lowQualScore                  :                                                                                                                                                                                                                                                                                                                                                                                   111111111111111111111111111111111111111111111111111111111111111111111111                 111111111111111111111111111111111111111111                                                                                                                                                                                                                                                                  1111111                                                                                                                                                                                                                                                                                                                                                                                                                                                   11111111                                                                                                                                                                                                                                                                                                                            22222222222222222222222222222                                                                                                  111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111                                             
lowQualScore                  :                                                                                                                                                                              22            11    222               11     2222                 1       55555555555555555555555555                    888888888888888                                                              000000000000000000000000000000000000000000000000000000000000000000000000                 000000000000000000000000000000000000000000            1              111111       222222222    2222222222       11      1111  222222  1111      11111                             1                                                                                                             4           3333333         1          1          22  1                                        222                                         1      1                 1        11                             1111             1                                            11  33       11    11                                                              1                                                                                                  1     00000000         1              444444  1                                            22                  1                                    111                   22222            444444444   1111111       33333333                 3333333                                                            1                        22222222222222222222222222222                      1    1                                                       1              666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666                                             
lowQualScore                  :                                                                                                                                                                              77  4         88    333               88     1111                 0       44444444444444444444444444 22        1        555555555555555             8                6                  2      6     000000000000000000000000000000000000000000000000000000000000000000000000            8  8 111111111111111111111111111111111111111111            0    888       777777  6    555555555    0000000000       33      4444  444444  4444      22222                             5              6   3                          6            6                       4                4   4     0         2 0000000         1        6 7          11  5                                        111  6     2                                7      3                 5        33                    6        8888    7        7   6                                6       88  99       88    88                  6         9                                 5                  8       6           7 88            7                                           3     77777777         5  3     2     222222  0                                            33                  5                                    777           555     11111      5     777777777   3333333       22222222                 4444444           4                                 2              7          8             66666666666666666666666666666        77            0    5          3             3                              5              000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000    4     6   3           4                  
lowQualScore                  :                                                                                                                                                                              ..  .         ..    ...               ..     ....                 .       .......................... ..        .        ...............             .                .                  .      .     ........................................................................            .  . ..........................................            .    ...       ......  .    .........    ..........       ..      ....  ......  ....      .....                             .              .   .                          .            .                       .                .   .     .         . .......         .        . .          ..  .                                        ...  .     .                                .      .                 .        ..                    .        ....    .        .   .                                .       ..  ..       ..    ..                  .         .                                 .                  .       .           . ..            .                                           .     ........         .  .     .     ......  .                                            ..                  .                                    ...           ...     .....      .     .........   .......       ........                 .......           .                                 .              .          .             .............................        ..            .    .          .             .                              .              ...........................................................................................................................    .     .   .           .                  
