTTAATCAATCC
Bu84802       CTTTAAAACAGATAGTTAGAAAATTAAGAGAACAATTTGGGA------------ATAAAACAATAGTCTTTAATCAATCC

              801
Bu84793       TCAGGAGGGGACCCAGAAATTGTAATGCACAGTTTTAATTGTCAAGGGGAATTTTTCTACTGTAATACAACAAAGCTGCT
Bu84792       TCAGGAGGGGACCCAGAAATTGTAATGCACAGTTTTAATTGCCAAGGGGAATTTTTCTACTGTAATACAACAAAGCTGTT
Bu84797       TCAGGAGGGGACCCAGAAATTGTAACGCATAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTT
Bu84796       TCAGGAGGGGACCCAGAAATTGTGACGCATAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCTACACAACTGTT
Bu84798       TCAGGAGGGGACCCAGAAATTGTAACGCATAGTCTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTT
Bu84807       TCAGGAGGGGACCCGGAAATTGCAATGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAACACAACAGCACTGTT
Bu84810       TCAGGAGGGGACCCGGAAATTGCAATGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAACACAACAGCACTGTT
Bu848103      TCAGGAGGGGACCCAGAAATTGCAACGCTCAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTT
Bu84801       TCAGGAGGGGACCCAGAAATTGTAATGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTT
Bu84802       TCAGGAGGGGACCCAGAAATTGTAATGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATACAACACAACTGTT

              881
Bu84793       TAATAGTACTTGGAATG------------------ATACTACAGAGTCAAATAACAATGATAGTACTATTACACTCCCAT
Bu84792       TAATAGTACTTGGAATAGCACT------TGGAATAATACTACAGAGTCAAATAACAATGATAGTACTATTACACTCCCAT
Bu84797       TAATAGTACTTGGAATTTAAATGGTACTTGGAATTTTACTGCAGGGTCAAATGAAACTGAAGGCAATATCACACTCCCAT
Bu84796       TAATAGTACTTGGAATTTAAATGGTACTTGGAATTTTACTGCGGGGTCAAATGAAACTGAAGGCAATATCACACTCCCAT
Bu84798       TAATAGTACTTGGAATTTAAATGGTACTTGGAATTTTACTGCAGGGTCAAATGAAACTGAAGGCAATATCACACTCCCAT
Bu84807       TAATAGTACCTGGAATGTTACTAAAAGGTTGAATAACACTGAAGGAAATAGCACAGGAGATGAAAATATCATACTCCCAT
Bu84810       TAATAGTACCTGGAATGTTACTAAAGGGTTGAATAACACTGAAGGAAATAGCACAGGAGATGAAAATATCATACTCCCAT
Bu848103      TAATAGTACTTGGAATAGTACTG---GGTCAAATAACACTAAAGG----AA--------AGGACACAATCACACTCCCAT
Bu84801       TAATAGTACTTGGAATAATACT------TGGAAGGATCCTAACAGG---AG---------CGACAATATCACACTCCCAT
Bu84802       TAATAGTACTTGGAATAATACT------TGGAAGGATCCTAACAGG---AG---------TGACAATATCACACTCCCAT

              961
Bu84793       GCAGAATAAAACAAATTATAAACATGTGGCAGGAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGAGGAGAAATTAAA
Bu84792       GCAGAATAAAACAAATTATAAACATGTGGCAGGAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGAGGAGAAATTAAA
Bu84797       GCAGAATAAAACAAATTATAAACAGGTGGCAGGAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACGAATAAGA
Bu84796       GCAGAATAAAACAAATTATAAACAGGTGGCAGGAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATAAGA
Bu84798       GCAGAATAAAACAAATTATAAACAGGTGGCAGGAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGA
Bu84807       GTAGAATAAAACAAATTATAAACATGTGGCAGGAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGA
Bu84810       GTAGAATAAAACAAATTATAAACATGTGGCAGGAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGA
Bu848103      GCAGAATAAGACAAATTATAAACATGTGGCAGAAAATAGGAAAAGCAATGTATGCCCCTCCCATCAAAGGGCAAATTAGA
Bu84801       GCAGAATAAAACAAATTATAAACATGTGGCAGGAAGTAGGAAAAGCAATGTACGCCCCTCCCATCAGAGGGGAAATTAGA
Bu84802       GCAGAATAAAACAAATTATAAACATGTGGCAGGAAGTAGGAAAAGCAATGTACGCCCCTCCCATCAGAGGGGAAATTAGA

