lowQualScore                  :                                      1111111                                                             11111111                                        11                                         1111   22222222       11111111               333333333333                               2222222222222222                  2222222                       1                  22222222                      11111                      1                              1111111111                                              11         11111                            
lowQualScore                  :                        3             1111111             6     11  1 5          44   6     777       1   99999999      4                     66   4      33    66                                   4444   77777777 55  4 11111111         7  4  333333333333            22   0    0      0 7777777777777777                  9999999                       5         3  9 1   11111111           3          22222    99    3 3  55     9   4  7       7 66            9999999999    0     1            4       4       8      22         22222      3 9  66         77    
lowQualScore                  :                        .             .......             .     ..  . .          ..   .     ...       .   ........      .                     ..   .      ..    ..                                   ....   ........ ..  . ........         .  .  ............            ..   .    .      . ................                  .......                       .         .  . .   ........           .          .....    ..    . .  ..     .   .  .       . ..            ..........    .     .            .       .       .      ..         .....      . .  ..         ..    
lowQualScore                  :                        6             8888888             7     77  0 2          66   0     555       9   66666666      7                     11   4      00    11                                   0000   55555555 55  0 44444444         0  6  000000000000            11   9    1      1 6666666666666666                  9999999                       0         3  0 8   00000000           3          66666    88    3 3  55     6   4  0       2 11            0000000000    1     1            4       4       0      33         55555      2 4  99         99    
consensus                     :                 NNTGATT-TTTGTTCTTTATT-------CTATAGTAAATAATAAAAGTTTGAANGCTTGTCATT--CATAGAGAG--ACCCAAATGAAA-GAAG---TGAAACTTACATTTTACTGTTTGTCAAC--CTC-TGCACTACCAAA--ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----T---T--TT-T----T---CTGCTCAGTGTGTACAC-TGTTGACAAAGTGAAAGTAGACTTCCGAAATCATGTATTC-----------ATA-CCCCAATTTCCAAGCATCA-A-TTT-TTTTTCTAAATTCACAATTCAAACATGACAATG-CTNTCAAAAT------GTTCAAAATAC-ATCAATAACG----CCATT-NAAAT-A-AA--AAATGAGCA-TTAAAATAAGGA--AAATGCATTTTT--AAA----GAAGAAGAAACGAGGATTATTTAT-AACCGCC-ATTATGCGACTACCCCACGGAAGCA-----CTTCCTNTTTC--CAATGGTGG--TACT
Reference ( gi|3 )            :                 AATGATT-TTTGTTCTTTATT-------CTATAGTAAATAATAAAAGTTTGAAGGCTTGTCATT--CATGGAGAG--ACCCAAATAAAA-AATG---TGAAACCTACATTTTACTGTTTGTCAAC--CTC-TGCACTGTCAAA--ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----T---T--TT-T----T---CTGCTCAGTATGTACGA-TGTTGACATAGTGAAAGTAGACTTCCGAAATCATGTATTC-----------ATA-CCCCAATTTCCAAGCATCA-A-TTTATTTTTCTAAATTCACAATTCAAAGATGACAATG-CTATCAAACT------GTTCAAAATAC-ATCAATAATG----TCATT-AAAAT-A-AA--AAATGTGCA-TTGAAATAAGAA--AAATGCATTTTT--AAA----GAAGAAGAAACGAGGATTATTTAT-AACCGCC-ATTATGCAACTACCTTACGGAAGCA-----CTTCCTTTCTC--CAATGGTGG--TACTT
gi|2                          :                   TGATT-TTTGTTCTTTATT-------CTATGGTAAATAATAAAAGTTTGAAGGCTTGTCATT--CAAAGAGAG--ACCTAAATGAAA-GAAG---TGAAACTTACATTTTACTGTTTGTTAAC--ATC-TGCACTATCAAA--ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----T---T--TT-T----TTTTCTGCTCAGTGTG-------------A-AGTGAAAGTAGACTTCCAAAATTATGTACTC-----------ATA-CCCCAATTTCCATGCATTA-T-TTTTTTTTTCTAACTTCACAATTCAAACATGAAAATG-CTGTCAGAAT------GTTCAAAATAC-ATCAATAATG----CCATT-TGAATAA-AA--AAATGAACA-TTAAAATAAGGA--AAATGCAGTTTT--AAA----GAAGAAAAAACGAGGATTATTTAT-AACTGCC-ATTATGCGACTACCCCACGGAAGCA-----CTTCCTTT-TC--CAATGGTGG--TACT
gi|1                          : aaggtgtaaaccaatcatTGCTT-TTTGTTCTTTATT-------CTATAGTAAATAATAAACGTTTGAAAGCTTGTCATT--CATAGAGGG--TCCCAAATGAAA-GAAG---TGAAACTTACATTTTACAATTTGTCAAC--CTC-TGCATTACCAAA--ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AAA----C---A--AT-T--------CTGCTCTGTGTGTACAC-TTTTGACAAAGTGAAAGTAGATTTCCGAAATCATGTATTC-----------ATA-ACCCAATTTCCAAGCATCATA-TTC--TTTTCTAAATTCACAATTCTAACATGATAATG-CTTTCAAAAT------GTTCAAAATAC-ACCGATAATG----CCATT-CAAAT-A-AA--AAATA-GCATTTAAAATAAGGA--AAATGCATTTTT--AAA----GAAGAAGAAACAAGAATTATTTAT-AACCGCC-ATTATGCGACAACCCCAATGAAGCA-----CTTCCTTTTTC--CAATGGTGG--TACTatgcc
gi|4                          :     tgtaagcccaccatTGAGT-TTTGTTATTTATT-------CTATTGTAAATAATAAAAGTTTGAAGGCTTGTCATT--CATAGAGAA--TCCCAAATGAAA-GAAG---TGAAACCTACATTTTACTGTTTGTCAAC--CTC-TGCACTATCAAA--ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGAGATTT---T--TT-T----T---CTGCTCAGTGTGTACAC-TGGTGACAAAGTGATAGTAGAC------AAT------TT------------------CCAA-------GCATC--A-TTTTTTTTTCTAAATTCACAATTCAAACATGACAATG-CTATCAAAAT------GTTCAAAATAC-ATTAATAATG----CCATT-CAAAT-A-AAATAAATGAGCA-TTTAAATAAGGA--AAATGCATTTTT--AAA----GAAAAAGAAATGAGGATTATTTAT-AACCGCC-ATCATGCGACTACCCCACGGAAGTA-----CTTCCTTTTTG--CAATGGTGG--TACTat
gi|7                          :  aggtgttacctcaccatTGATT-TTTGTTCTTTATT-------CTATTGTAAATAATAAAAGTTTGAAGGCTTGTCATT--CATAGAGAA--TCCCAAATGAAA-GAAG---TGAAACCTACATTTTACTGTTTGTCAAC--CTC-TGCACTATCAAA--ATATGATGAGAAAAGTAGGGGTCATGTGTCATATAAG--AGA----TTG-T--TT-T----T---CTGCTCAGTGTGTACAC-TGGTGACAAAGTGAAAGTAGACTTCCGAAATCATGTATTC-----------ATA-TCCCAGTTTCCAAGCATCA-ATTTTTTTTTTCTAAATTCATGATTCAAACATGAAAATG-CTATCAAAAT------GCTCAAAATAC-ATCAATGATG----CCATT-CAAAA-A-AA--AAATGAGCA-TAAAAATAAGGA--AAATGCATTTTT--AAA----GAAGAatgc
gi|10                         : aaagtgtcaacccaccatTGATTGTTTGTCCTTTATT-------CTATAGTAAATAATACAAGTTTGAAGGCTTGTCATT--TATAGAGAG--ACCTAAATGAAA-GCAG---TGAAACATACATTTTACTGTTTGTCAA---CTC-TGTACTTCTAAA--ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGATAT-T---T--TT-T----T---CTGCTCAGTGTGTACAC-TGTTGACAAAGTGAAAGTAGACTTCCGAAATCATGTATTCCGAAATCATGTATT-CTCCAATTTCCAAGCAT-A---------TTTCTAAATTCACAATTCAAACCTGACAATG-CTATAAAAAT------GTTAATAATATGAACAATAATG----GCATT-CCAAT-A-AA--
gi|9                          :   ggtgtaagtccaccatTGATT-TTTGTTCTTTGTT-------GTATAGTAAATAA-AAAAGTATACATGCTTGTCATT--CATAGAGAT--ACCCAACTGAAA-GAAGT--TG--GCTTGCATTTAATTACTTAT
gi|11                         :         agctcaccatTGATT-GTTGCTCTTTATTGAAATTTCTATAGTAAATAA--AGAGC----ATGTTTGTCATT--CATAGAGAGAGACACAAATGAAA-GAAG---TGAAACTTACATTTAATTGTTTCTCAAC--CAC-TGCAATA-CAGAATATATGATGAGAAAAGTAGGGTTCATATGGCATATA----AAA----C---TAGTT-T----T---CTGTTCAGTGTG-ACCACTGCTGACAAAGTGAAAGTACACATCCAAAATCataagatttttttctgctcagtgtgtacagtgttggcaaagtgagagtagacttccgaaatcgtgtatccaatttccaaacatcattattttcctaaacatttcaatgttttccaagtgttcaaaatacatcaataatgccattcaaatataacaatgagtgttaaaataaggaaagtttttttttcaaataagaaacacggattatttataaatcgccattaagccactacctcacagaagct
gi|8                          :   ggtgtaagaccaccatTGATT-TCTGTTCTTTTTT-------C-ATAGT---CAATAAAAC-----ACGCATTTCATT--CATAAAGAG--ACCCAAATGAAAGAAAGAAATGAAACTTACATATTATTGATTTTCAACAACTCCTGCACTACCAAA--ATATGATGAGAAAAGTA--AGTTATGTAATATATGATACACA----T---T--TT-T----T---CTGTTCAG
gi|16                         :               ccatTGATG-TTTGTTCTTTATT-------CTATAGTAAATAA-AACAATTTACGTGCTTGTCATT--CATggttctttttttctaaattaacaattcaaacatgactgtgctcttaaatgtttgaaatagatcccttatggagttcaaaaataaaaatgagcattaaaagaaaggagatgatttttttaaatattaaagagaaacaagtattatttataactaccattatacgtctactccacgaaagcatttcctgtgtccaatggtgggatactatgca
gi|5                          :      tgtaagcccgccatGATT-TTT--TCTTTAAG-------CTATAGTAAAAAAAAGAAA---GAATACTTGTCGTTATCACAGAGAA-----CAAAGAAAT-AA-G---TGAAACTCATATTTTTATGTTTGTCAAC--CTC-TGCACTAATATA--ATATGACGAGAAAAATGGGGATTATGTGTCATTCA----AGA----TAG-T--TT-TCGTGT---CTGTT---TGTGTAC---TGTTTAC------GAAGT----TTACAAAA----ATATGC-----------ATACCCCCAATTTCCAAGCATCA-A-TTTCTGTTTCTAATTTCACAATTTAAACATGAAAATGTTTAT-AAATTTATAAAGTTCAAATTAT-ACCAATAATG----CCATTCAAAAT-A-AA--ATATAAGCA-ATAAAATAAGGA--AAATGC-TTTTT-----------------------------TTAT-AACCGTC-ATTAT-----------------GCA-----TTTCATGTCTC--CAATGGT----TACTa
gi|6                          :    aaggcgtaagtccatcattg-TTTGTTGTTTATT-------CTATAGTAAATAATAAAAGTTTGAAAGCTTGCCATT--CATAGAGAG--ACCCAAATAAAA-GAAA---TGAAACTTACAGTTTACTATTTGTCAAC--CTC-TGCACTACCAAA--ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----TATTT--TT-T----T---CTGCT-----------------------GTGAAAGTAGA-------AATCATATATTC-----------ATT-CCCAAATGTCCAAGCATTA-A-TTT--TTTTCTAAATTCACAATTCAA------------------AA-T------GTTCAAAATAC-ATCAATAATG----CCATTCAAAAT-A-AA--AAATGAGCA-TTAAAATAAGGAGAAAATGCATTTTT--GGA----GAAGAAGAAACGAGGATTATTTAT-AACCGCC-ATTATGCGACTACTCCACAGAAGCG-----CATCCTATTTC--CAACGGTGC--TA
gi|17                         :                                                            AACGTTTGCATGCTTGTTATT--CACAGAAAC--ACCCAA-TAAAA-GACG---TGAAATGTATATTTTATTGT
gi|9                          :                                                                                                                                                                                              TTATATA----AGA----T---T--TTTT----T---CTGCTCAGTGTGTACAG-TGTTGGCAAAGTGAGAGTAGACTTCCGAAATCGTGTAT-------------------CCAATTTCCAAACATCA----TTATTTTCCTAA----ACATTT---------CAATG-TTTTCCAAGT------GTTCAAAATAC-ATCAATAATG----CCATT-CAAAT-ATAA--CAATGAGTG-TTAAAATAAGGA--AAGTTTTTTTTT--CA------AATAAGAAACACGGATTATTTATAAATCGCC-ATTAAGCCACTACCTCACAGAAGC
gi|14                         :                                                                                                                                                                                                          agctcaccattgatttttgttctttgttgtatagtaaataaaaaagtatacatgcttgtcattcatagagatacccaactgaaagaagttggcttgcatttaattacCCAAGCATCA----TT-TTTTTCTAAATTCACAATTCACACATGGCAATG-CTTTCAAAAT------GTTCAAAACAC-ATCAATAACA----CCATT-ACAAT-A-AC--AAATGAGTA-TTAAAATACGTA--AAATGCATTATC--A-------ATGAAGAAACAATGGCTATTTAT-AACGGCCAATCA-GCGATTATCCCACGGAAGCATTAATTTTCCTGTTTG--CAATGGTt