lowQualScore                  :                                                                                                                                                                              55  0         33    333               33     2222                 0       88888888888888888888888888 22        4        222222222222222             8                0                  5      0     000000000000000000000000000000000000000000000000000000000000000000000000            0  0 222222222222222222222222222222222222222222            8    555       333333  7    333333333    5555555555       88      2222  888888  2222      44444                             0              0   0                          0            0                       0                0   0     0         5 0000000         5        0 0          00  0                                        000  0     5                                0      3                 0        00                    7        3333    0        0   0                                0       33  77       33    33                  0         7                                 0                  3       0           7 33            3                                           3     55555555         5  0     5     222222  0                                            88                  0                                    444           888     66666      0     111111111   0000000       33333333                 3333333           8                                 2              0          8             00000000000000000000000000000        00            0    0          2             2                              0              000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000    0     0   0           0                  
consensus                     :                                                                                                                                                                          ACTACTAANATATAATAA--TAAA---TAATTAAAACTAACT--GTAAT----AAATAACTGAATAAATA-ATTAAAA--N--NAT-AA-TAAGCATGAACAANTAACTGAATAAATAATTAGAC-T---TATAGACTCTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNT-----ACTACTGTAATA-AA-TTA---AAA-------AAATAATTAAAACTAACTGTA------ATAAATAACTGAATAAATA-ATTAAAA-----ATA-AATA-A-------ATAA--GC------ATGAACACTACTGAA----TAA----TTA----GACTCTGTATTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTACACAAGACACAAAGTGATTTTGCGCACGACTTTTCTATTTTTAGATATAGCATNTCACAACCATTGCATCNGTCNAACCC-ACGCTAAGANATTAGTGTCAAGCCTAGNATGTGTCTCCTTACTGTCTGCTCTTGTATTGGCACGATACATAATCCCTAAGCGGATTAGGCAGCACATGCCGGATANACCGCAATGGCCTATTGATACGTCAGAGTTAATACCTTT-ACGTGACCCCAGTATGTCTAGCGTCTACCGGATATGAACACAATAGCCCATTCATCAGCCAAAAGGTAATCTCCTTAACGTCGCCAGTATGTCTAGCGTTTGTTTATTTAGGCACGGAA--GTGTAACAATG--GTGT--ATTCAAGTGTCAAACTTAACGACTGGACGTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATAGTCATGATTGGACTAAATAACTCGAGCAAAGTTAGNTGTATTTGGTATATCTGTGTCCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAA-TACTTTANTTAAAAATAAAATGATTNTTGTTNTTGTTG---T-TT-TTAGTATCGTAGATGTTGCCTTAACTGTGTAACACGAATTTTAC-GGGAAAATCGGGTGTATTGAATTTTTATAGCAGGAGGTAAATACTTAATTTTAGAGGACCACAGGGAAGA---TTGGA-NATTGTTCCAACTGTG---------TTT-------AAATAAAGACTTAA-TTATTATTATTATTACTATA---ATCATTATTATTATTATTAAAGATGAAATATGTTCTTTTTAGTATCGTAAATGTTGCCTTAACTGTGTAACACGAATTTTACGGAAAATTAATGGGTT-GAATT-ATGGGTTCGATCCTAAAACCGGAAGTTGAAAA-TAATTGTTTCGAAGTAGGGCAAGTTATATATTTTTGAAAAGGTATGACCGAGTACATTACGAAAAATATGGTTCC-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAAAATANTTTTCGATTNATGTCAGAAATNAGAAATGGAAACCCTAGA
Reference ( gi|1 )            :                                                                                                                                                                          ACTA--AAAATATAATAA--TAAA---TAATTAAAACTAACT--GTAAT----AAATAACTGAATAAATA-ATTAAAA--A--AAT-AA-TAATTATGGACAAATAACTGAATAAATAATTAAACGTAAATATAGACTCTATAAATAACTTATATGTTTCTTCTCCAACAGCCAACACTCAAATGAACGCCCTACATTTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNA-----ACTACTGTAATA-AA-TTAAAAAAA-------AAAAAATTAAACTTAACTGTG------ATAAATAACTGAGTAAACA-ATTAAAA-----ATA-AATA-A-------ATAA--GC------ATGAACACTACTGAA----TAA----TTA----GACTCTGTATTATAAATAACTTACATGTTTCTTCTCCAACTGCCAACACTCAAATAAATTCCCTACGTTACACAAGACACAAAGTGGTTTTGCGCACGATTTTTCTATTTTTAGATATAGCATTTCACAACCATTGCATCAGTCAAACCCCACGCTAAGAGA-------CAAGCCTAGTATGTGTCTTCATACTGTCTGCCATTTTATTGACACGATACATAATCTCTAAGCGGATTAGGCAACACATGCTGGATACACCACAATGGCCTATTGATATGTCAGAGTTAAAACCTTT-ACGTGACCCCAGTATGTGTAGCGTCTGACGGATATGAACACAATAGCCCATTCATCAGCCCAAAGTTAATCTCCATAATGTCGCCAGTATGTCTAGCGTTTGTTTATTTAGACACGGAA--GTTAAACAATG--GTGT--ATTCAAGTGTCAAACTTAGCGACTGGACATCTTAACAATAGATTAATGGGTCCTTTGTTGTAAATAGTCATGATTGGACTATATAACTCAAGCAAAGTTAGTTATATTTGGTATATCTGTGTCCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAA-TACTT--------AATAAAATGATTTTTGTTGTTGTT----T-TT-TTAGTATCGTAGATGTTGCCTTAACTGTATAACACGAATTTTATGGGGAAAATCGGATGTATTGCATTTTTATAGCAAGAGGTAAATATTTAATTTTAGAGCAACACAGGGAAGA---TTGGA-GATAGTTCCAGCTGTG---------TTT-------AAATAAAGTCTTAA-TTATTATTATTATTACTGTT---GTCATTATTATTGTTATTAAAGATGAAATATGTTCTTTTTAGTATCATAAATGTTACCTTATCTGTGTAACATGAATTTTACGGAA--------------A--------------TCCTAAAACTGGAAGTTGAAAA-TAATGGTTTCGAAATAGGGCAAGTTATATATTTTTGAAAAGGTATGACTGAGTACATTACTAAAAATATGGTTCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTGCAATATTTTTCAATTTATGTCAGAAATAAAAAATGAAAACCTTAGA
gi|2                          :                                                                                                                                                                          ATTA--AATAAATAATAA--TAAA---TAATTAAAAGTATTTTTGTAATTCATAAATAACTGAATAAATA-ATTAAAA--ATAAAT-AAATAAGCATG-ACCACTA-CTGAATAAATAATTAGACTT---TGTA----TTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAAGGAATTCCATACGTT
gi|6                          :                                                                                                                                                            actactgtaaaaaaACTACTAAAATATAATAA--TAAA---TAATTAAAACTAACT--GTAAT----AAATAACTGAATAAATA-ATTAAAA--C--TTT-AA-T------GAACAAGTTACTGAATAAATAATTAAA------TATAGACTCTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTACTGTAATA-AA-TT-----------------AAAT-----------------------AATAACTAA-TAAATG-ATTAAAA-----CTA-ATTGTA-------ATAA--AT------A--------ACTGAA----TAA----ATA----AAacacaagacacaaagtgattttacgcacgacttttctatttttagatatagcatatcacaaccattgcatcagtttaatccacgctaagagattagtgtcaagtctagcatgtgtctccttactgtctgctcttgtattgacacgatacataatctctaagcggattaggcagcaaccggatacaccgcaattgcctattgatatgtcagagttaatacctttatgtgaccgcagtatgtctagggtataccggataggaacacaatagccaaaaggtaatctctttaacgtcaccagtatgtctagcgtttgtttatttaggcacggaagtgtatcaatgatgtattaaagtctcaaacttaacgactggacgtcttaacaatagattaatgggtcctttgttgtacattgtcatgattggactatttaactcgagcaaagttaggtattggtataactgtccacggtgtgaatattggagttttatagcaagaggtaaattattttaaaataaaatgttgttgttttttttgtagtttttagtatcgtagatgttgccttaattgtataacacgaattttattgggaaaattggatgtattgaatttttatggcaggaggtaaatatttaattttagaggaccacagggaatattggagttccagctgtgttttttctttaaacaagaacttaattattataattattactataatcattattgttattattaatgatgaaatatgttctttttagtatcataaatgttgccttaactgtgtaacacgaattttacggaaaattaatgggttcgatcctaaaaccggaagttgaaaataattgtttcgaagtagggcaagttatattttttgaaaaggtatgaccgattacattacgaaaaatatggtt
gi|7                          :                                                                                                                                                                                   tTGTAATAAATTAAAACATAATTAAAACTAACT--GTAAT----AAATAACAGAAAAAAAATATTAAAAATA--AATAAA-TAAGCATGAAC-ACTAA-TGAATAATTAATTAGACtaaaacaaagtaaatgaactataa
gi|7                          : aataaattaaaaataaaaaactgaatcaataattaaaactataatgaacatataactgaataaataattaaatataaactctataaataacttaaatgtttcttctccaacggccaacactcaaatgaacgccctacgtttatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntactacAAT----AAAAAACTGAATCAATA-ATTAAAA--C--TAT-AA-T------GAACATATAACTGAATAAATAATTAAA------TATAAACTCTATAAATAACTTAAATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNT-----ACTACTGTAATA-AA-TT----AAA-------ACATAATTAAAACTAACTGTA------ATAAATAACAGAAAAAAAATATTAAAA-----ATA-AATA-A-------ATAA--GC------ATGAACACTAATGAATAATTAA----TTA----GACTCTGTATTtctgtatt