              1041
Bu84793       TGTTCATCAAATATTACAGGACTACTGTTAACAAGAGATGGTGGTATTAACA-CT-----------AGCGATGCCA---C
Bu84792       TGTTCATCAAATATTACAGGACTACTGTTAACAAGAGATGGTGGTATTAACA-CT-----------AGCGATGCCA---C
Bu84797       TGCTCATCAAACATTACAGGGATGATATTAACAAGGGATGGTGGTAACGAGAACAATAATGA---GAGCACTAATA---C
Bu84796       TGCTCATCAAACATTACAGGGATGATATTAACAAGGGATGGTGGTAACGAGAACAATAATGA---GAGCAGTACTA---C
Bu84798       TGCTCATCAAACATTACAGGGATGATATTAACAAGGGATGGTGGTAACGAGAACAATAATGA---GAGCAGTACTA---C
Bu84807       TGTTCATCGAATATTACAGGGCTGCTACTAACAAGAGATGGTGGTAGTAAGAAC------GA---GAGCATCACCA---C
Bu84810       TGTTCATCAAATATTACAGGGCTGCTACTAACAAGAGATGGTGGTAGTAAGAAC------GA---GAGCATCACCA---C
Bu848103      TGTTCATCAAATATTACAGGGCTAATATTAATAAGAGATGGTGGTAACAACAACA-T--------GAGCAAGACCA---C
Bu84801       TGTTCATCAAATATCACAGGGCTGCTACTAACAAGAGATGGTGGTAATGACGATGGTAATGACACGACCACAAACAGGAC
Bu84802       TGTTCATCAAATATCACAGGGCTGCTACTAACAAGAGATGGTGGTAATGACGATGGTAATGACACGACCACAAACAGGAC

              1121
Bu84793       CGAGACCTTCAGACCGGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTGAAAATTG
Bu84792       CGAGACCTTCAGACCGGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTGAAAATTG
Bu84797       TGAGATCTTCAGACCGGGAGGAGGAGATACGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTG
Bu84796       TGAGACCTTCAGACCGGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTG
Bu84798       TGAGACCTTCAGACCGGGAGGAGGAGATATGAGGAACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTG
Bu84807       CGAGGTCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTG
Bu84810       CGAGGTCTTCAGACCTGGAGGAGGTGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTG
Bu848103      CGAGACCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTG
Bu84801       CGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAGATATAAAGTAGTAAAAATTG
Bu84802       CGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAGATATAAAGTAGTAATAATTG

              1201
Bu84793       AGCCATTAGGAGTAGCACCCACCAAGGCCAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGT---AACACTAGGAGCT
Bu84792       AGCCATTAGGAGTAGCACCCACCAAGGCTAAGAGGAGAGTGGTGCAGAGAGAAAAGAGAGCAGT---TACACTAGGAGCT
Bu84797       AGCCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGG-------------
Bu84796       AGCCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAGCGCTAGGAGCT
Bu84798       AACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAGCGCTAGGAGCT
Bu84807       AACCATTAGGAGTAGCGCCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAACAATAGGAGCT
Bu84810       AACCATTAGGAGTAGCGCCCACCAAGCCAAAGAGAAGAGTGGTG------------------------------------
Bu848103      AACCATTAGGAGTAGCACCCACCAGGCCAAAGAGAAGAGTGGT-------------------------------------
Bu84801       AACCATTAGGAATAGCACCCACCAGGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGT---AGGACTAGGAGCT
Bu84802       AACCATTAGGAATAGCACCCACCAGGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGT---AGGACTAGGAGCT

              1281
Bu84793       ATGTTCCTT--------------------
Bu84792       ATGTTCCTT--------------------
Bu84797       -----------------------------
Bu84796       ATGTTCCTTGGGTTCT-------------
Bu84798       ATGTTCCTTGGGTTCT-------------
Bu84807       ATGTTCCTTGGGTTCTTGGG---------
Bu84810       -----------------------------
Bu848103      -----------------------------
Bu84801       TTGTTCCTTGGGTTCTTGGGAGCAGCAGG
Bu84802       TTGTTCCTTGGGTTCTTGGGAGCAGCAGG

>Bconserve:

-------AAAGCCATGTGTAAAATTAACCCCACTCTGTGTTACTTTAAATTGCATGATA-
--GAATGTACTAAA---------------------TTTACATATAGTAGGGAAATAGGGA
GAAATAAAAAACTGCTCTTTCAATATCACCACAAGCATAAGAGATAAGTGCAGAAAGAAT
ATGCACTTTTTATAAACTTGATGTAGTACCAATAGATAATGAT---AATACAGCTATAGT
TGATAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAA
TTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAGTGTAATGATAAGAAGT
TCAATGGAAAGGACCATGTAAAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCC
AGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAG
ATCTGCAATTTCACAGACAATCTAAAACCATAATAGTACAGCTGAAGAATCTGTAGAAAT
TAATTGTACAAGACCCAACAACAATACAAGAAAAGTATACATATAGGACCAGGGAGAGCA
TTTATGCAACAGGAGAAATATAGGAGATATAAGACAAGCACATTGTAACATTAGTAGAAC
AAAATGGAATAACACTTTAAAAGATAGTTAAAAATTAAAGAACAATTTAA----------
--ATAAAACAATAGTCTTTAATCATCCTCAGGAGGGGACCCAGAAATTGTAATGCACAGT
TTTAATTGTGGAGGGGAATTTTTCTACTGTAATCAACACAACTGTTTAATAGTACTTGGA
ATACTTGGAATATACTAGGGAAGAGCAATATCACACTCCCATGCAGAATAAAACAAATTA
TAAACATGTGGCAGGAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGGGACAAATTAG
ATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAAACTGA---G
AGCAACCA---CCGAGACTTCAGACCGGAGGAGGAGATATGAGGGACAATTGGAGAAGTG
AATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAA
AGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGT---ACTAGGAGCTTGTTCCTT-----
--------
 
 
 
 

intrasubtype E 

              1
Eu48278       GCCAGTGGTATCAACTCAATTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGATAATAATCAGATCTGAGAATCTCACAA
Eu48275       GCCAGTGGTATCAACTCAATTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGATAATAATCAGATCTGAAAATCTCACAA
Eu48277       GCCAGTGGTATCAACTCAATTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGATAATAATCAGATCTGAAAATCTCACAA
Eu48268       GCCAGTGGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGATAATAATCAGATCTGAAAATCTCACAA
Eu48273       GCCAGTGGTATCAACTCAATTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGATAATAATCAGATCTGAAAATCTCACAG
Eu48269       GCCAGTGGTATCAACTCAATTGCTGTTAAATGGCAGTCTTGCAGAAGAAGAGATAATAATCAGATCTGAAAATCTCACAA
Eu48265       GCCAGTGGTATCAACTCAATTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGATAATAATCAGATCTGAAAATCTCACAA
Eu48267       GCCAGTGGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGATAATAATCAGATCTGAAAATCTCACAA
Eu48274       GCCAGTGGTATCAACTCAATTGCTGTTAAATGGCAGTCTAGSAGAAGAAGAGATAATAATCAGATCTGAAAATCTCACAA
Eu48272       -------------------------------------------GAAGAAGAGATAATAATCAGATCTGAAAATCTCACAA

              81
Eu48278       ACAATGCCAAAACCATAATAGTGCATCTTAATAAATCTGTAGAAATCAATTGTACCAGACCCTCCAACAATACAAGAACA
Eu48275       ACAATGCCAAAACCATAATAGTGCACCTTAATAAATCTGTAGAAATCAATTGTACCAGACCCTCCAACAATACAAGAACA
Eu48277       ACAATGCCAAAACCATAATAGTGCACCTTAATAAATCTGTAGAAATCAATTGTACCAGACCCTCCAACAATACAAGAACA
Eu48268       ACAATGCCAAAACCATAATAGTGCACCTTAATAAATCTGTAGAAATCAATTGTACCAGACCCTCCAACAAGAAAAGACAA
Eu48273       ACAATACCAAAACCATAATAGTGCACCTTAATAAATCTGTAGAAATCAATTGTACCAGACCCTCCAACAATAAAAGAACA
Eu48269       ACAATGCCAAAACCATAATAGTGCACCTTAATAAATCTGTGGAAATCAATTGTACCAGACCCTCCGACAGGATGAGAACA
Eu48265       ACAATGCCAAAACCATAATAGTGCACCTTAATAAATCTGTAGAAATCAATTGTACCAGACCCTCCGATATTACAAGAATA
Eu48267       ACAATGCCAAAACCATAATAGTGCACCTTAATAAATCTGTAGAAATCAATTGTACCAGACCCTTCTATA---CAAGAATA
Eu48274       ACAATGCCAAAACCATAATAGTGCACCTTAATAAATCTGTAGAAATCAATTGTACCAGACCCTCCAACAATACAAGAACA
Eu48272       ACAATGCCAAAACCATAATAGTGCACCTTAATGAATCTGTAGAAATCAATTGTACCAGACCCTCCAACAATACAAGAACA
  