gi|12                         :                                                                                                                                                                                                                                                                                                                     CCAAGCATCA----TT-TTTTTCTAAATTCACAATTCACACATGGCAATG-CTTTCAAAAT------GTTCAAAACAC-ATCAATAACA----CCATT-ACAAT-A-
gi|13                         :                                                                                                                                                                                aaaaatagaatttacataattatataaatatattttttatctttaattttattttgtgtttgtatattttagcaaacatgaaaccccaaatcccttacatcaccaaatgcattaccaagaatcgtatgaaccaaacactgcatgc-TTTGATTTTCTAGATTCAAAATTCAAACATGGCAATG-TT---------------TTCTAAATAT-AGCAATTACG----CCATT-AAAGT-A-A
gi|8                          :                                                                                                                                                                                                                                                                                                                        ccaaatgtgcctatTTTTTCTAAATTAACAATTCAAACATGACTGTG-CTCTTAAA-T------GTTTGAAATAG-ATCCCTTATGGAGTTCA---AAAAT-A-AA--AA-TGAGCA-TTAAAAGAAAGG--AGATG-ATTTTTTTAAATATTAAAGA-GAAACAAGTATTATTTAT-AACTACC-ATTATACGTCTACTCCACGAAAGCA-----TTTCCTGTGTC--CAATGGTGGGATACTcatactagtatcataacaactaaacttaagaaagtgtattgttgttttttgaaaataaacacaaacaaaacctattgatgccagacatcatacgcgacaggagcgacatattatatcta
gi|15                         :                                                                                                                                                                                                                                                                                                    ccattgatttctgttcttttttcatagtcaataaaacacgcatttcattcataaagagacccaaatgaaagaaagaaatgaaacttacatattattgattttcaacaactcctgcactaccaaaatatgatgagaaaagtaagttatgtaatatatgatacacattttttctgttcagggttcttAGGACTATTTAT-AACCGCC-ATCATACGACTACCCCACGGAAGCA-----CTTCCTTTTTTTACAATGGTGG--TACTatgca

lowQualScore                  :                                                                                                                                                                                                           1111111                                                                 1111                                                                                  1111   22222222                                                                    22222222222                       111                                                                                                             111111111                             1111111111111                                                           11111                            
lowQualScore                  :                                                                                                                                                                                             3             0000000             5     11    1          44         777               1111                            55   4            4                                   2222   44444444 55  3  666            0      2                  4                1 11111111111  666                  444   3 44 3   3                              5     555  555           3        2      44   3  6  44   3      3 444444444           55         7777   7777777777777          0            3       3  55                       11111      5    66         66    
lowQualScore                  :                                                                                                                                                                                             .             .......             .     ..    .          ..         ...               ....                            ..   .            .                                   ....   ........ ..  .  ...            .      .                  .                . ...........  ...                  ...   . .. .   .                              .     ...  ...           .        .      ..   .  .  ..   .      . .........           ..         ....   .............          .            .       .  ..                       .....      .    ..         ..    
lowQualScore                  :                                                                                                                                                                                             3             8888888             4     77    0          66         555               4444                            55   0            0                                   7777   22222222 00  6  444            9      1                  1                8 11111111111  777                  333   1 22 1   1                              1     444  444           1        3      11   1  2  66   6      6 555555555           00         7777   9999999999999          5            6       6  00                       11111      3    11         99    
consensus                     :                                                                                                                                                                                      NNTGATT-TTTGTTCTTTATT-------CTATAGTAAATAATAAAAGTTTGAANGCTTGTCATT--CATAGAGAGA--CCCAAATGAAAGAAG----TGAAACTTACATTTTACTGTTTGTCAAC--CTC-TGCACTACCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----T---T--TT-TT---CTGCTCAGTGTGTACACTGTTGACAAAGTGAAAGTAGACTTCCGAAATCATGTATTC-----------ATA-CCCCAATTTCCAAGCATCAA--TTT-T--T-TTT-CTAAATTCACAATTCAAACATGACAATGCTNTCAAA---AT---GTTCAAAATAC-ATCAATAATGCCATT-CAAA-TA-AA--AAA-TGAGCA-T---------TAAAATAAGGA--AAATGCATT----TTT-----AAA----GAAGAAGAAACGAGGATTATTTAT-AACCGCC-AT--TATGCGACTACCCCACGGAAGCA-----CTTCCTNTTTC--CAATGGTGG--TACT
Reference ( family-1110 )     :                                                                                                                                                                                      NNTGATT-TTTGTTCTTTATT-------CTATAGTAAATAATAAAAGTTTGAANGCTTGTCATT--CATAGAGAGA--CCCAAATGAAAGAAG----TGAAACTTACATTTTACTGTTTGTCAAC--CTC-TGCACTACCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----T---T--TT-TT---CTGCTCAGTGTGTACACTGTTGACAAAGTGAAAGTAGACTTCCGAAATCATGTATTC-----------ATA-CCCCAATTTCCAAGCATCAA--TTT-T--T-TTT-CTAAATTCACAATTCAAACATGACAATGCTNTCAAA---AT---GTTCAAAATAC-ATCAATAACGCCATT-NAAA-TA-AA--AAA-TGAGCA-T---------TAAAATAAGGA--AAATGCATT----TTT-----AAA----GAAGAAGAAACGAGGATTATTTAT-AACCGCC-AT--TATGCGACTACCCCACGGAAGCA-----CTTCCTNTTTC--CAATGGTGG--TACT
gi|1                          :                                                                                                                                                                                        TGCTT-TTTGTTCTTTATT-------CTATAGTAAATAATAAACGTTTGAAAGCTTGTCATT--CATAGAGGGT--CCCAAATGAAAGAAG----TGAAACTTACATTTTACAATTTGTCAAC--CTC-TGCATTACCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AAA----C---A--AT-T----CTGCTCTGTGTGTACACTTTTGACAAAGTGAAAGTAGATTTCCGAAATCATGTATTC-----------ATA-ACCCAATTTCCAAGCATCAT--ATT-C--T-TTT-CTAAATTCACAATTCTAACATGATAATGCTTTCAAA---AT---GTTCAAAATAC-ACCGATAATGCCATT-CAAA-TA-AA--AAA-T-AGCATT---------TAAAATAAGGA--AAATGCATT----TTT-----AAA----GAAGAAGAAACAAGAATTATTTAT-AACCGCC-AT--TATGCGACAACCCCAATGAAGCA-----CTTCCTTTTTC--CAATGGTGG--TACT
gi|10                         :                                                                                                                                                                          tgtaagcccaccatTGATTGTTTGTCCTTTATT-------CTATAGTAAATAATACAAGTTTGAAGGCTTGTCATT--TATAGAGAGA--CCTAAATGAAAGCAG----TGAAACATACATTTTACTGTTTGTCAA---CTC-TGTACTTCTAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGATAT-T---T--TT-TT---CTGCTCAGTGTGTACACTGTTGACAAAGTGAAAGTAGACTTCCGAAATCATGTATTCCGAAATCATGTATT-CTCCAATTTCCAAGCAT-A------------TTT-CTAAATTCACAATTCAAACCTGACAATGCTATAAAA---AT---GTTAATAATATGAACAATAATGGCATT-CCAA-TA-AA--at
gi|11                         :                                                                                                                                                                        ggtgtaagtccaccatTGATT-GTTGCTCTTTATTGAAATTTCTATAGTAAATAA--AGAGC----ATGTTTGTCATT--CATAGAGAGAGACACAAATGAAAGAAG----TGAAACTTACATTTAATTGTTTCTCAAC--CAC-TGCAATACAGAATATATGATGAGAAAAGTAGGGTTCATATGGCATATA----AAA----C---TAGTT-TT---CTGTTCAGTGTGACCACTGCTGACAAAGTGAAAGTACACATCCAAAATC
gi|12                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                    ggtgtaagaccaccatCCAAGCATCA----TT-T--T-TTT-CTAAATTCACAATTCACACATGGCAATGCTTTCAAA---AT---GTTCAAAACAC-ATCAATAACACCATT-ACAA-TA-
gi|13                         :                                                                                                                                                                                                                                                                                                                                             aaaaatagaatttacataattatataaatatattttttatctttaattttattttgtgtttgtatattttagcaaacatgaaaccccaaatcccttacatcaccaaatgcattaccaagaatcgtatgaaccaaacactgcatgcA--TTT-TGAT-TTT-CTAGATTCAAAATTCAAACATGGCAATGTT---------------TTCTAAATAT-AGCAATTACGCCATT-AAAG-TA-AC--ATA-CTAGTA-TCATAACAACTAAACTTAAGA--AAGTGTATTGTTGTTTTTTGAAAA----TAAACACAAACAAAACCTATTGAT-GCCAGAC-ATCATACGCGAC