gi|4                          :                                                                                                                                                                                                                                                       aataaattaaaA-TAAGCATGAACA--CTACTGAATAATTAATTAGAC-TCTGTAT------TATAAATAACTTACATGTTTTTTCTCCAACGGCCAACACTCAAATGAATTCCCTACGTT
gi|2                          :                                                                                                                                                                                                                                                                                                                                                                   tactgtaataaattannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn-----ACTACTGTAAAA-AAATTAAATAAATAATAATAAATAATTAAAAGTATTTTTGTAATTCATAAATAACTGAATAAATA-ATTAAAA-----ATA-AATA-A-------ATAA--GC------ATGACCACTACTGAA----TAAATAATTA----GACTTTGTATTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAAGGAATTCCATACGTTACACAAGACACAAAGTGATTTTACGCACGACTTTTCTATTTTTAGATATAGCATATCACAACCATTGCATCAGTTTAATCC-ACGCTAAGAGATTAGTGTCAAGTCTAGCATGTGTCTCCTTACTGTCTGCTCTTGTATTGACACGATACATAATCTCTAAGCGGATTAGGCAGCA---ACCGGATACACCGCAATTGCCTATTGATATGTCAGAGTTAATACCTTT-ATGTGACCGCAGTATGTCTAGGGTATACCGGATAGGAACACAATAGCC--------A----AAAGGTAATCTCTTTAACGTCACCAGTATGTCTAGCGTTTGTTTATTTAGGCACGGAA--GTGTATCAATG--ATGT--ATTAAAGTCTCAAACTTAACGACTGGACGTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATTGTCATGATTGGACTATTTAACTCGAGCAAAGTTAGGTA---TTGGTATAAC--TGTCCACGGTGTGAATATTGGAGTTTTATAGCAAGAGGTAAATTATTTTAA-----AATAAAATG-TTGTTGTTTTTTTTGTAGT-TT-TTAGTATCGTAGATGTTGCCTTAATTGTATAACACGAATTTTATTGGGAAAATTGGATGTATTGAATTTTTATGGCAGGAGGTAAATATTTAATTTTAGAGGACCACAGGGAATA---TTGG-----AGTTCCAGCTGTGTTTTTTC--TTT-------AAACAAGAACTTAA-TTATTATAATTATTACTATA---ATCATTATTGTTATTATTAATGATGAAATATGTTCTTTTTAGTATCATAAATGTTGCCTTAACTGTGTAACACGAATTTTACGGAAAATTAATGGGTTCGA--------------TCCTAAAACCGGAAGTTGAAAA-TAATTGTTTCGAAGTAGGGCAAGTTATAT-TTTTTGAAAAGGTATGACCGATTACATTACGAAAAATATGGTTacacaagacacaaagtaattttgcgcacgacttttctatttttagatatagcatttcacaaccattgcatctgtcaaacccacgctaagatattagtgtcaaacctagaatgtgtctccttactgtctgctcttgtattggcacgatacataatccctaagcggattaggcaacacatgccggatagaccacaatggcctattgatatgtcagagttaatacctttacgtgaccccagtatgtctagcgtctaatggatatgaacacaatagcccattcatcagccaaaaggtaatctccttaacgtcgccagtatgtctagcgtttgtttatttaggcacggaagtgtaataatggtgtgtattcaagtgtcaaacttaacgactggacgtcttaacaatagattaatgggtcctttgttgtacatagtcatgattggactaaataactcgagcaaagttagttgtatttggtatatctgtgtccacggtgtgtgtattggagttttatagcaagaggtaaatact
gi|6                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                      -----ACTACTAAAATATAA-T-----AAT-------AAATAATTAAAACTAACTGTA------ATAAATAACTGAATAAATA-ATTAAAA-----CTTTAATG-A-------ACAA--GTTACTGAATAAATA--ATTAAA----TA------TA----GACTCT-----ATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTT
gi|4                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                            tTACTGTAATA-AA-TTANNNNNN-------NNNNNNNNNNNNNNNNNNNNN------NNNNNNNNNNNNNNNNNNN-NNNNNNN-----NNN-NNNN-NNNNNNNNATAA--GC------ATGAACACTACTGAA----TAA----TTAATTAGACTCTGTATTATAAATAACTTACATGTTTTTTCTCCAACGGCCAACACTCAAATGAATTCCCTACGTTACACAAGACACAAAGTAATTTTGCGCACGACTTTTCTATTTTTAGATATAGCATTTCACAACCATTGCATCTGTCAAACCC-ACGCTAAGATATTAGTGTCAAACCTAGAATGTGTCTCCTTACTGTCTGCTCTTGTATTGGCACGATACATAATCCCTAAGCGGATTAGGCAACACATGCCGGATAGACCACAATGGCCTATTGATATGTCAGAGTTAATACCTTT-ACGTGACCCCAGTATGTCTAGCGTCTAATGGATATGAACACAATAGCCCATTCATCAGCCAAAAGGTAATCTCCTTAACGTCGCCAGTATGTCTAGCGTTTGTTTATTTAGGCACGGAA--GTGTAATAATGGTGTGT--ATTCAAGTGTCAAACTTAACGACTGGACGTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATAGTCATGATTGGACTAAATAACTCGAGCAAAGTTAGTTGTATTTGGTATATCTGTGTCCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAA-TACTtatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntactactgtaataaattaaataataactaataaatgattaaaactaattgtaataaataactgaataaataaataaaacaaagtaaatgaactataa
gi|7                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    -------AATAAATTAAA---------A------ATAAAAAACTGAATCAATA-ATTAAAACTATAATG-AACA-T-------ATAACTGA------ATAAATA--ATTAAA----TA------TA----AACTCT-----ATAAATAACTTAAATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTT
gi|9                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       ACCACAAGGGCCTATTGAAACGCCATAGTTAATACTTTTTACGTGATCCCCGTATGGCTAGCGTCTACCGGACATGAACACAATAtatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntactactgtaataaattaaaacataattaaaactaactgtaataaataacagaaaaaaaatattaaaaataaataaataagcatgaacactaatgaataattaattagactctgtatt
gi|3                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         ATAGCCCATTCATCAGCCAAAAGTTAATCTCCTTAACGTCGCAAATATGTCTAGCGTTTGTTTATTTAGGCACGGGATAGT--AACAATG--GTGTGTATTCAAGTGTCAAACTTAACGACTGAACTTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATAGTCATGATTGGACTAAATAACTCGAGCAAAGTTAGATGTATTTGGTATATCTGTGTTCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAA-TACTTTATTTAAAAATAAAATGATTTTTGTTGTGGTTG---TATT-TTAGTATCGTAGATGTTGCCTTAACTGTATAACAAGAATTTTATGGGGGAAATCGGGTGTATTGAATTTTTATAGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN---NNNNN-NNNNNNNNNNNNNNNN---------NNN-------NNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNTTAATCATAATAATTACTATTAAAGATGAAATCTGTTCTTTTTAGTATCGTAAATGTTACCTTAACTGTGTAACAAGAATTTTACGGAAAATTAATGGGTTAGA--------------TCCTAAAACTGGAAGTTGAAAA-TAATTGTTTCGAAGTAGGGCAAGTTATATATTTTTGAAAAGGTATAACTGAGTACATTACGAAAAATATCGTTTCa
gi|5                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TGTTC---T-TT-TTAGTATCGTAAATGTTGCCTTAACTGTGTAACACGAATTTTAC--GGAAAATcgccnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctaaaataattttcgattgatgttagaaataaaaaatggaaaccttaga
gi|8                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 tcattattattattattaaagatgaaataTGTT----T-TTCTTAGTATCGTAAATGTTACCTTAACTGTGTAACACGAATTTTAC--GGAAAATtaatgggttcgatcctaaaaccggaagttaaaaaataattgtttcgaaatagggcaagttatatatttttgaaaaagtatgaccgagtacattacgaaaaatatggttccnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctaaaatatttttcgatttatgtcagaaattagaaatgaaaactcta
gi|4                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             cttaatannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaagatgaaataTGTATTGGAGTTTTATAGCAAGAGGTAAATACTttatgggttcgatcctaaaagttaaaaataattgtttcgaaatggcaagttatatatttttgaaaaggtatgactgagtacattacgacaaatatggt
gi|16                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      tactgtaataaattannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnataagcatgaacactactgaataattaattagactctgtattataaataacttacatgttttttctccaacggccaacactcaaatgaattccctacgttacacaagacacaaagtaattttgcgcacgacttttctatttttagatatagcatttcacaaccattgcatctgtcaaacccacgctaagatattagtgtcaaacctagaatgtgtctccttactgtctgctcttgtattggcacgatacataatccctaagcggattaggcaacacatgccggatagaccacaatggcctattgatatgtcagagttaatacctttacgtgaccccagtatgtctagcgtctaatggatatgaacacaatagcccattcatcagccaaaaggtaatctccttaacgtcgccagtatgtctagcgtttgtttatttaggcacggaagtgtaataatggtgtgtattcaagtgtcaaacttaacgactggacgtcttaacaatagattaatgggtcctttgttgtacatagtcatgattggactaaataactcgagcaaagttagttgtatttggtatatctgtgtccacggtgtgTAAAGGACCACAGGGAAGA---TTGGACAAT-GTTCTAACTGTG---------TTT-------