  161
Eu48278       AGTATAACTATGGGACCAGGACAAGTATTCTATAGAACAGGAGACATAATAGGAGATATAAGAAAAGCATATTGTGAGAT
Eu48275       AGTATAACTATGGGACCAGGACAAGTATTCTATAGAACAGGAGACATAATAGGAGATATAAGAAAAGCATATTGTGAGAT
Eu48277       AGTATAAATATAGGACCAGGACAAGTATTTTATAGAACAGGAGACATAATAGGAGATATAAGAAAAGCATATTGTGAGAT
Eu48268       AGGGTAACTATAGGGCCAGGACGAGTATACTATAGCACAGGAGACATAATGGGAGATATAAGAAAAGCACATTGTGAAAT
Eu48273       AGGATAACTATAGGACCAGGACGAGTATTCTATAGAACAGGAGAAATAATAGGAGATATAAGAAAAGCATATTGTGAAAT
Eu48269       CCTATGAGAATAGGACCAGGACGAGTATTCTATAAAACAGGAAACATAATGGGAGATAGAAGAACAGCATACTGTGAAAT
Eu48265       AGTACAAGAATAGGACCAGGACGAGTATTCTATAAAACAGGAAACATACTAGGAGATATAAGAAAAGCATATTGTGAGAT
Eu48267       AGTATGACTAGGGGACCAGGACACGTATTCTATAGAACAGGAAAAATAGTAGGAGATCCAAGAAAAGCATATTGTGAGAT
Eu48274       AGTATAACTATAGGACCAGGACGAGTATTCTATAGAACAGGAGACATAACAGGAGATATAAGAAAAGCATATTGTGAGAT
Eu48272       AGTGTAAGAATAGGACCAGGACAAGTATTCTATAGAACAGGAGACATAACAGGAGACATAAGAAAAGCATATTGTGAGAT

              241
Eu48278       TAATGGAACAAAATGGAATGAAGCTTTAAAACAGGTAACTGGAAAACTAAAAGAGCACTTTAA---TAAGACAATAATCT
Eu48275       TAATGGAACAAAATGGAATGAAGCTTTAAAACAGGTAACTGGAAAACTAAAAGAGCACTTTAA---TAAGACAATAATCT
Eu48277       TAATGAAACAAAATGGACTAAAGTTTTAAAACAGGTAACTGAAAAATTAAAAGAGCACTTTAAGAATAAGACAATAATCT
Eu48268       TAATGGAACAAAATGGAATAAAGTTTTAAAACAGGTAACTGAAAAATTAAAAGAGCACTTTAATAA---GACAATAGTCT
Eu48273       TAATGGAACAAAATGGAATAAAGTTTTAAAACAGGTAACTGAAAAATTAAAAGGGCACTTTAATAA---GACAATAGTCT
Eu48269       TAATGGAACAAAATGGAATAGAGTTTTAAAACAGGTAATGGGAAAATTAAAAGAGCACTTTAATAATAAGACAATAACCT
Eu48265       TAATGGAACAAAATGGAATGAAACTTTAAAACAGGTAGCTGGAAAATTAAAAGAGCACTTTAATAA---GACAATAATCT
Eu48267       TAATGGAACAAAATGGAATGAAGCTTTAAAACAGGTAACTGAAAAATTAAAAGAGCACTTTAATAA---GACAATAATCT
Eu48274       TAATGGAACAAAATGGAATGAAGTTYTAAAACAGGTAACTGAAAAATTAAAAGAGCACTTTAAGAATAAGACAATAATCT
Eu48272       TAATGAAACAAAATGGAATGAAACTTTAAAACAGGTAACTGAAAAATTGAAAGAGCACTTTAAAAATAAGACAATAATCT