gi|14                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                        ccaaatgtgcctCCAAGCATCA----TT-T--T-TTT-CTAAATTCACAATTCACACATGGCAATGCTTTCAAA---AT---GTTCAAAACAC-ATCAATAACACCATT-ACAA-TA-AC--AAA-TGAGTA-T---------TAAAATACGTA--AAATGCATT----ATC-----A-------ATGAAGAAACAATGGCTATTTAT-AACGGCCAAT--CA-GCGATTATCCCACGGAAGCATTAATTTTCCTGTTTG--CAATGGTaggagcgacatattatatcta
gi|15                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            AGGACTATTTAT-AACCGCC-AT--CATACGACTACCCCACGGAAGCA-----CTTCCTTTTTTTACAATGGTGG--TACT
gi|16                         :                                                                                                                                                                                        TGATG-TTTGTTCTTTATT-------CTATAGTAAATAA-AACAATTTACGTGCTTGTCATT--CATAatgcc
gi|2                          :                                                                                                                                                                          tgtaagcccgccatTGATT-TTTGTTCTTTATT-------CTATGGTAAATAATAAAAGTTTGAAGGCTTGTCATT--CAAAGAGAGA--CCTAAATGAAAGAAG----TGAAACTTACATTTTACTGTTTGTTAAC--ATC-TGCACTATCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----T---T--TT-TTTTTCTGCTCAGTGTG-------------AAGTGAAAGTAGACTTCCAAAATTATGTACTC-----------ATA-CCCCAATTTCCATGCATTAT--TTT-T--T-TTTTCTAACTTCACAATTCAAACATGAAAATGCTGTCAGA---AT---GTTCAAAATAC-ATCAATAATGCCATT-TGAA-TA-AA--AAAATGAACA-T---------TAAAATAAGGA--AAATGCAGT----TTT-----AAA----GAAGAAAAAACGAGGATTATTTAT-AACTGCC-AT--TATGCGACTACCCCACGGAAGCA-----CTTCCT-TTTC--CAATGGTGG--TACT
gi|3                          :                                                                                                                                                                      aaggtgtaaaccaatcatTGATT-TTTGTTCTTTATT-------CTATAGTAAATAATAAAAGTTTGAAGGCTTGTCATT--CATGGAGAGA--CCCAAATAAAAAATG----TGAAACCTACATTTTACTGTTTGTCAAC--CTC-TGCACTGTCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----T---T--TT-TT---CTGCTCAGTATGTACGATGTTGACATAGTGAAAGTAGACTTCCGAAATCATGTATTC-----------ATA-CCCCAATTTCCAAGCATCAA--TTTAT--T-TTT-CTAAATTCACAATTCAAAGATGACAATGCTATCAAA---CT---GTTCAAAATAC-ATCAATAATGTCATT-AAAA-TA-AA--AAA-TGTGCA-T---------TGAAATAAGAA--AAATGCATT----TTT-----AAA----GAAGAAGAAACGAGGATTATTTAT-AACCGCC-AT--TATGCAACTACCTTACGGAAGCA-----CTTCCTTTCTC--CAATGGTGG--TACTatgcc
gi|4                          :                                                                                                                                                                                      aaTGAGT-TTTGTTATTTATT-------CTATTGTAAATAATAAAAGTTTGAAGGCTTGTCATT--CATAGAGAAT--CCCAAATGAAAGAAG----TGAAACCTACATTTTACTGTTTGTCAAC--CTC-TGCACTATCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGAGATTT---T--TT-TT---CTGCTCAGTGTGTACACTGGTGACAAAGTGATAGTAGA-------------------------------------CAATTTCCAAGCATCAT--TTT-T--T-TTT-CTAAATTCACAATTCAAACATGACAATGCTATCAAA---AT---GTTCAAAATAC-ATTAATAATGCCATT-CAAA-TA-AAATAAA-TGAGCA-T---------TTAAATAAGGA--AAATGCATT----TTT-----AAA----GAAAAAGAAATGAGGATTATTTAT-AACCGCC-AT--CATGCGACTACCCCACGGAAGTA-----CTTCCTTTTTG--CAATGGTGG--TACTt
gi|5                          :                                                                                                                                                                        aggtgttacctcaccatGATT-TTT--TCTTTAAG-------CTATAGTAAAAAAAAGAAA---GAATACTTGTCGTTATCACAGAGAA-----CAAA-GAAATAAG----TGAAACTCATATTTTTATGTTTGTCAAC--CTC-TGCACTAATATA-ATATGACGAGAAAAATGGGGATTATGTGTCATTCA----AGA----TAG-T--TT-TC---GTG-TCTGTTTGTGTACTGTTTACGAAGT----------TTACAAAA----ATATGC-----------ATACCCCCAATTTCCAAGCATCAA--TTT-C--TGTTT-CTAATTTCACAATTTAAACATGAAAATGTTTATAAATTTATAAAGTTCAAATTAT-ACCAATAATGCCATTCAAAA-TA-AA--ATA-TAAGCA-A---------TAAAATAAGGA--AAATGC-TT----TT--------------------------------TTTAT-AACCGTC-AT--TAT-----------------GCA-----TTTCATGTCTC--CAATGGT----TACTatgc
gi|6                          :                                                                                                                                                                         aaggcgtaagtccatcattg-TTTGTTGTTTATT-------CTATAGTAAATAATAAAAGTTTGAAAGCTTGCCATT--CATAGAGAGA--CCCAAATAAAAGAAA----TGAAACTTACAGTTTACTATTTGTCAAC--CTC-TGCACTACCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----TATTT--TT-TT---CTGCT----------------------GTGAAAGTAGA-------AATCATATATTC-----------ATT-CCCAAATGTCCAAGCATTAA--TTT-T--T-TT--CTAAATTCACAATTCAAA---------------------AT---GTTCAAAATAC-ATCAATAATGCCATT-CAAAATA-AA--AAA-TGAGCA-T---------TAAAATAAGGAGAAAATGCATT----TTT-----GGA----GAAGAAGAAACGAGGATTATTTAT-AACCGCC-AT--TATGCGACTACTCCACAGAAGCG-----CATCCTATTTC--CAACGGTGC--TA
gi|7                          :                                                                                                                                                                                        TGATT-TTTGTTCTTTATT-------CTATTGTAAATAATAAAAGTTTGAAGGCTTGTCATT--CATAGAGAAT--CCCAAATGAAAGAAG----TGAAACCTACATTTTACTGTTTGTCAAC--CTC-TGCACTATCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATAAG--AGA----TTG-T--TT-TT---CTGCTCAGTGTGTACACTGGTGACAAAGTGAAAGTAGACTTCCGAAATCATGTATTC-----------ATA-TCCCAGTTTCCAAGCATCAATTTTT-T--T-TTT-CTAAATTCATGATTCAAACATGAAAATGCTATCAAA---AT---GCTCAAAATAC-ATCAATGATGCCATT-CAAA-AA-AA--AAA-TGAGCA-T---------AAAAATAAGGA--AAATGCATT----TTT-----AAA----GAAGA
gi|8                          :                                                                                                                                                                      aaagtgtcaacccaccatTGATT-TCTGTTCTTTTTT-------C-ATAGT---CAATAAAAC-----ACGCATTTCATT--CATAAAGAGA--CCCAAATGAAAGAAAGAAATGAAACTTACATATTATTGATTTTCAACAACTCCTGCACTACCAAA-ATATGATGAGAAAAGTA--AGTTATGTAATATATGATACACA----T---T--TT-TT---CTGTTCAGGGT
gi|8                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ccatTT-T--T-TTT-CTAAATTAACAATTCAAACATGACTGTGCTCTTAAA----T---GTTTGAAATAG-ATCCCTTATGGAGTT-CAAA-AATAA--AAA-TGAGCA-T---------TAAAAGAAAGG--AGATG-ATT----TTTTT---AAATATTAAAGA-GAAACAAGTATTATTTAT-AACTACC-AT--TATACGTCTACTCCACGAAAGCA-----TTTCCTGTGTC--CAATGGTGGGATACTtctttttttctaaattaacaattcaaacatgactgtgctcttaaatgtttgaaatagatcccttatggagttcaaaaataaaaatgagcattaaaagaaaggagatgatttttttaaatattaaagagaaacaagtattatttataactaccattatacgtctactccacgaaagcatttcctgtgtccaatggtgggatactatgca
gi|9                          : ccattgatttctgttcttttttcatagtcaataaaacacgcatttcattcataaagagacccaaatgaaagaaagaaatgaaacttacatattattgattttcaacaactcctgcactaccaaaatatgatgagaaaagtaagttatgtaatatatgatacacattttttctgttcagggttcTGATT-TTTGTTCTTTGTT-------GTATAGTAAATAA-AAAAGTATACATGCTTGTCATT--CATAGAGATA--CCCAACTGAAAGAAGT---TG--GCTTGCATTTAATTACTTATatgca
gi|9                          :                                                                                                                                                                                                                                                                                                                                                        agctcaccatTTATATA----AGA----T---T--TTTTT---CTGCTCAGTGTGTACAGTGTTGGCAAAGTGAGAGTAGACTTCCGAAATCGTGTAT-------------------CCAATTTCCAAACATC-A--TTA-T--T-TTC-CTAA----ACATTT---------CAATGTTTTCCAA---GT---GTTCAAAATAC-ATCAATAATGCCATT-CAAA-TATAA--CAA-TGAGTG-T---------TAAAATAAGGA--AAGTTTTTT----TTT-----CA------AATAAGAAACACGGATTATTTATAAATCGCC-AT--TAAGCCACTACCTCACAGAAGCataagatttttttctgctcagtgtgtacagtgttggcaaagtgagagtagacttccgaaatcgtgtatccaatttccaaacatcattattttcctaaacatttcaatgttttccaagtgttcaaaatacatcaataatgccattcaaatataacaatgagtgttaaaataaggaaagtttttttttcaaataagaaacacggattatttataaatcgccattaagccactacctcacagaagct

Unaligned ( gi|17 ): AACGTTTGCATGCTTGTTATTCACAGAAACACCCAATAAAAGACGTGAAATGTATATTTTATTGT

lowQualScore                  :                                                                                                                                                                                                           1111111                                                                 1111                                                                                  1111   22222222                                                                    22222222222                       111                                                                                                             111111111                             1111111111111                                                           11111                            
lowQualScore                  :                                                                                                                                                                                             3             0000000             5     11    1          44         777               1111                            55   4            4                                   2222   44444444 55  3  666            0      2                  4                1 11111111111  666                  444   3 44 3   3                              5     555  555           3                3   3  6  44   3      3 444444444           55         7777   7777777777777          0            3       3  55                       11111      5    66         66    
lowQualScore                  :                                                                                                                                                                                             .             .......             .     ..    .          ..         ...               ....                            ..   .            .                                   ....   ........ ..  .  ...            .      .                  .                . ...........  ...                  ...   . .. .   .                              .     ...  ...           .                .   .  .  ..   .      . .........           ..         ....   .............          .            .       .  ..                       .....      .    ..         ..    