gi|15                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        tcaTAAAGGACCTCAGGGAAGA---TTGGACAAT-GTTCTAACTGTG---------TTT-------cct
gi|10                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           aAGAGGACCACAGGGAAGA---TTGGA-GATTGTTCCAAATGTGTTTGCTCC-TTT-------AAATAAA----TAATTTATTATTGTTATcctcttt
gi|17                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   CACAGGGAAGA---TTGGA-AATTGTTCCAACTGTG---------Taataa
gi|20                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   CACAGGGAAGA---TTGGA-CATTGTTCCAACTATG---------Tatcctct
gi|12                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   CACAGGGGAGA---CTAGA-CATTGTTCCAACTCTGTTTCCTA--TTT-------AAATAAAAAC---A-TTATTATT
gi|14                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   CACAGAGAAGAGTGTTGGA-CACTGTTCTAACTGTG---------TTT-------
gi|11                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               taagacCAGGAAAGA---TTGGA-CATTGTTCCAAAGGTGTTTTTCCTCTTT-------AAATAAAG----A---TATTATTATTtctctttcaa
gi|18                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    gacccGAAGA---TTGGA-GACTGTTCCAACTGTG---------TTT-------
gi|13                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           AGA---TTGGA-CATTGTTCCATGTGTG---------TTTCCTCTTTGAATAAAGACTTTA-TTATTATTATTcctctttaaa
gi|8                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   CTTAA-TANNNNNNNNNNNNNNNNNN---NNNNNNNNNNNNNNNNNNNAAGATGAAATATGTTTTTCTTAGTATCGTAAATGTTACCTTAACTGTGTAACACGAATTTTACGGAA--------------AATTTATGGGTTCGATCCTAAAA------GTTAAAAA-TAATTGTTTCGAAAT--GGCAAGTTATATATTTTTGAAAAGGTATGACTGAGTACATTACGACAAATATGGT
gi|5                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 TCATTATTATTATTATTAAAGATGAAATATGTTCTTTTTAGTATCGTAAATGTTGCCTTAACTGTGTAACACGAATTTTACGGAA--------------AATTAATGGGTTCGATCCTAAAACCGGAAGTTAAAAAATAATTGTTTCGAAATAGGGCAAGTTATATATTTTTGAAAAAGTATGACCGAGTACATTACGAAAAATATGGTTCC-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAAAATATTTTTCGATTTATGTCAGAAATTAGAAATGAAAACTCTA
gi|3                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                AATAATTTTCGATTGATGTTAGAAATAAAAAATGGAAACCTTAGA
2 sequences could not be aligned to this particular reference sequence:
Unaligned ( gi|19 ): TTTTAAATATTCATTTTTGTTAGCATGAATATAAT
Unaligned ( gi|21 ): GCAGAGGGGTAAATGTCCATATATCACATAA






Alignments
lowQualScore                  :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           11111111111111111111                                                                                                     11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111                                                 
lowQualScore                  :     11                                                                   777777                           666666                                                                       99999999999999999999999999999999999999999999999999999999999999999999999                     33333333333      111111    11     22222222       1111                                 3333333333                     2222   333333333                                                            22                                                                                          1                                                                                                                                                 1                                                                                                                                  11    11                                                                                                     1                                                                111111                          333333                                             444                                                                                              33333333333333333333                                111                                                                                            66666666666666666666                                                                                                     33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333                                                 
lowQualScore                  :     88  1                                                         22     111111      1                  6 777777                      3                                                99999999999999999999999999999999999999999999999999999999999999999999999               8  0  88888888888      888888    11     99999999       7777               1 8               5555555555                     1111   333333333                                                            11                                                               1                1   1     3         1 7               1                               0              0                0  6          1   2                2                  0                           2                    2                2                                                                33    33                            0                                                    4                   0    3          3                                           3    777777           7  1     1     444444                              6              666           0                               4                          555     4               33333333333333333333       8888 1  1              0 444                                                                                        0   22222222222222222222            1            8               0             0                                             11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111    7   1   7     1           1 0     0     0    
lowQualScore                  :     ..  .                                                         ..     ......      .                  . ......                      .                                                .......................................................................               .  .  ...........      ......    ..     ........       ....               . .               ..........                     ....   .........                                                            ..                                                               .                .   .     .         . .               .                               .              .                .  .          .   .                .                  .                           .                    .                .                                                                ..    ..                            .                                                    .                   .    .          .                                           .    ......           .  .     .     ......                              .              ...           .                               .                          ...     .               ....................       .... .  .              . ...                                                                                        .   ....................            .            .               .             .                                             .......................................................................................................................    .   .   .     .           . .     .     .    