              321
Eu48278       TTCAGCCACCCTCAGGAGGAGATCTAGAAATTACAATGCATCATTTTAGTTGTAGAGGGGAATTTTTCTATTGCAATACA
Eu48275       TTCAACCACCCTCAGGAGGAGATCTAGAAATTACAATGCATCATTTTACTTGTAGAGGGGAATTTTTCTATTGCAATACA
Eu48277       TTCAACCACCCTCAGGAGGAGATCTAGAAATTACAATGCATCACTTTAATTGTAAAGGGGAATTTTTCTATTGCAATACA
Eu48268       TTCAACCACCCTCAGGAGGAGATCTAGAAATTACAATGCATCATTTTAATTGTAGAGGGGAATTTTTCTATTGCAATACA
Eu48273       TTCAACCACCCTCAGGAGGAGATCTAGAAATTACAATGCATCATTTTAATTGTAGAGGGGAATTTTTCTATTGCAATACA
Eu48269       TTCAACCACCCTCAGGAAGAGATCTAGAAATCACAATGCATCATTTTAATTGTAGAGGGGAATTTTTCTATTGCAATACA
Eu48265       TTAAACCACCCTCAGGAGGAGATCTAGAAATTACAATGCATCATTTTAATTGTAGAGGGGAATTTTTCTATTGCAATACA
Eu48267       TTCAACCACCATCAGGAGGAGACCTAGAAATTACAATGCATCATTTTAATTGTAGAGGGGAATTTTTCTATTGCAATACA
Eu48274       YTAAACCACCCTCAGGAGGAGATCTAGAAATTACAATGCATCATTTTAATTGTAGAGGGGAGTTTTTCTATTGCAATACA
Eu48272       TTCAACCACCCTCAGGAGGAGATCTAGAAATTACAATGCTTCATTTTAATTGTAGAGGGGAATTTTTCTATTGCAATACA

              401
Eu48278       ACACAACTGTTTAATAGTACTTGCATAAGAAATGAAAGCATGGAGGGGTGTAATGGCACTATCATACTTCCATGCAAGAT
Eu48275       ACACAACTGTTTAATAATACTTGCATAGGAAATGAAACCATGGAGGGGTGTAATGGCACTATCATACTTCCATGCAAGAT
Eu48277       ACACAACTGTTTAATAATACTTGCATAAAAAATGAAACCATGGGGGGGTGTAATGGCACTATCATACTTCCATGCAAGAT
Eu48268       ACAAGTCTGTTTAATAATACTTGCATAGGAAGTGAAACCCTG------TGTAATGGCAAGATCACACTTCCATGCAAGAT
Eu48273       ACAAAACTGTTTAATAATACTTGCATA---AATGAAACCATGGGGGGGTGTAATGACACTATCACACTTCCATGCAAGAT
Eu48269       ACACGACTGTTTAATAATACTTGCATAGGAAATGAAACTAAGGAGGGGTGTAATGGCACTATCACACTTCCATGCAAGAT
Eu48265       ACACAACTGTTTAATAGTACTTGGCCAGGAAATGAAACCATGGAGAAGTATAATGGCACTATCACACTTCCATGCAAAAT
Eu48267       ACAAAACTGTTTAATAGTACCGGGATAGGAAATGAAACCATGAAGGGGTATAATGACACTATCACACTTCCATGCAGGAT
Eu48274       ACAAATTTGTTTAATAATACTTGCATA---AATGAAACCATGRGAGGGTGTAATGACACTATCACACTTCCATGCAAGAT
Eu48272       TCAAAACTGTTTAATACCACTCGCATAGGAAATGAAACCAAGGAGGAGGGTAATGGCACTATCATACTTCCATGCAGGAT

              481
Eu48278       AAAACAAATTATAAACATGTGGCAAGGCGCAGGACAAGCAATGTATGCTCCTCCCATCAGTGGAAGAATTAATTGTGTAT
Eu48275       AAAGCAAATTATAAACATGTGGCAGGGAGCAGGACAAGCAATGTATGCTCCTCCCATCAGTGGAAGAATTAATTGTGTAT
Eu48277       AAAGCAAATTATAAACATGTGGCAGGGAGCAGGACAAGCAATGTATGCTCCTCCCATCAGTGGAAGAATTAATTGTGTAT
Eu48268       AAAGCAAATTATAAACATGTGGCAGGGAGTAGGACAAGCTATGTATGCTCCTCCCATTACTGGAAAAATTAATTGTGTAT
Eu48273       AAAGCAAATTGTAAACATGTGGCAGGGAGCAGGACAAGCAATGTATGCTCCTCCCATCAGTGGAAGAATTAATTGTGTAT
Eu48269       AAAGCAAATTATAAAAATGTGGCAGGGAGTAGGACAAGCAATGTATGCTCCTCCCATCAGTGGAATAATTAATTGTTTAT
Eu48265       AAAGCAAATTATAAACATGTGGCAGGGAGCAGGACAAGCAATGTATGCTCCTCCCATCAGTGGAACAATTAATTGTGTAT
Eu48267       AAAGCAAATTATAAACATGTGGCAGGGAGCAGGACAAGCAATGTACGCTCCTCCAATCAAAGAAAGAATTAATTGTGTAT
Eu48274       AAAGCAAATTATAAACATGTGGCAGGGAGCAGGACAAGCAATGTATGCTCCTCCCATCAGTGGAAGAATTAATTGTGTAT
Eu48272       AAAGCAAATTATAAACATGTGGCAGGGAGTAGGACAAGCAATGTATGCTCCTCCCATCAGTGGAAGCATTAATTGTGTAT