lowQualScore                  :                                                                                                                                                                                             3             8888888             4     77    0          66         555               4444                            55   0            0                                   7777   22222222 00  6  444            9      1                  1                8 11111111111  777                  333   1 22 1   1                              1     444  444           1                1   1  2  66   6      6 555555555           00         7777   9999999999999          5            6       6  00                       11111      3    11         99    
consensus                     :                                                                                                                                                                                      NNTGATT-TTTGTTCTTTATT-------CTATAGTAAATAATAAAAGTTTGAANGCTTGTCATT--CATAGAGAGA--CCCAAATGAAAGAAG----TGAAACTTACATTTTACTGTTTGTCAAC--CTC-TGCACTACCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----T---T--TT-TT---CTGCTCAGTGTGTACACTGTTGACAAAGTGAAAGTAGACTTCCGAAATCATGTATTC-----------ATA-CCCCAATTTCCAAGCATCAA--TTT-T--T-TTT-CTAAATTCACAATTCAAACATGACAATGCTNTCAAA---AT---GTTCAAAATAC-ATCAATAATGCCATTC-AAA-TA-AA--AAA-TGAGCA-T---------TAAAATAAGGA--AAATGCATT----TTT-----AAA----GAAGAAGAAACGAGGATTATTTAT-AACCGCC-AT--TATGCGACTACCCCACGGAAGCA-----CTTCCTNTTTC--CAATGGTGG--TACT
Reference ( family-1110 )     :                                                                                                                                                                                      NNTGATT-TTTGTTCTTTATT-------CTATAGTAAATAATAAAAGTTTGAANGCTTGTCATT--CATAGAGAGA--CCCAAATGAAAGAAG----TGAAACTTACATTTTACTGTTTGTCAAC--CTC-TGCACTACCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----T---T--TT-TT---CTGCTCAGTGTGTACACTGTTGACAAAGTGAAAGTAGACTTCCGAAATCATGTATTC-----------ATA-CCCCAATTTCCAAGCATCAA--TTT-T--T-TTT-CTAAATTCACAATTCAAACATGACAATGCTNTCAAA---AT---GTTCAAAATAC-ATCAATAATGCCATTC-AAA-TA-AA--AAA-TGAGCA-T---------TAAAATAAGGA--AAATGCATT----TTT-----AAA----GAAGAAGAAACGAGGATTATTTAT-AACCGCC-AT--TATGCGACTACCCCACGGAAGCA-----CTTCCTNTTTC--CAATGGTGG--TACT
gi|1                          :                                                                                                                                                                                        TGCTT-TTTGTTCTTTATT-------CTATAGTAAATAATAAACGTTTGAAAGCTTGTCATT--CATAGAGGGT--CCCAAATGAAAGAAG----TGAAACTTACATTTTACAATTTGTCAAC--CTC-TGCATTACCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AAA----C---A--AT-T----CTGCTCTGTGTGTACACTTTTGACAAAGTGAAAGTAGATTTCCGAAATCATGTATTC-----------ATA-ACCCAATTTCCAAGCATCAT--ATT-C--T-TTT-CTAAATTCACAATTCTAACATGATAATGCTTTCAAA---AT---GTTCAAAATAC-ACCGATAATGCCATTC-AAA-TA-AA--AAA-T-AGCATT---------TAAAATAAGGA--AAATGCATT----TTT-----AAA----GAAGAAGAAACAAGAATTATTTAT-AACCGCC-AT--TATGCGACAACCCCAATGAAGCA-----CTTCCTTTTTC--CAATGGTGG--TACT
gi|10                         :                                                                                                                                                                          tgtaagcccaccatTGATTGTTTGTCCTTTATT-------CTATAGTAAATAATACAAGTTTGAAGGCTTGTCATT--TATAGAGAGA--CCTAAATGAAAGCAG----TGAAACATACATTTTACTGTTTGTCAA---CTC-TGTACTTCTAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGATAT-T---T--TT-TT---CTGCTCAGTGTGTACACTGTTGACAAAGTGAAAGTAGACTTCCGAAATCATGTATTCCGAAATCATGTATT-CTCCAATTTCCAAGCAT-A------------TTT-CTAAATTCACAATTCAAACCTGACAATGCTATAAAA---AT---GTTAATAATATGAACAATAATGGCATTC-CAA-TA-AA--at
gi|11                         :                                                                                                                                                                        ggtgtaagtccaccatTGATT-GTTGCTCTTTATTGAAATTTCTATAGTAAATAA--AGAGC----ATGTTTGTCATT--CATAGAGAGAGACACAAATGAAAGAAG----TGAAACTTACATTTAATTGTTTCTCAAC--CAC-TGCAATACAGAATATATGATGAGAAAAGTAGGGTTCATATGGCATATA----AAA----C---TAGTT-TT---CTGTTCAGTGTGACCACTGCTGACAAAGTGAAAGTACACATCCAAAATC
gi|12                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                    ggtgtaagaccaccatCCAAGCATCA----TT-T--T-TTT-CTAAATTCACAATTCACACATGGCAATGCTTTCAAA---AT---GTTCAAAACAC-ATCAATAACACCATTA-CAA-TA-
gi|13                         :                                                                                                                                                                                                                                                                                                                                             aaaaatagaatttacataattatataaatatattttttatctttaattttattttgtgtttgtatattttagcaaacatgaaaccccaaatcccttacatcaccaaatgcattaccaagaatcgtatgaaccaaacactgcatgcA--TTT-TGAT-TTT-CTAGATTCAAAATTCAAACATGGCAATGTT---------------TTCTAAATAT-AGCAATTACGCCATTA-AAG-TA-AC--ATA-CTAGTA-TCATAACAACTAAACTTAAGA--AAGTGTATTGTTGTTTTTTGAAAA----TAAACACAAACAAAACCTATTGAT-GCCAGAC-ATCATACGCGAC
gi|14                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                        ccaaatgtgcctCCAAGCATCA----TT-T--T-TTT-CTAAATTCACAATTCACACATGGCAATGCTTTCAAA---AT---GTTCAAAACAC-ATCAATAACACCATTA-CAA-TA-AC--AAA-TGAGTA-T---------TAAAATACGTA--AAATGCATT----ATC-----A-------ATGAAGAAACAATGGCTATTTAT-AACGGCCAAT--CA-GCGATTATCCCACGGAAGCATTAATTTTCCTGTTTG--CAATGGTaggagcgacatattatatcta
gi|15                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            AGGACTATTTAT-AACCGCC-AT--CATACGACTACCCCACGGAAGCA-----CTTCCTTTTTTTACAATGGTGG--TACT
gi|16                         :                                                                                                                                                                                        TGATG-TTTGTTCTTTATT-------CTATAGTAAATAA-AACAATTTACGTGCTTGTCATT--CATAatgcc
gi|2                          :                                                                                                                                                                          tgtaagcccgccatTGATT-TTTGTTCTTTATT-------CTATGGTAAATAATAAAAGTTTGAAGGCTTGTCATT--CAAAGAGAGA--CCTAAATGAAAGAAG----TGAAACTTACATTTTACTGTTTGTTAAC--ATC-TGCACTATCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----T---T--TT-TTTTTCTGCTCAGTGTG-------------AAGTGAAAGTAGACTTCCAAAATTATGTACTC-----------ATA-CCCCAATTTCCATGCATTAT--TTT-T--T-TTTTCTAACTTCACAATTCAAACATGAAAATGCTGTCAGA---AT---GTTCAAAATAC-ATCAATAATGCCATTT-GAA-TA-AA--AAAATGAACA-T---------TAAAATAAGGA--AAATGCAGT----TTT-----AAA----GAAGAAAAAACGAGGATTATTTAT-AACTGCC-AT--TATGCGACTACCCCACGGAAGCA-----CTTCCT-TTTC--CAATGGTGG--TACT
gi|3                          :                                                                                                                                                                      aaggtgtaaaccaatcatTGATT-TTTGTTCTTTATT-------CTATAGTAAATAATAAAAGTTTGAAGGCTTGTCATT--CATGGAGAGA--CCCAAATAAAAAATG----TGAAACCTACATTTTACTGTTTGTCAAC--CTC-TGCACTGTCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----T---T--TT-TT---CTGCTCAGTATGTACGATGTTGACATAGTGAAAGTAGACTTCCGAAATCATGTATTC-----------ATA-CCCCAATTTCCAAGCATCAA--TTTAT--T-TTT-CTAAATTCACAATTCAAAGATGACAATGCTATCAAA---CT---GTTCAAAATAC-ATCAATAATGTCATTA-AAA-TA-AA--AAA-TGTGCA-T---------TGAAATAAGAA--AAATGCATT----TTT-----AAA----GAAGAAGAAACGAGGATTATTTAT-AACCGCC-AT--TATGCAACTACCTTACGGAAGCA-----CTTCCTTTCTC--CAATGGTGG--TACTatgcc
gi|4                          :                                                                                                                                                                                      aaTGAGT-TTTGTTATTTATT-------CTATTGTAAATAATAAAAGTTTGAAGGCTTGTCATT--CATAGAGAAT--CCCAAATGAAAGAAG----TGAAACCTACATTTTACTGTTTGTCAAC--CTC-TGCACTATCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGAGATTT---T--TT-TT---CTGCTCAGTGTGTACACTGGTGACAAAGTGATAGTAGA-------------------------------------CAATTTCCAAGCATCAT--TTT-T--T-TTT-CTAAATTCACAATTCAAACATGACAATGCTATCAAA---AT---GTTCAAAATAC-ATTAATAATGCCATTC-AAA-TA-AAATAAA-TGAGCA-T---------TTAAATAAGGA--AAATGCATT----TTT-----AAA----GAAAAAGAAATGAGGATTATTTAT-AACCGCC-AT--CATGCGACTACCCCACGGAAGTA-----CTTCCTTTTTG--CAATGGTGG--TACTt
gi|5                          :                                                                                                                                                                        aggtgttacctcaccatGATT-TTT--TCTTTAAG-------CTATAGTAAAAAAAAGAAA---GAATACTTGTCGTTATCACAGAGAA-----CAAA-GAAATAAG----TGAAACTCATATTTTTATGTTTGTCAAC--CTC-TGCACTAATATA-ATATGACGAGAAAAATGGGGATTATGTGTCATTCA----AGA----TAG-T--TT-TC---GTG-TCTGTTTGTGTACTGTTTACGAAGT----------TTACAAAA----ATATGC-----------ATACCCCCAATTTCCAAGCATCAA--TTT-C--TGTTT-CTAATTTCACAATTTAAACATGAAAATGTTTATAAATTTATAAAGTTCAAATTAT-ACCAATAATGCCATTCAAAA-TA-AA--ATA-TAAGCA-A---------TAAAATAAGGA--AAATGC-TT----TT--------------------------------TTTAT-AACCGTC-AT--TAT-----------------GCA-----TTTCATGTCTC--CAATGGT----TACTatgc
gi|6                          :                                                                                                                                                                         aaggcgtaagtccatcattg-TTTGTTGTTTATT-------CTATAGTAAATAATAAAAGTTTGAAAGCTTGCCATT--CATAGAGAGA--CCCAAATAAAAGAAA----TGAAACTTACAGTTTACTATTTGTCAAC--CTC-TGCACTACCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----TATTT--TT-TT---CTGCT----------------------GTGAAAGTAGA-------AATCATATATTC-----------ATT-CCCAAATGTCCAAGCATTAA--TTT-T--T-TT--CTAAATTCACAATTCAAA---------------------AT---GTTCAAAATAC-ATCAATAATGCCATTC-AAAATA-AA--AAA-TGAGCA-T---------TAAAATAAGGAGAAAATGCATT----TTT-----GGA----GAAGAAGAAACGAGGATTATTTAT-AACCGCC-AT--TATGCGACTACTCCACAGAAGCG-----CATCCTATTTC--CAACGGTGC--TA