lowQualScore                  :     00  0                                                         00     777777      0                  0 000000                      7                                                33333333333333333333333333333333333333333333333333333333333333333333333               0  8  22222222222      000000    00     00000000       0000               2 0               0000000000                     2222   555555555                                                            00                                                               0                0   0     3         0 3               0                               7              7                7  7          0   0                0                  0                           5                    5                5                                                                88    88                            2                                                    0                   8    2          2                                           2    777777           3  0     0     333333                              0              000           7                               3                          444     0               11111111111111111111       0000 5  6              2 000                                                                                        8   22222222222222222222            4            0               8             8                                             33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333    3   0   3     0           0 7     7     7    
consensus                     : ACTACTAAAATATAATAATAAATAATTAAAACTAACTGTAATAAATAACTGAATAAATAATTAAAACTATAAT------GAACAAATAACTGAATAAATAATTAAA------TATAGACTCTATAAATAACTTANATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTTAT-----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTACTGTAATAAA-TTAAA-A---------AAATAA---T--TAAA--ACTAA--------CTGTAAT----AAATAACTGAATAAANA-ATTAAAAATAAATAA----------ATAAGCATGAACACTACTGAA----TAA----T----TAGACTCTGTATTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAATGAATTCCCTACGTTACACAAGACACAAAGTGATTTTGCGCACGACTTTTCTATTTTTAGATATAGCATTTCACAACCATTGCATCAGTCAAACCC-ACGCTAAGAGATTAGTGTCAAGCCTAGNATGTGTCTCCTTACTGTCTGCTCTTGTATTGACACGATACATAATCTCTAAGCGGATTAGGCAACACATGCCGGATACACCACAATGGCCTATTGATATGTCAGAGTTAATACCTTT-ACGTGACCCCAGTATGTCTAGCGTCTANCGGATATGAACACAATAGCCCATTCATCAGCCAAAAGNTAATCTCCTTAACGTCGCCAGTATGTCTAGCGTTTGTTTATTTAGGCACGGAAGTGTAACAATG--GTGT--ATTCAAGTGTCAAACTTAACGACTGGACGTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATAGTCATGATTGGACTANATAACTCGAGCAAAGTTAGTTGTATTTGGTATATCTGTGTCCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACTTTATTT-AAAATAAAATGATTTTTGTTGTTGTT---GT-TTTTAGTATCGTAGATGTTGCCTTAACTGTATAACACGAATTTTA-TGGGGAAAATCGGATGTATTGAATTTTTATAGCAGGAGGTAAATATTTAATTTTAGAGGACCACAGGGAAGA---TTGGACATTGTTCCAACTGTG--------TTT---------AAATAAAGACTTAATTATTATTATTATTACTA---TAATCATTATTATTATTATTAAAGATGAAATATGTTCTTTTTAGTATCGTAAATGTTACCTTAACTGTGTAACACGAATTTTACGGAAAATTAATGGGTT-----ATGGGTTCGATCCTAAAACCGGAAGTTGAAAA-TAATTGTTTCGAAATAGGGCAAGTTATATATTTTTGAAAAGGTATGACCGAGTACATTACGAAAAATATGGTTCC-CGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAAACTAAAATATTTTTCGATTTATGTCAGAAATAAAAAATGAAAACCTTAGA
Reference ( family-761 )      : ACTACTAANATATAATAATAAATAATTAAAACTAACTGTAATAAATAACTGAATAAATAATTAAAANNATAATAAGCATGAACAANTAACTGAATAAATAATTAGAC-T---TATAGACTCTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTTAT-----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTACTGTAATAAA-TTAAA-A---------AAATAA---T--TAAA--ACTAA--------CTGTAAT----AAATAACTGAATAAATA-ATTAAAAATAAATAA----------ATAAGCATGAACACTACTGAA----TAA----T----TAGACTCTGTATTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTACACAAGACACAAAGTGATTTTGCGCACGACTTTTCTATTTTTAGATATAGCATNTCACAACCATTGCATCNGTCNAACCC-ACGCTAAGANATTAGTGTCAAGCCTAGNATGTGTCTCCTTACTGTCTGCTCTTGTATTGGCACGATACATAATCCCTAAGCGGATTAGGCAGCACATGCCGGATANACCGCAATGGCCTATTGATACGTCAGAGTTAATACCTTT-ACGTGACCCCAGTATGTCTAGCGTCTACCGGATATGAACACAATAGCCCATTCATCAGCCAAAAGGTAATCTCCTTAACGTCGCCAGTATGTCTAGCGTTTGTTTATTTAGGCACGGAAGTGTAACAATG--GTGT--ATTCAAGTGTCAAACTTAACGACTGGACGTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATAGTCATGATTGGACTAAATAACTCGAGCAAAGTTAGNTGTATTTGGTATATCTGTGTCCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACTTTANTTAAAAATAAAATGATTNTTGTTNTTGTT---GT-TTTTAGTATCGTAGATGTTGCCTTAACTGTGTAACACGAATTTTA-C-GGGAAAATCGGGTGTATTGAATTTTTATAGCAGGAGGTAAATACTTAATTTTAGAGGACCACAGGGAAGA---TTGGANATTGTTCCAACTGTG--------TTT---------AAATAAAGACTTAATTATTATTATTATTACTA---TAATCATTATTATTATTATTAAAGATGAAATATGTTCTTTTTAGTATCGTAAATGTTGCCTTAACTGTGTAACACGAATTTTACGGAAAATTAATGGGTTGAATTATGGGTTCGATCCTAAAACCGGAAGTTGAAAA-TAATTGTTTCGAAGTAGGGCAAGTTATATATTTTTGAAAAGGTATGACCGAGTACATTACGAAAAATATGGTTCC-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAAAATANTTTTCGATTNATGTCAGAAATNAGAAATGGAAACCCTAGA
gi|1                          : ACTA--AAAATATAATAATAAATAATTAAAACTAACTGTAATAAATAACTGAATAAATAATTAAAAAAATAATAATTATGGACAAATAACTGAATAAATAATTAAACGTAAATATAGACTCTATAAATAACTTATATGTTTCTTCTCCAACAGCCAACACTCAAATGAACGCCCTACATTTAT-----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAACTACTGTAATAAA-TTAAA-A---------AAAAAAAAAT--TAAA--CTTAA--------CTGTGAT----AAATAACTGAGTAAACA-ATTAAAAATAAATAA----------ATAAGCATGAACACTACTGAA----TAA----T----TAGACTCTGTATTATAAATAACTTACATGTTTCTTCTCCAACTGCCAACACTCAAATAAATTCCCTACGTTACACAAGACACAAAGTGGTTTTGCGCACGATTTTTCTATTTTTAGATATAGCATTTCACAACCATTGCATCAGTCAAACCCCACGCTAAGAGA-------CAAGCCTAGTATGTGTCTTCATACTGTCTGCCATTTTATTGACACGATACATAATCTCTAAGCGGATTAGGCAACACATGCTGGATACACCACAATGGCCTATTGATATGTCAGAGTTAAAACCTTT-ACGTGACCCCAGTATGTGTAGCGTCTGACGGATATGAACACAATAGCCCATTCATCAGCCCAAAGTTAATCTCCATAATGTCGCCAGTATGTCTAGCGTTTGTTTATTTAGACACGGAAGTTAAACAATG--GTGT--ATTCAAGTGTCAAACTTAGCGACTGGACATCTTAACAATAGATTAATGGGTCCTTTGTTGTAAATAGTCATGATTGGACTATATAACTCAAGCAAAGTTAGTTATATTTGGTATATCTGTGTCCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACTT--------AATAAAATGATTTTTGTTGTTGTT----T-TTTTAGTATCGTAGATGTTGCCTTAACTGTATAACACGAATTTTA-TGGGGAAAATCGGATGTATTGCATTTTTATAGCAAGAGGTAAATATTTAATTTTAGAGCAACACAGGGAAGA---TTGGAGATAGTTCCAGCTGTG--------TTT---------AAATAAAGTCTTAATTATTATTATTATTACTG---TTGTCATTATTATTGTTATTAAAGATGAAATATGTTCTTTTTAGTATCATAAATGTTACCTTATCTGTGTAACATGAATTTTACGGAA--------------------------ATCCTAAAACTGGAAGTTGAAAA-TAATGGTTTCGAAATAGGGCAAGTTATATATTTTTGAAAAGGTATGACTGAGTACATTACTAAAAATATGGTTCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTGCAATATTTTTCAATTTATGTCAGAAATAAAAAATGAAAACCTTAGA