              561
Eu48278       CAAATATTACAGGAATACTATTGACAAGAGATGGTGGTG------CTAATAACACGGCTAACGAGACCTTCAGACCTGGA
Eu48275       CAAATATTACAGGAATACTATTGACAAGAGATGGTGGTG------CTAATAATACGGCTAACGAGACCTTCAGACCTGGA
Eu48277       CAAATATTACAGGAATACTATTGACAAGAGATGGTGGTG------CTAATAATACGACTAACGAGACCTTCAGACCTGGA
Eu48268       CAAATATTACAGGAATACTATTGACAAGAGATGGTGGT---------AATAATACGAATAACGAGACCTTCAGACCTGGA
Eu48273       CAAATATTACAGGAATACTATTGACAAGAGATGGTGGTGGTGATGCTAATAATAGGAAGAACGAGACCTTCAGACCTGGA
Eu48269       CAAATATTACAGGAATACTATTGACAAGAGATGGTGGTC------CTAATAATATGACTAATGAGACCTTCAGACCTGGA
Eu48265       CAAATATTACAGGAATACTATTGACAAGAGATGGTGGTC------CTAATAGTACGAATAATGAGACCTTCAGACCTGGA
Eu48267       CAAATATTACAGGAATACTATTGACAAGAGATGGTGGTA------TTAATAGTACGACTAACGAGACCTTCAGACCTGGA
Eu48274       CAAATATTACAGGAATACTATTGACAAGAGATGGTGGTG------CTCATAATGATACTAAGGAGATCTTCAGACCTGGA
Eu48272       CAAATATTACAGGAATACTATTGACAAGAGATGGTGGTG------ATAATAGTGATACTAATGA----------------

              641
Eu48278       GGAGGAAA-----
Eu48275       GGAGGAAA-----
Eu48277       GGAGGAAA-----
Eu48268       GGAGGAAA-----
Eu48273       GGAGGAAA-----
Eu48269       GGAGGAAA-----
Eu48265       GGAGGAAA-----
Eu48267       GGAGGAAAAAGCC
Eu48274       GGAGGAAAAAGCC
Eu48272       -------------

>Econserve:

GCCAGTGGTATCAACTCAATTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGATAATAAT

CAGATCTGAAAATCTCACAAACAATGCCAAAACCATAATAGTGCACCTTAATAAATCTGT

AGAAATCAATTGTACCAGACCCTCCAACAATACAAGAACAAGTATAACTATAGGACCAG

GAC*AGTATTCTATAGAACAGGAGACATAATAGGAGATATAAGAAAAGCATATTGTGAG

ATTAATGGAACAAAATGGAATGAAG*TTTAAAACAGGTAACTGAAAAATTAAAAGAGCA

CTTTAA*AATAAGACAATAATCTTTCAACCACCCTCAGGAGGAGATCTAGAAATTACAAT

GCATCATTTTAATTGTAGAGGGGAATTTTTCTATTGCAATACAACA*AACTGTTTAATAAT

ACTTGCATAGGAAATGAAACCATGGAGGGGTGTAATGGCACTATCACACTTCCATGCAAG

ATAAAGCAAATTATAAACATGTGGCAGGGAGCAGGACAAGCAATGTATGCTCCTCCCATC

AGTGGAAGAATTAATTGTGTATCAAATATTACAGGAATACTATTGACAAGAGATGGTGGT

G------CTAATAATACGATAACGAGACCTTCAGACCTGGAGGAGGAAA-----
 
H1 H2 H3 H4 H5 H6 H7 H8 H9-H13