gi|7                          :                                                                                                                                                                                        TGATT-TTTGTTCTTTATT-------CTATTGTAAATAATAAAAGTTTGAAGGCTTGTCATT--CATAGAGAAT--CCCAAATGAAAGAAG----TGAAACCTACATTTTACTGTTTGTCAAC--CTC-TGCACTATCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATAAG--AGA----TTG-T--TT-TT---CTGCTCAGTGTGTACACTGGTGACAAAGTGAAAGTAGACTTCCGAAATCATGTATTC-----------ATA-TCCCAGTTTCCAAGCATCAATTTTT-T--T-TTT-CTAAATTCATGATTCAAACATGAAAATGCTATCAAA---AT---GCTCAAAATAC-ATCAATGATGCCATTC-AAA-AA-AA--AAA-TGAGCA-T---------AAAAATAAGGA--AAATGCATT----TTT-----AAA----GAAGA
gi|8                          :                                                                                                                                                                      aaagtgtcaacccaccatTGATT-TCTGTTCTTTTTT-------C-ATAGT---CAATAAAAC-----ACGCATTTCATT--CATAAAGAGA--CCCAAATGAAAGAAAGAAATGAAACTTACATATTATTGATTTTCAACAACTCCTGCACTACCAAA-ATATGATGAGAAAAGTA--AGTTATGTAATATATGATACACA----T---T--TT-TT---CTGTTCAGGGT
gi|8                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ccatTT-T--T-TTT-CTAAATTAACAATTCAAACATGACTGTGCTCTTAAA----T---GTTTGAAATAG-ATCCCTTATGGAGTTC-AAA-AATAA--AAA-TGAGCA-T---------TAAAAGAAAGG--AGATG-ATT----TTTTT---AAATATTAAAGA-GAAACAAGTATTATTTAT-AACTACC-AT--TATACGTCTACTCCACGAAAGCA-----TTTCCTGTGTC--CAATGGTGGGATACTtctttttttctaaattaacaattcaaacatgactgtgctcttaaatgtttgaaatagatcccttatggagttcaaaaataaaaatgagcattaaaagaaaggagatgatttttttaaatattaaagagaaacaagtattatttataactaccattatacgtctactccacgaaagcatttcctgtgtccaatggtgggatactatgca
gi|9                          : ccattgatttctgttcttttttcatagtcaataaaacacgcatttcattcataaagagacccaaatgaaagaaagaaatgaaacttacatattattgattttcaacaactcctgcactaccaaaatatgatgagaaaagtaagttatgtaatatatgatacacattttttctgttcagggttcTGATT-TTTGTTCTTTGTT-------GTATAGTAAATAA-AAAAGTATACATGCTTGTCATT--CATAGAGATA--CCCAACTGAAAGAAGT---TG--GCTTGCATTTAATTACTTATatgca
gi|9                          :                                                                                                                                                                                                                                                                                                                                                        agctcaccatTTATATA----AGA----T---T--TTTTT---CTGCTCAGTGTGTACAGTGTTGGCAAAGTGAGAGTAGACTTCCGAAATCGTGTAT-------------------CCAATTTCCAAACATC-A--TTA-T--T-TTC-CTAA----ACATTT---------CAATGTTTTCCAA---GT---GTTCAAAATAC-ATCAATAATGCCATTC-AAA-TATAA--CAA-TGAGTG-T---------TAAAATAAGGA--AAGTTTTTT----TTT-----CA------AATAAGAAACACGGATTATTTATAAATCGCC-AT--TAAGCCACTACCTCACAGAAGCataagatttttttctgctcagtgtgtacagtgttggcaaagtgagagtagacttccgaaatcgtgtatccaatttccaaacatcattattttcctaaacatttcaatgttttccaagtgttcaaaatacatcaataatgccattcaaatataacaatgagtgttaaaataaggaaagtttttttttcaaataagaaacacggattatttataaatcgccattaagccactacctcacagaagct

Unaligned ( gi|17 ): AACGTTTGCATGCTTGTTATTCACAGAAACACCCAATAAAAGACGTGAAATGTATATTTTATTGT

lowQualScore                  :                                                                                                                                                                                                           1111111                                                                 1111                                                                                  1111   22222222                                                                    22222222222                       111                                                                                                             111111111                             1111111111111                                                           11111                            
lowQualScore                  :                                                                                                                                                                                             3             0000000             5     11    1          44         777               1111                            55   4            4                                   2222   44444444 55  3  666            0      2                  4                1 11111111111  666                  444   3 44 3   3                              5     555  555           3                3   3  6  44   3      3 444444444           55         7777   7777777777777          0            3       3  55                       11111      5    66         66    
lowQualScore                  :                                                                                                                                                                                             .             .......             .     ..    .          ..         ...               ....                            ..   .            .                                   ....   ........ ..  .  ...            .      .                  .                . ...........  ...                  ...   . .. .   .                              .     ...  ...           .                .   .  .  ..   .      . .........           ..         ....   .............          .            .       .  ..                       .....      .    ..         ..    
lowQualScore                  :                                                                                                                                                                                             3             8888888             4     77    0          66         555               4444                            55   0            0                                   7777   22222222 00  6  444            9      1                  1                8 11111111111  777                  333   1 22 1   1                              1     444  444           1                1   1  2  66   6      6 555555555           00         7777   9999999999999          5            6       6  00                       11111      3    11         99    
consensus                     :                                                                                                                                                                                      NNTGATT-TTTGTTCTTTATT-------CTATAGTAAATAATAAAAGTTTGAANGCTTGTCATT--CATAGAGAGA--CCCAAATGAAAGAAG----TGAAACTTACATTTTACTGTTTGTCAAC--CTC-TGCACTACCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----T---T--TT-TT---CTGCTCAGTGTGTACACTGTTGACAAAGTGAAAGTAGACTTCCGAAATCATGTATTC-----------ATA-CCCCAATTTCCAAGCATCAA--TTT-T--T-TTT-CTAAATTCACAATTCAAACATGACAATGCTNTCAAA---AT---GTTCAAAATAC-ATCAATAATGCCATTC-AAA-TA-AA--AAA-TGAGCA-T---------TAAAATAAGGA--AAATGCATT----TTT-----AAA----GAAGAAGAAACGAGGATTATTTAT-AACCGCC-AT--TATGCGACTACCCCACGGAAGCA-----CTTCCTNTTTC--CAATGGTGG--TACT
Reference ( family-1110 )     :                                                                                                                                                                                      NNTGATT-TTTGTTCTTTATT-------CTATAGTAAATAATAAAAGTTTGAANGCTTGTCATT--CATAGAGAGA--CCCAAATGAAAGAAG----TGAAACTTACATTTTACTGTTTGTCAAC--CTC-TGCACTACCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----T---T--TT-TT---CTGCTCAGTGTGTACACTGTTGACAAAGTGAAAGTAGACTTCCGAAATCATGTATTC-----------ATA-CCCCAATTTCCAAGCATCAA--TTT-T--T-TTT-CTAAATTCACAATTCAAACATGACAATGCTNTCAAA---AT---GTTCAAAATAC-ATCAATAATGCCATTC-AAA-TA-AA--AAA-TGAGCA-T---------TAAAATAAGGA--AAATGCATT----TTT-----AAA----GAAGAAGAAACGAGGATTATTTAT-AACCGCC-AT--TATGCGACTACCCCACGGAAGCA-----CTTCCTNTTTC--CAATGGTGG--TACT
gi|1                          :                                                                                                                                                                                        TGCTT-TTTGTTCTTTATT-------CTATAGTAAATAATAAACGTTTGAAAGCTTGTCATT--CATAGAGGGT--CCCAAATGAAAGAAG----TGAAACTTACATTTTACAATTTGTCAAC--CTC-TGCATTACCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AAA----C---A--AT-T----CTGCTCTGTGTGTACACTTTTGACAAAGTGAAAGTAGATTTCCGAAATCATGTATTC-----------ATA-ACCCAATTTCCAAGCATCAT--ATT-C--T-TTT-CTAAATTCACAATTCTAACATGATAATGCTTTCAAA---AT---GTTCAAAATAC-ACCGATAATGCCATTC-AAA-TA-AA--AAA-T-AGCATT---------TAAAATAAGGA--AAATGCATT----TTT-----AAA----GAAGAAGAAACAAGAATTATTTAT-AACCGCC-AT--TATGCGACAACCCCAATGAAGCA-----CTTCCTTTTTC--CAATGGTGG--TACT
gi|10                         :                                                                                                                                                                          tgtaagcccaccatTGATTGTTTGTCCTTTATT-------CTATAGTAAATAATACAAGTTTGAAGGCTTGTCATT--TATAGAGAGA--CCTAAATGAAAGCAG----TGAAACATACATTTTACTGTTTGTCAA---CTC-TGTACTTCTAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGATAT-T---T--TT-TT---CTGCTCAGTGTGTACACTGTTGACAAAGTGAAAGTAGACTTCCGAAATCATGTATTCCGAAATCATGTATT-CTCCAATTTCCAAGCAT-A------------TTT-CTAAATTCACAATTCAAACCTGACAATGCTATAAAA---AT---GTTAATAATATGAACAATAATGGCATTC-CAA-TA-AA--at
gi|11                         :                                                                                                                                                                        ggtgtaagtccaccatTGATT-GTTGCTCTTTATTGAAATTTCTATAGTAAATAA--AGAGC----ATGTTTGTCATT--CATAGAGAGAGACACAAATGAAAGAAG----TGAAACTTACATTTAATTGTTTCTCAAC--CAC-TGCAATACAGAATATATGATGAGAAAAGTAGGGTTCATATGGCATATA----AAA----C---TAGTT-TT---CTGTTCAGTGTGACCACTGCTGACAAAGTGAAAGTACACATCCAAAATC
gi|12                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                    ggtgtaagaccaccatCCAAGCATCA----TT-T--T-TTT-CTAAATTCACAATTCACACATGGCAATGCTTTCAAA---AT---GTTCAAAACAC-ATCAATAACACCATTA-CAA-TA-