gi|10                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              AGAGGACCACAGGGAAGA---TTGGAGATTGTTCCAAATGTGTTTGCTCCTTT---------AAATAAA----TAAT--TTATTATTGTTATAA---TAA
gi|11                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  GACCCCAGGAAAGA---TTGGACATTGTTCCAAAGGTG--------TTTTTCCTCTTTAAATAAAGA------TATTATTATT
gi|12                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     CACAGGGGAGA---CTAGACATTGTTCCAACTCTGTTTCCTA-TTT---------AAATAAAAAC---ATTATTATT
gi|13                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             AGA---TTGGACATTGTTCCATGTGTG--------TTTCCTCTTT--GAATAAAGACTTTATTATTATTATT
gi|14                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                AAGACCACAGAGAAGAGTGTTGGACACTGTTCTAACTGTG--------TTT---------
gi|15                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            tTAAAGGACCTCAGGGAAGA---TTGGACAATGTTCTAACTGTG--------TTT---------tctctttcaa
gi|16                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            aTAAAGGACCACAGGGAAGA---TTGGACAATGTTCTAACTGTG--------TTT---------cctcttt
gi|17                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  tcaCACAGGGAAGA---TTGGAAATTGTTCCAACTGTG--------Tcct
gi|18                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           GAAGA---TTGGAGACTGTTCCAACTGTG--------TTT---------atcctct
gi|2                          :                                                                                                                                                                                                                                                                ACTACTGTAAAAAAATTAAA-T---------AAATAA---TAATAAATAATTAAAAGTATTTTTGTAATTCATAAATAACTGAATAAATA-ATTAAAAATAAATAA----------ATAAGCATGACCACTACTGAA----TAAATAAT----TAGACTTTGTATTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAAGGAATTCCATACGTTACACAAGACACAAAGTGATTTTACGCACGACTTTTCTATTTTTAGATATAGCATATCACAACCATTGCATCAGTTTAATCC-ACGCTAAGAGATTAGTGTCAAGTCTAGCATGTGTCTCCTTACTGTCTGCTCTTGTATTGACACGATACATAATCTCTAAGCGGATTAGGCAGCA---ACCGGATACACCGCAATTGCCTATTGATATGTCAGAGTTAATACCTTT-ATGTGACCGCAGTATGTCTAGGGTATACCGGATAGGAACACAATAGCC------------AAAAGGTAATCTCTTTAACGTCACCAGTATGTCTAGCGTTTGTTTATTTAGGCACGGAAGTGTATCAATG--ATGT--ATTAAAGTCTCAAACTTAACGACTGGACGTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATTGTCATGATTGGACTATTTAACTCGAGCAAAGTTAG--GTA-TTGGTATAAC--TGTCCACGGTGTGAATATTGGAGTTTTATAGCAAGAGGTAAA----TTATTTTAAAATAAAATG-TTGTTGTTTTTTTTGTAGT-TTTTAGTATCGTAGATGTTGCCTTAATTGTATAACACGAATTTTATT-GGGAAAATTGGATGTATTGAATTTTTATGGCAGGAGGTAAATATTTAATTTTAGAGGACCACAGGGAATA---TTGGA----GTTCCAGCTGTGTTTTTTC-TTT---------AAACAAGAACTTAATTATTATAATTATTACTA---TAATCATTATTGTTATTATTAATGATGAAATATGTTCTTTTTAGTATCATAAATGTTGCCTTAACTGTGTAACACGAATTTTACGGAAAATTA------------ATGGGTTCGATCCTAAAACCGGAAGTTGAAAA-TAATTGTTTCGAAGTAGGGCAAGTTATAT-TTTTTGAAAAGGTATGACCGATTACATTACGAAAAATATGGTTcctctttaaa
gi|20                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     CACAGGGAAGA---TTGGACATTGTTCCAACTATG--------T
gi|3                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ATAGCCCATTCATCAGCCAAAAGTTAATCTCCTTAACGTCGCAAATATGTCTAGCGTTTGTTTATTTAGGCACGGGATAGTAACAATG--GTGTGTATTCAAGTGTCAAACTTAACGACTGAACTTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATAGTCATGATTGGACTAAATAACTCGAGCAAAGTTAGATGTATTTGGTATATCTGTGTTCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACTTTATTTAAAAATAAAATGATTTTTGTTGTGGTT---GTATTTTAGTATCGTAGATGTTGCCTTAACTGTATAACAAGAATTTTA-TGGGGGAAATCGGGTGTATTGAATTTTTATAGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN---NNNNNNNNNNNNNNNNNNNNN--------NNN---------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTAATCATAATAATTACTATTAAAGATGAAATCTGTTCTTTTTAGTATCGTAAATGTTACCTTAACTGTGTAACAAGAATTTTACGGAAAATTAATGGGTTA------------GATCCTAAAACTGGAAGTTGAAAA-TAATTGTTTCGAAGTAGGGCAAGTTATATATTTTTGAAAAGGTATAACTGAGTACATTACGAAAAATATCGTTTC-CGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAAAATAA----TTTT-CGATTGATGTTAGAAATAAAAAATGGAAACCTTAGA
gi|4                          :                                                                                                                                                                                                                                                                  TACTGTAATAAA-TTANN-N---------NNNNNN---N--NNNN--NNNNN--------NNNNNNN----NNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNNNNNATAAGCATGAACACTACTGAA----TAA----TTAATTAGACTCTGTATTATAAATAACTTACATGTTTTTTCTCCAACGGCCAACACTCAAATGAATTCCCTACGTTACACAAGACACAAAGTAATTTTGCGCACGACTTTTCTATTTTTAGATATAGCATTTCACAACCATTGCATCTGTCAAACCC-ACGCTAAGATATTAGTGTCAAACCTAGAATGTGTCTCCTTACTGTCTGCTCTTGTATTGGCACGATACATAATCCCTAAGCGGATTAGGCAACACATGCCGGATAGACCACAATGGCCTATTGATATGTCAGAGTTAATACCTTT-ACGTGACCCCAGTATGTCTAGCGTCTAATGGATATGAACACAATAGCCCATTCATCAGCCAAAAGGTAATCTCCTTAACGTCGCCAGTATGTCTAGCGTTTGTTTATTTAGGCACGGAAGTGTAATAATGGTGTGT--ATTCAAGTGTCAAACTTAACGACTGGACGTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATAGTCATGATTGGACTAAATAACTCGAGCAAAGTTAGTTGTATTTGGTATATCTGTGTCCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACT
gi|5                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  TCATTATTATTATTATTAAAGATGAAATATGTTCTTTTTAGTATCGTAAATGTTGCCTTAACTGTGTAACACGAATTTTACGGAAAATTAATGGGTT------------CGATCCTAAAACCGGAAGTTAAAAAATAATTGTTTCGAAATAGGGCAAGTTATATATTTTTGAAAAAGTATGACCGAGTACATTACGAAAAATATGGTTCC-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAAAATATTTTTCGATTTATGTCAGAAATTAGAAATGAAAACTCTA
gi|6                          : ACTACTAAAATATAATAATAAATAATTAAAACTAACTGTAATAAATAACTGAATAAATAATTAAAACTTTAAT------GAACAAGTTACTGAATAAATAATTAAA------TATAGACTCTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTACTGTAATAAA-TTAAATAATAACTAATAAATGA---T--TAAA--ACTAA--------TTGTAAT----AAATAACTGAATAAATA-AATAAAACAAAGTAA----------ATGAAC