gi|13                         :                                                                                                                                                                                                                                                                                                                                             aaaaatagaatttacataattatataaatatattttttatctttaattttattttgtgtttgtatattttagcaaacatgaaaccccaaatcccttacatcaccaaatgcattaccaagaatcgtatgaaccaaacactgcatgcA--TTT-TGAT-TTT-CTAGATTCAAAATTCAAACATGGCAATGTT---------------TTCTAAATAT-AGCAATTACGCCATTA-AAG-TA-AC--ATA-CTAGTA-TCATAACAACTAAACTTAAGA--AAGTGTATTGTTGTTTTTTGAAAA----TAAACACAAACAAAACCTATTGAT-GCCAGAC-ATCATACGCGAC
gi|14                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                        ccaaatgtgcctCCAAGCATCA----TT-T--T-TTT-CTAAATTCACAATTCACACATGGCAATGCTTTCAAA---AT---GTTCAAAACAC-ATCAATAACACCATTA-CAA-TA-AC--AAA-TGAGTA-T---------TAAAATACGTA--AAATGCATT----ATC-----A-------ATGAAGAAACAATGGCTATTTAT-AACGGCCAAT--CA-GCGATTATCCCACGGAAGCATTAATTTTCCTGTTTG--CAATGGTaggagcgacatattatatcta
gi|15                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            AGGACTATTTAT-AACCGCC-AT--CATACGACTACCCCACGGAAGCA-----CTTCCTTTTTTTACAATGGTGG--TACT
gi|16                         :                                                                                                                                                                                        TGATG-TTTGTTCTTTATT-------CTATAGTAAATAA-AACAATTTACGTGCTTGTCATT--CATAatgcc
gi|2                          :                                                                                                                                                                          tgtaagcccgccatTGATT-TTTGTTCTTTATT-------CTATGGTAAATAATAAAAGTTTGAAGGCTTGTCATT--CAAAGAGAGA--CCTAAATGAAAGAAG----TGAAACTTACATTTTACTGTTTGTTAAC--ATC-TGCACTATCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----T---T--TT-TTTTTCTGCTCAGTGTG-------------AAGTGAAAGTAGACTTCCAAAATTATGTACTC-----------ATA-CCCCAATTTCCATGCATTAT--TTT-T--T-TTTTCTAACTTCACAATTCAAACATGAAAATGCTGTCAGA---AT---GTTCAAAATAC-ATCAATAATGCCATTT-GAA-TA-AA--AAAATGAACA-T---------TAAAATAAGGA--AAATGCAGT----TTT-----AAA----GAAGAAAAAACGAGGATTATTTAT-AACTGCC-AT--TATGCGACTACCCCACGGAAGCA-----CTTCCT-TTTC--CAATGGTGG--TACT
gi|3                          :                                                                                                                                                                      aaggtgtaaaccaatcatTGATT-TTTGTTCTTTATT-------CTATAGTAAATAATAAAAGTTTGAAGGCTTGTCATT--CATGGAGAGA--CCCAAATAAAAAATG----TGAAACCTACATTTTACTGTTTGTCAAC--CTC-TGCACTGTCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----T---T--TT-TT---CTGCTCAGTATGTACGATGTTGACATAGTGAAAGTAGACTTCCGAAATCATGTATTC-----------ATA-CCCCAATTTCCAAGCATCAA--TTTAT--T-TTT-CTAAATTCACAATTCAAAGATGACAATGCTATCAAA---CT---GTTCAAAATAC-ATCAATAATGTCATTA-AAA-TA-AA--AAA-TGTGCA-T---------TGAAATAAGAA--AAATGCATT----TTT-----AAA----GAAGAAGAAACGAGGATTATTTAT-AACCGCC-AT--TATGCAACTACCTTACGGAAGCA-----CTTCCTTTCTC--CAATGGTGG--TACTatgcc
gi|4                          :                                                                                                                                                                                      aaTGAGT-TTTGTTATTTATT-------CTATTGTAAATAATAAAAGTTTGAAGGCTTGTCATT--CATAGAGAAT--CCCAAATGAAAGAAG----TGAAACCTACATTTTACTGTTTGTCAAC--CTC-TGCACTATCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGAGATTT---T--TT-TT---CTGCTCAGTGTGTACACTGGTGACAAAGTGATAGTAGA-------------------------------------CAATTTCCAAGCATCAT--TTT-T--T-TTT-CTAAATTCACAATTCAAACATGACAATGCTATCAAA---AT---GTTCAAAATAC-ATTAATAATGCCATTC-AAA-TA-AAATAAA-TGAGCA-T---------TTAAATAAGGA--AAATGCATT----TTT-----AAA----GAAAAAGAAATGAGGATTATTTAT-AACCGCC-AT--CATGCGACTACCCCACGGAAGTA-----CTTCCTTTTTG--CAATGGTGG--TACTt
gi|5                          :                                                                                                                                                                        aggtgttacctcaccatGATT-TTT--TCTTTAAG-------CTATAGTAAAAAAAAGAAA---GAATACTTGTCGTTATCACAGAGAA-----CAAA-GAAATAAG----TGAAACTCATATTTTTATGTTTGTCAAC--CTC-TGCACTAATATA-ATATGACGAGAAAAATGGGGATTATGTGTCATTCA----AGA----TAG-T--TT-TC---GTG-TCTGTTTGTGTACTGTTTACGAAGT----------TTACAAAA----ATATGC-----------ATACCCCCAATTTCCAAGCATCAA--TTT-C--TGTTT-CTAATTTCACAATTTAAACATGAAAATGTTTATAAATTTATAAAGTTCAAATTAT-ACCAATAATGCCATTCAAAA-TA-AA--ATA-TAAGCA-A---------TAAAATAAGGA--AAATGC-TT----TT--------------------------------TTTAT-AACCGTC-AT--TAT-----------------GCA-----TTTCATGTCTC--CAATGGT----TACTatgc
gi|6                          :                                                                                                                                                                         aaggcgtaagtccatcattg-TTTGTTGTTTATT-------CTATAGTAAATAATAAAAGTTTGAAAGCTTGCCATT--CATAGAGAGA--CCCAAATAAAAGAAA----TGAAACTTACAGTTTACTATTTGTCAAC--CTC-TGCACTACCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----TATTT--TT-TT---CTGCT----------------------GTGAAAGTAGA-------AATCATATATTC-----------ATT-CCCAAATGTCCAAGCATTAA--TTT-T--T-TT--CTAAATTCACAATTCAAA---------------------AT---GTTCAAAATAC-ATCAATAATGCCATTC-AAAATA-AA--AAA-TGAGCA-T---------TAAAATAAGGAGAAAATGCATT----TTT-----GGA----GAAGAAGAAACGAGGATTATTTAT-AACCGCC-AT--TATGCGACTACTCCACAGAAGCG-----CATCCTATTTC--CAACGGTGC--TA
gi|7                          :                                                                                                                                                                                        TGATT-TTTGTTCTTTATT-------CTATTGTAAATAATAAAAGTTTGAAGGCTTGTCATT--CATAGAGAAT--CCCAAATGAAAGAAG----TGAAACCTACATTTTACTGTTTGTCAAC--CTC-TGCACTATCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATAAG--AGA----TTG-T--TT-TT---CTGCTCAGTGTGTACACTGGTGACAAAGTGAAAGTAGACTTCCGAAATCATGTATTC-----------ATA-TCCCAGTTTCCAAGCATCAATTTTT-T--T-TTT-CTAAATTCATGATTCAAACATGAAAATGCTATCAAA---AT---GCTCAAAATAC-ATCAATGATGCCATTC-AAA-AA-AA--AAA-TGAGCA-T---------AAAAATAAGGA--AAATGCATT----TTT-----AAA----GAAGA
gi|8                          :                                                                                                                                                                      aaagtgtcaacccaccatTGATT-TCTGTTCTTTTTT-------C-ATAGT---CAATAAAAC-----ACGCATTTCATT--CATAAAGAGA--CCCAAATGAAAGAAAGAAATGAAACTTACATATTATTGATTTTCAACAACTCCTGCACTACCAAA-ATATGATGAGAAAAGTA--AGTTATGTAATATATGATACACA----T---T--TT-TT---CTGTTCAGGGT
gi|8                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ccatTT-T--T-TTT-CTAAATTAACAATTCAAACATGACTGTGCTCTTAAA----T---GTTTGAAATAG-ATCCCTTATGGAGTTC-AAA-AATAA--AAA-TGAGCA-T---------TAAAAGAAAGG--AGATG-ATT----TTTTT---AAATATTAAAGA-GAAACAAGTATTATTTAT-AACTACC-AT--TATACGTCTACTCCACGAAAGCA-----TTTCCTGTGTC--CAATGGTGGGATACTtctttttttctaaattaacaattcaaacatgactgtgctcttaaatgtttgaaatagatcccttatggagttcaaaaataaaaatgagcattaaaagaaaggagatgatttttttaaatattaaagagaaacaagtattatttataactaccattatacgtctactccacgaaagcatttcctgtgtccaatggtgggatactatgca
gi|9                          : ccattgatttctgttcttttttcatagtcaataaaacacgcatttcattcataaagagacccaaatgaaagaaagaaatgaaacttacatattattgattttcaacaactcctgcactaccaaaatatgatgagaaaagtaagttatgtaatatatgatacacattttttctgttcagggttcTGATT-TTTGTTCTTTGTT-------GTATAGTAAATAA-AAAAGTATACATGCTTGTCATT--CATAGAGATA--CCCAACTGAAAGAAGT---TG--GCTTGCATTTAATTACTTATatgca
gi|9                          :                                                                                                                                                                                                                                                                                                                                                        agctcaccatTTATATA----AGA----T---T--TTTTT---CTGCTCAGTGTGTACAGTGTTGGCAAAGTGAGAGTAGACTTCCGAAATCGTGTAT-------------------CCAATTTCCAAACATC-A--TTA-T--T-TTC-CTAA----ACATTT---------CAATGTTTTCCAA---GT---GTTCAAAATAC-ATCAATAATGCCATTC-AAA-TATAA--CAA-TGAGTG-T---------TAAAATAAGGA--AAGTTTTTT----TTT-----CA------AATAAGAAACACGGATTATTTATAAATCGCC-AT--TAAGCCACTACCTCACAGAAGCataagatttttttctgctcagtgtgtacagtgttggcaaagtgagagtagacttccgaaatcgtgtatccaatttccaaacatcattattttcctaaacatttcaatgttttccaagtgttcaaaatacatcaataatgccattcaaatataacaatgagtgttaaaataaggaaagtttttttttcaaataagaaacacggattatttataaatcgccattaagccactacctcacagaagct


blockSeqs                     :                                                                                                                                                                                             G             GAAATTT             T     TT    G          AT         AGA               GAAA                            AA   C            T                                   ATAC   GATTT    AG  T  TTT                   T                  C                T CGAAATCATGT  ACC                  ATT   A GA G   T                              A     TTT  AAA           G                A   A  T  AT   A      . CATAACAAC           GA         GTTG   TTAAATATTA                          A       A  CA                       TTAAT      G    TA         GA
blockSeqs                     :                                                                                                                                                                                             .             .                   T     TT    T          .          A                 T                               .    .            .                                   AG     TATT     .   .  .                     C                  C                T .            TC                   A     . .  .   .                              T     .    .             .                .   .  T  .    .      . .                   .          .      TTTGAAAAT                           .       .  .                        .          T    .          . 
blockSeqs                     :                                                                                                                                                                                             .             .                   T     TT    T          .          A                 .                               .    .            .                                   .      TATT     .   .  .                     T                  C                T .            AC                   T     . .  .   .                              T     .    .             .                .   .  .  .    .      . .                   .          .      AAAG                                .       .  .                        .          T    .          . 
blockSeqs                     :                                                                                                                                                                                             .             .                   T     TT    G          .          A                 .                               .    .            .                                   .      TAG      .   .  .                     G                  C                G .            AC                   A     . .  .   .                              G     .    .             .                .   .  .  .    .      . .                   .          .      AAAG                                .       .  .                        .          T    .          . 
blockSeqs                     :                                                                                                                                                                                             .             .                   A     TT    G          .          T                 .                               .    .            .                                   .      TTG      .   .  .                     T                  C                T .            TC                   T     . .  .   .                              A     .    .             .                .   .  .  .    .      . .                   .          .      AAAG                                .       .  .                        .          G    .          . 
blockSeqs                     :                                                                                                                                                                                             .             .                   T     TT    G          .          A                 .                               .    .            .                                   .      C        .   .  .                     G                  C                T .            AT                   A     . .  .   .                              A     .    .             .                .   .  .  .    .      . .                   .          .      GGAG                                .       .  .                        .          A    .          . 
blockSeqs                     :                                                                                                                                                                                             .             .                   T     TT    T          .          T                 .                               .    .            .                                   .      T        .   .  .                     T                  .                . .            .                    A     . .  .   .                              T     .    .             .                .   .  .  .    .      . .                   .          .      AAAG                                .       .  .                        .          G    .          . 
blockSeqs                     :                                                                                                                                                                                             .             .                   T     TA    A          .          A                 .                               .    .            .                                   .      T        .   .  .                     .                  .                . .            .                    A     . .  .   .                              A     .    .             .                .   .  .  .    .      . .                   .          .      CA                                  .       .  .                        .          .    .            
blockSeqs                     :                                                                                                                                                                                             .             .                   .     C     G          .          A                 .                               .    .            .                                   .      T        .   .  .                     .                  .                                                    .     . .  .   .                              C     .    .             .                .   .  .  .    .      . .                   .          .      A                                   .       .  .                                                     
blockSeqs                     :                                                                                                                                                                                             .             .                   .     .     C          .          .                 .                                                                                     .      T        .   .  .                                                                                             .     . .  .   .                              T     .    .             .                .   .  .  .    .      . .                   .          .      .                                   .       .  .                                                     
blockSeqs                     :                                                                                                                                                                                             .             .                   .     .     T          .                                                                                                                                                                                                                                       .     . .  .   .                              .     .    .             .                .   .  .  .                                                                                                                                                        
blockSeqs                     :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    . .  .   .                              .     .    .             .                .   .  .                                                                                                                                                           


blockSeqCons                  :                                                                                                                                                                                      
originalCons                  :                                                                                                                                                                                      NNTGATT-TTTGTTCTTTATT-------CTATAGTAAATAATAAAAGTTTGAANGCTTGTCATT--CATAGAGAGA--CCCAAATGAAAGAAG----TGAAACTTACATTTTACTGTTTGTCAAC--CTC-TGCACTACCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----T---T--TT-TT---CTGCTCAGTGTGTACACTGTTGACAAAGTGAAAGTAGACTTCCGAAATCATGTATTC-----------ATA-CCCCAATTTCCAAGCATCAA--TTT-T--T-TTT-CTAAATTCACAATTCAAACATGACAATGCTNTCAAA---AT---GTTCAAAATAC-ATCAATAATGCCATTC-AAA-TA-AA--AAA-TGAGCA-T---------TAAAATAAGGA--AAATGCATT----TTT-----AAA----GAAGAAGAAACGAGGATTATTTAT-AACCGCC-AT--TATGCGACTACCCCACGGAAGCA-----CTTCCTNTTTC--CAATGGTGG--TACT
finalCons                     :                                                                                                                                                                                      NNTGATT-TTTGTTCTTTATT-------CTATAGTAAATAATAAAAGTTTGAANGCTTGTCATT--CATAGAGAGA--CCCAAATGAAAGAAG----TGAAACTTACATTTTACTGTTTGTCAAC--CTC-TGCACTACCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----T---T--TT-TT---CTGCTCAGTGTGTACACTGTTGACAAAGTGAAAGTAGACTTCCGAAATCATGTATTC-----------ATA-CCCCAATTTCCAAGCATCAA--TTT-T--T-TTT-CTAAATTCACAATTCAAACATGACAATGCTNTCAAA---AT---GTTCAAAATAC-ATCAATAATGCCATTC-AAA-TA-AA--AAA-TGAGCA-T---------TAAAATAAGGA--AAATGCATT----TTT-----AAA----GAAGAAGAAACGAGGATTATTTAT-AACCGCC-AT--TATGCGACTACCCCACGGAAGCA-----CTTCCTNTTTC--CAATGGTGG--TACT

Unaligned ( gi|17 ): AACGTTTGCATGCTTGTTATTCACAGAAACACCCAATAAAAGACGTGAAATGTATATTTTATTGT

lowQualScore                  :                                                                                                                                                                                                           1111111                                                                 1111                                                                                  1111   22222222                                                                    22222222222                       111                                                                                                             111111111                             1111111111111                                                           11111                            
lowQualScore                  :                                                                                                                                                                                             3             0000000             5     11    1          44         777               1111                            55   4            4                                   2222   44444444 55  3  666            0      2                  4                1 11111111111  666                  444   3 44 3   3                              5     555  555           3                3   3  6  44   3      3 444444444           55         7777   7777777777777          0            3       3  55                       11111      5    66         66    
lowQualScore                  :                                                                                                                                                                                             .             .......             .     ..    .          ..         ...               ....                            ..   .            .                                   ....   ........ ..  .  ...            .      .                  .                . ...........  ...                  ...   . .. .   .                              .     ...  ...           .                .   .  .  ..   .      . .........           ..         ....   .............          .            .       .  ..                       .....      .    ..         ..    
lowQualScore                  :                                                                                                                                                                                             3             8888888             4     77    0          66         555               4444                            55   0            0                                   7777   22222222 00  6  444            9      1                  1                8 11111111111  777                  333   1 22 1   1                              1     444  444           1                1   1  2  66   6      6 555555555           00         7777   9999999999999          5            6       6  00                       11111      3    11         99    