gi|7                          :                                       tAATAAAAAACTGAATCAATAATTAAAACTATAAT------GAACATATAACTGAATAAATAATTAAA------TATAAACTCTATAAATAACTTAAATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTTAT-----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTACTGTAATAAA-TT-AA-A---------ACATAA---T--TAAA--ACTAA--------CTGTAAT----AAATAACAGAAAAAAAATATTAAAAATAAATAA----------ATAAGCATGAACACTAATGAATAATTAA----T----TAGACTCTGTATTtataa
gi|8                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          aataaattaaaCTTAATANNNNNNNNNNNNNNNN---NNNNNNNNNNNNNNNNNNNNNAAGATGAAATATGTTTTTCTTAGTATCGTAAATGTTACCTTAACTGTGTAACACGAATTTTACGGAAAATT------------TATGGGTTCGATCCTAAAA------GTTAAAAA-TAATTGTTTCGAAAT--GGCAAGTTATATATTTTTGAAAAGGTATGACTGAGTACATTACGACAAATATGGT
gi|9                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            ACCACAAGGGCCTATTGAAACGCCATAGTTAATACTTTTTACGTGATCCCCGTATGGCTAGCGTCTACCGGACATGAACACAATA
2 sequences could not be aligned to this reference sequence:
Unaligned ( gi|19 ): TTTTAAATATTCATTTTTGTTAGCATGAATATAAT
Unaligned ( gi|21 ): GCAGAGGGGTAAATGTCCATATATCACATAA






Alignments
lowQualScore                  :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111                                                      
lowQualScore                  :     11                                                                   333333                           333333                                                                       99999999999999999999999999999999999999999999999999999999999999999999999                     33333333333      111111    11     22222222       1111                                 3333333333                     2222   333333333                                                                                                                                                        1                                                                                                                                                 1                                                                                                                                  11    11                                                                                                                                                                      3333333                          333333                                                                                                                                             33333333333333333333                                111                                                                                           8888888888888888                                                                                                     111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111                                                      
lowQualScore                  :     88                                                                   888888                           888888                      1                                                99999999999999999999999999999999999999999999999999999999999999999999999               8  0  88888888888      888888    11     99999999       7777               1 8               5555555555                     1111   333333333                                                                                                                                                        3           7               1                                                                  6                                                  0                           1                    2                1                                                                33    33                            0                                                    1                   9    3          3                                           3    0000000           7              444444                                                                                                                     555     2               33333333333333333333       8888 1  1              0 444                                                                                        0  0000000000000000         0  1            8               0             0                                             111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111         7                                            
lowQualScore                  :     ..                                                                   ......                           ......                      .                                                .......................................................................               .  .  ...........      ......    ..     ........       ....               . .               ..........                     ....   .........                                                                                                                                                        .           .               .                                                                  .                                                  .                           .                    .                .                                                                ..    ..                            .                                                    .                   .    .          .                                           .    .......           .              ......                                                                                                                     ...     .               ....................       .... .  .              . ...                                                                                        .  ................         .  .            .               .             .                                             ..................................................................................................................         .                                            