consensus                     :                                                                                                                                                                                      NNTGATT-TTTGTTCTTTATT-------CTATAGTAAATAATAAAAGTTTGAANGCTTGTCATT--CATAGAGAGA--CCCAAATGAAAGAAG----TGAAACTTACATTTTACTGTTTGTCAAC--CTC-TGCACTACCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----T---T--TT-TT---CTGCTCAGTGTGTACACTGTTGACAAAGTGAAAGTAGACTTCCGAAATCATGTATTC-----------ATA-CCCCAATTTCCAAGCATCAA--TTT-T--T-TTT-CTAAATTCACAATTCAAACATGACAATGCTNTCAAA---AT---GTTCAAAATAC-ATCAATAATGCCATTC-AAA-TA-AA--AAA-TGAGCA-T---------TAAAATAAGGA--AAATGCATT----TTT-----AAA----GAAGAAGAAACGAGGATTATTTAT-AACCGCC-AT--TATGCGACTACCCCACGGAAGCA-----CTTCCTNTTTC--CAATGGTGG--TACT
Reference ( family-1110 )     :                                                                                                                                                                                      NNTGATT-TTTGTTCTTTATT-------CTATAGTAAATAATAAAAGTTTGAANGCTTGTCATT--CATAGAGAGA--CCCAAATGAAAGAAG----TGAAACTTACATTTTACTGTTTGTCAAC--CTC-TGCACTACCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----T---T--TT-TT---CTGCTCAGTGTGTACACTGTTGACAAAGTGAAAGTAGACTTCCGAAATCATGTATTC-----------ATA-CCCCAATTTCCAAGCATCAA--TTT-T--T-TTT-CTAAATTCACAATTCAAACATGACAATGCTNTCAAA---AT---GTTCAAAATAC-ATCAATAATGCCATTC-AAA-TA-AA--AAA-TGAGCA-T---------TAAAATAAGGA--AAATGCATT----TTT-----AAA----GAAGAAGAAACGAGGATTATTTAT-AACCGCC-AT--TATGCGACTACCCCACGGAAGCA-----CTTCCTNTTTC--CAATGGTGG--TACT
gi|1                          :                                                                                                                                                                                        TGCTT-TTTGTTCTTTATT-------CTATAGTAAATAATAAACGTTTGAAAGCTTGTCATT--CATAGAGGGT--CCCAAATGAAAGAAG----TGAAACTTACATTTTACAATTTGTCAAC--CTC-TGCATTACCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AAA----C---A--AT-T----CTGCTCTGTGTGTACACTTTTGACAAAGTGAAAGTAGATTTCCGAAATCATGTATTC-----------ATA-ACCCAATTTCCAAGCATCAT--ATT-C--T-TTT-CTAAATTCACAATTCTAACATGATAATGCTTTCAAA---AT---GTTCAAAATAC-ACCGATAATGCCATTC-AAA-TA-AA--AAA-T-AGCATT---------TAAAATAAGGA--AAATGCATT----TTT-----AAA----GAAGAAGAAACAAGAATTATTTAT-AACCGCC-AT--TATGCGACAACCCCAATGAAGCA-----CTTCCTTTTTC--CAATGGTGG--TACT
gi|10                         :                                                                                                                                                                          tgtaagcccaccatTGATTGTTTGTCCTTTATT-------CTATAGTAAATAATACAAGTTTGAAGGCTTGTCATT--TATAGAGAGA--CCTAAATGAAAGCAG----TGAAACATACATTTTACTGTTTGTCAA---CTC-TGTACTTCTAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGATAT-T---T--TT-TT---CTGCTCAGTGTGTACACTGTTGACAAAGTGAAAGTAGACTTCCGAAATCATGTATTCCGAAATCATGTATT-CTCCAATTTCCAAGCAT-A------------TTT-CTAAATTCACAATTCAAACCTGACAATGCTATAAAA---AT---GTTAATAATATGAACAATAATGGCATTC-CAA-TA-AA--at
gi|11                         :                                                                                                                                                                        ggtgtaagtccaccatTGATT-GTTGCTCTTTATTGAAATTTCTATAGTAAATAA--AGAGC----ATGTTTGTCATT--CATAGAGAGAGACACAAATGAAAGAAG----TGAAACTTACATTTAATTGTTTCTCAAC--CAC-TGCAATACAGAATATATGATGAGAAAAGTAGGGTTCATATGGCATATA----AAA----C---TAGTT-TT---CTGTTCAGTGTGACCACTGCTGACAAAGTGAAAGTACACATCCAAAATC
gi|12                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                    ggtgtaagaccaccatCCAAGCATCA----TT-T--T-TTT-CTAAATTCACAATTCACACATGGCAATGCTTTCAAA---AT---GTTCAAAACAC-ATCAATAACACCATTA-CAA-TA-
gi|13                         :                                                                                                                                                                                                                                                                                                                                             aaaaatagaatttacataattatataaatatattttttatctttaattttattttgtgtttgtatattttagcaaacatgaaaccccaaatcccttacatcaccaaatgcattaccaagaatcgtatgaaccaaacactgcatgcA--TTT-TGAT-TTT-CTAGATTCAAAATTCAAACATGGCAATGTT---------------TTCTAAATAT-AGCAATTACGCCATTA-AAG-TA-AC--ATA-CTAGTA-TCATAACAACTAAACTTAAGA--AAGTGTATTGTTGTTTTTTGAAAA----TAAACACAAACAAAACCTATTGAT-GCCAGAC-ATCATACGCGAC
gi|14                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                        ccaaatgtgcctCCAAGCATCA----TT-T--T-TTT-CTAAATTCACAATTCACACATGGCAATGCTTTCAAA---AT---GTTCAAAACAC-ATCAATAACACCATTA-CAA-TA-AC--AAA-TGAGTA-T---------TAAAATACGTA--AAATGCATT----ATC-----A-------ATGAAGAAACAATGGCTATTTAT-AACGGCCAAT--CA-GCGATTATCCCACGGAAGCATTAATTTTCCTGTTTG--CAATGGTaggagcgacatattatatcta
gi|15                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            AGGACTATTTAT-AACCGCC-AT--CATACGACTACCCCACGGAAGCA-----CTTCCTTTTTTTACAATGGTGG--TACT
gi|16                         :                                                                                                                                                                                        TGATG-TTTGTTCTTTATT-------CTATAGTAAATAA-AACAATTTACGTGCTTGTCATT--CATAatgcc
gi|2                          :                                                                                                                                                                          tgtaagcccgccatTGATT-TTTGTTCTTTATT-------CTATGGTAAATAATAAAAGTTTGAAGGCTTGTCATT--CAAAGAGAGA--CCTAAATGAAAGAAG----TGAAACTTACATTTTACTGTTTGTTAAC--ATC-TGCACTATCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----T---T--TT-TTTTTCTGCTCAGTGTG-------------AAGTGAAAGTAGACTTCCAAAATTATGTACTC-----------ATA-CCCCAATTTCCATGCATTAT--TTT-T--T-TTTTCTAACTTCACAATTCAAACATGAAAATGCTGTCAGA---AT---GTTCAAAATAC-ATCAATAATGCCATTT-GAA-TA-AA--AAAATGAACA-T---------TAAAATAAGGA--AAATGCAGT----TTT-----AAA----GAAGAAAAAACGAGGATTATTTAT-AACTGCC-AT--TATGCGACTACCCCACGGAAGCA-----CTTCCT-TTTC--CAATGGTGG--TACT
gi|3                          :                                                                                                                                                                      aaggtgtaaaccaatcatTGATT-TTTGTTCTTTATT-------CTATAGTAAATAATAAAAGTTTGAAGGCTTGTCATT--CATGGAGAGA--CCCAAATAAAAAATG----TGAAACCTACATTTTACTGTTTGTCAAC--CTC-TGCACTGTCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----T---T--TT-TT---CTGCTCAGTATGTACGATGTTGACATAGTGAAAGTAGACTTCCGAAATCATGTATTC-----------ATA-CCCCAATTTCCAAGCATCAA--TTTAT--T-TTT-CTAAATTCACAATTCAAAGATGACAATGCTATCAAA---CT---GTTCAAAATAC-ATCAATAATGTCATTA-AAA-TA-AA--AAA-TGTGCA-T---------TGAAATAAGAA--AAATGCATT----TTT-----AAA----GAAGAAGAAACGAGGATTATTTAT-AACCGCC-AT--TATGCAACTACCTTACGGAAGCA-----CTTCCTTTCTC--CAATGGTGG--TACTatgcc
gi|4                          :                                                                                                                                                                                      aaTGAGT-TTTGTTATTTATT-------CTATTGTAAATAATAAAAGTTTGAAGGCTTGTCATT--CATAGAGAAT--CCCAAATGAAAGAAG----TGAAACCTACATTTTACTGTTTGTCAAC--CTC-TGCACTATCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGAGATTT---T--TT-TT---CTGCTCAGTGTGTACACTGGTGACAAAGTGATAGTAGA-------------------------------------CAATTTCCAAGCATCAT--TTT-T--T-TTT-CTAAATTCACAATTCAAACATGACAATGCTATCAAA---AT---GTTCAAAATAC-ATTAATAATGCCATTC-AAA-TA-AAATAAA-TGAGCA-T---------TTAAATAAGGA--AAATGCATT----TTT-----AAA----GAAAAAGAAATGAGGATTATTTAT-AACCGCC-AT--CATGCGACTACCCCACGGAAGTA-----CTTCCTTTTTG--CAATGGTGG--TACTt
gi|5                          :                                                                                                                                                                        aggtgttacctcaccatGATT-TTT--TCTTTAAG-------CTATAGTAAAAAAAAGAAA---GAATACTTGTCGTTATCACAGAGAA-----CAAA-GAAATAAG----TGAAACTCATATTTTTATGTTTGTCAAC--CTC-TGCACTAATATA-ATATGACGAGAAAAATGGGGATTATGTGTCATTCA----AGA----TAG-T--TT-TC---GTG-TCTGTTTGTGTACTGTTTACGAAGT----------TTACAAAA----ATATGC-----------ATACCCCCAATTTCCAAGCATCAA--TTT-C--TGTTT-CTAATTTCACAATTTAAACATGAAAATGTTTATAAATTTATAAAGTTCAAATTAT-ACCAATAATGCCATTCAAAA-TA-AA--ATA-TAAGCA-A---------TAAAATAAGGA--AAATGC-TT----TT--------------------------------TTTAT-AACCGTC-AT--TAT-----------------GCA-----TTTCATGTCTC--CAATGGT----TACTatgc
gi|6                          :                                                                                                                                                                         aaggcgtaagtccatcattg-TTTGTTGTTTATT-------CTATAGTAAATAATAAAAGTTTGAAAGCTTGCCATT--CATAGAGAGA--CCCAAATAAAAGAAA----TGAAACTTACAGTTTACTATTTGTCAAC--CTC-TGCACTACCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATA----AGA----TATTT--TT-TT---CTGCT----------------------GTGAAAGTAGA-------AATCATATATTC-----------ATT-CCCAAATGTCCAAGCATTAA--TTT-T--T-TT--CTAAATTCACAATTCAAA---------------------AT---GTTCAAAATAC-ATCAATAATGCCATTC-AAAATA-AA--AAA-TGAGCA-T---------TAAAATAAGGAGAAAATGCATT----TTT-----GGA----GAAGAAGAAACGAGGATTATTTAT-AACCGCC-AT--TATGCGACTACTCCACAGAAGCG-----CATCCTATTTC--CAACGGTGC--TA
gi|7                          :                                                                                                                                                                                        TGATT-TTTGTTCTTTATT-------CTATTGTAAATAATAAAAGTTTGAAGGCTTGTCATT--CATAGAGAAT--CCCAAATGAAAGAAG----TGAAACCTACATTTTACTGTTTGTCAAC--CTC-TGCACTATCAAA-ATATGATGAGAAAAGTAGGGGTCATGTGTCATATAAG--AGA----TTG-T--TT-TT---CTGCTCAGTGTGTACACTGGTGACAAAGTGAAAGTAGACTTCCGAAATCATGTATTC-----------ATA-TCCCAGTTTCCAAGCATCAATTTTT-T--T-TTT-CTAAATTCATGATTCAAACATGAAAATGCTATCAAA---AT---GCTCAAAATAC-ATCAATGATGCCATTC-AAA-AA-AA--AAA-TGAGCA-T---------AAAAATAAGGA--AAATGCATT----TTT-----AAA----GAAGA
gi|8                          :                                                                                                                                                                      aaagtgtcaacccaccatTGATT-TCTGTTCTTTTTT-------C-ATAGT---CAATAAAAC-----ACGCATTTCATT--CATAAAGAGA--CCCAAATGAAAGAAAGAAATGAAACTTACATATTATTGATTTTCAACAACTCCTGCACTACCAAA-ATATGATGAGAAAAGTA--AGTTATGTAATATATGATACACA----T---T--TT-TT---CTGTTCAGGGT
gi|8                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ccatTT-T--T-TTT-CTAAATTAACAATTCAAACATGACTGTGCTCTTAAA----T---GTTTGAAATAG-ATCCCTTATGGAGTTC-AAA-AATAA--AAA-TGAGCA-T---------TAAAAGAAAGG--AGATG-ATT----TTTTT---AAATATTAAAGA-GAAACAAGTATTATTTAT-AACTACC-AT--TATACGTCTACTCCACGAAAGCA-----TTTCCTGTGTC--CAATGGTGGGATACTtctttttttctaaattaacaattcaaacatgactgtgctcttaaatgtttgaaatagatcccttatggagttcaaaaataaaaatgagcattaaaagaaaggagatgatttttttaaatattaaagagaaacaagtattatttataactaccattatacgtctactccacgaaagcatttcctgtgtccaatggtgggatactatgca
gi|9                          : ccattgatttctgttcttttttcatagtcaataaaacacgcatttcattcataaagagacccaaatgaaagaaagaaatgaaacttacatattattgattttcaacaactcctgcactaccaaaatatgatgagaaaagtaagttatgtaatatatgatacacattttttctgttcagggttcTGATT-TTTGTTCTTTGTT-------GTATAGTAAATAA-AAAAGTATACATGCTTGTCATT--CATAGAGATA--CCCAACTGAAAGAAGT---TG--GCTTGCATTTAATTACTTATatgca
gi|9                          :                                                                                                                                                                                                                                                                                                                                                        agctcaccatTTATATA----AGA----T---T--TTTTT---CTGCTCAGTGTGTACAGTGTTGGCAAAGTGAGAGTAGACTTCCGAAATCGTGTAT-------------------CCAATTTCCAAACATC-A--TTA-T--T-TTC-CTAA----ACATTT---------CAATGTTTTCCAA---GT---GTTCAAAATAC-ATCAATAATGCCATTC-AAA-TATAA--CAA-TGAGTG-T---------TAAAATAAGGA--AAGTTTTTT----TTT-----CA------AATAAGAAACACGGATTATTTATAAATCGCC-AT--TAAGCCACTACCTCACAGAAGCataagatttttttctgctcagtgtgtacagtgttggcaaagtgagagtagacttccgaaatcgtgtatccaatttccaaacatcattattttcctaaacatttcaatgttttccaagtgttcaaaatacatcaataatgccattcaaatataacaatgagtgttaaaataaggaaagtttttttttcaaataagaaacacggattatttataaatcgccattaagccactacctcacagaagct

Unaligned ( gi|17 ): AACGTTTGCATGCTTGTTATTCACAGAAACACCCAATAAAAGACGTGAAATGTATATTTTATTGT