lowQualScore                  :     00                                                                   333333                           333333                      0                                                33333333333333333333333333333333333333333333333333333333333333333333333               0  8  22222222222      000000    00     00000000       0000               0 0               0000000000                     2222   555555555                                                                                                                                                        3           3               0                                                                  7                                                  0                           0                    5                0                                                                88    88                            2                                                    0                   8    2          2                                           2    0000000           3              333333                                                                                                                     444     4               11111111111111111111       0000 5  6              2 000                                                                                        8  0000000000000000         8  4            0               8             8                                             777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777         3                                            
consensus                     : ACTACTAAAATATAATAATAAATAATTAAAACTAACTGTAATAAATAACTGAATAAATAATTAAAACTATAAT------GAACAAATAACTGAATAAATAATTAAA------TATAGACTCTATAAATAACTTANATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTTAT-----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTACTGTAATAAA-TTAAA-A---------AAATAA---T--TAAA--ACTAA--------CTGTAAT----AAATAACTGAATAAANA-ATTAAAAATAAATAA----------ATAAGCATGAACACTACTGAA----TAA----T----TAGACTCTGTATTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAATGAATTCCCTACGTTACACAAGACACAAAGTGATTTTGCGCACGACTTTTCTATTTTTAGATATAGCATTTCACAACCATTGCATCAGTCAAACCC-ACGCTAAGAGATTAGTGTCAAGCCTAGNATGTGTCTCCTTACTGTCTGCTCTTGTATTGACACGATACATAATCTCTAAGCGGATTAGGCAACACATGCCGGATACACCACAATGGCCTATTGATATGTCAGAGTTAATACCTTT-ACGTGACCCCAGTATGTCTAGCGTCTANCGGATATGAACACAATAGCCCATTCATCAGCCAAAAGNTAATCTCCTTAACGTCGCCAGTATGTCTAGCGTTTGTTTATTTAGGCACGGAAGTGTAACAATG--GTGT--ATTCAAGTGTCAAACTTAACGACTGGACGTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATAGTCATGATTGGACTANATAACTCGAGCAAAGTTAGTTGTATTTGGTATATCTGTGTCCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACTTTA-TTT-AAAATAAAATGATTTTTGTTGTTGTT---GT-TTTTAGTATCGTAGATGTTGCCTTAACTGTATAACACGAATTTTATGGGGAAAATCGGATGTATTGAATTTTTATAGCAGGAGGTAAATATTTAATTTTAGAGGACCACAGGGAAGA---TTGGACATTGTTCCAACTGTG--------TTT---------AAATAAAGACTTAATTATTATTATTATTACTA---TAATCATTATTATTATTATTAAAGATGAAATATGTTCTTTTTAGTATCGTAAATGTTACCTTAACTGTGTAACACGAATTTTACGGAAAATTAATGGGTTATGGGTTCGATCCTAAAACCGGAAGTTGAAAA-TAATTGTTTCGAAATAGGGCAAGTTATATATTTTTGAAAAGGTATGACCGAGTACATTACGAAAAATATGGTTCC-CGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAAACTAAAATATTTTTCGATTTATGTCAGAAATAAAAAATGAAAACCTTAGA
Reference ( family-761 )      : ACTACTAAAATATAATAATAAATAATTAAAACTAACTGTAATAAATAACTGAATAAATAATTAAAACTATAAT------GAACAAATAACTGAATAAATAATTAAA------TATAGACTCTATAAATAACTTANATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTTAT-----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTACTGTAATAAA-TTAAA-A---------AAATAA---T--TAAA--ACTAA--------CTGTAAT----AAATAACTGAATAAANA-ATTAAAAATAAATAA----------ATAAGCATGAACACTACTGAA----TAA----T----TAGACTCTGTATTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAATGAATTCCCTACGTTACACAAGACACAAAGTGATTTTGCGCACGACTTTTCTATTTTTAGATATAGCATTTCACAACCATTGCATCAGTCAAACCC-ACGCTAAGAGATTAGTGTCAAGCCTAGNATGTGTCTCCTTACTGTCTGCTCTTGTATTGACACGATACATAATCTCTAAGCGGATTAGGCAACACATGCCGGATACACCACAATGGCCTATTGATATGTCAGAGTTAATACCTTT-ACGTGACCCCAGTATGTCTAGCGTCTANCGGATATGAACACAATAGCCCATTCATCAGCCAAAAGNTAATCTCCTTAACGTCGCCAGTATGTCTAGCGTTTGTTTATTTAGGCACGGAAGTGTAACAATG--GTGT--ATTCAAGTGTCAAACTTAACGACTGGACGTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATAGTCATGATTGGACTANATAACTCGAGCAAAGTTAGTTGTATTTGGTATATCTGTGTCCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACTTTA-TTT-AAAATAAAATGATTTTTGTTGTTGTT---GT-TTTTAGTATCGTAGATGTTGCCTTAACTGTATAACACGAATTTTATGGGGAAAATCGGATGTATTGAATTTTTATAGCAGGAGGTAAATATTTAATTTTAGAGGACCACAGGGAAGA---TTGGACATTGTTCCAACTGTG--------TTT---------AAATAAAGACTTAATTATTATTATTATTACTA---TAATCATTATTATTATTATTAAAGATGAAATATGTTCTTTTTAGTATCGTAAATGTTACCTTAACTGTGTAACACGAATTTTACGGAAAATTAATGGGTTATGGGTTCGATCCTAAAACCGGAAGTTGAAAA-TAATTGTTTCGAAATAGGGCAAGTTATATATTTTTGAAAAGGTATGACCGAGTACATTACGAAAAATATGGTTCC-CGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAAACTAAAATATTTTTCGATTTATGTCAGAAATAAAAAATGAAAACCTTAGA
gi|1                          : ACTA--AAAATATAATAATAAATAATTAAAACTAACTGTAATAAATAACTGAATAAATAATTAAAAAAATAATAATTATGGACAAATAACTGAATAAATAATTAAACGTAAATATAGACTCTATAAATAACTTATATGTTTCTTCTCCAACAGCCAACACTCAAATGAACGCCCTACATTTAT-----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAACTACTGTAATAAA-TTAAA-A---------AAAAAAAAAT--TAAA--CTTAA--------CTGTGAT----AAATAACTGAGTAAACA-ATTAAAAATAAATAA----------ATAAGCATGAACACTACTGAA----TAA----T----TAGACTCTGTATTATAAATAACTTACATGTTTCTTCTCCAACTGCCAACACTCAAATAAATTCCCTACGTTACACAAGACACAAAGTGGTTTTGCGCACGATTTTTCTATTTTTAGATATAGCATTTCACAACCATTGCATCAGTCAAACCCCACGCTAAGAGA-------CAAGCCTAGTATGTGTCTTCATACTGTCTGCCATTTTATTGACACGATACATAATCTCTAAGCGGATTAGGCAACACATGCTGGATACACCACAATGGCCTATTGATATGTCAGAGTTAAAACCTTT-ACGTGACCCCAGTATGTGTAGCGTCTGACGGATATGAACACAATAGCCCATTCATCAGCCCAAAGTTAATCTCCATAATGTCGCCAGTATGTCTAGCGTTTGTTTATTTAGACACGGAAGTTAAACAATG--GTGT--ATTCAAGTGTCAAACTTAGCGACTGGACATCTTAACAATAGATTAATGGGTCCTTTGTTGTAAATAGTCATGATTGGACTATATAACTCAAGCAAAGTTAGTTATATTTGGTATATCTGTGTCCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACTT---------AATAAAATGATTTTTGTTGTTGTT----T-TTTTAGTATCGTAGATGTTGCCTTAACTGTATAACACGAATTTTATGGGGAAAATCGGATGTATTGCATTTTTATAGCAAGAGGTAAATATTTAATTTTAGAGCAACACAGGGAAGA---TTGGAGATAGTTCCAGCTGTG--------TTT---------AAATAAAGTCTTAATTATTATTATTATTACTG---TTGTCATTATTATTGTTATTAAAGATGAAATATGTTCTTTTTAGTATCATAAATGTTACCTTATCTGTGTAACATGAATTTTACGGAA---------------------ATCCTAAAACTGGAAGTTGAAAA-TAATGGTTTCGAAATAGGGCAAGTTATATATTTTTGAAAAGGTATGACTGAGTACATTACTAAAAATATGGTTCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTGCAATATTTTTCAATTTATGTCAGAAATAAAAAATGAAAACCTTAGA
gi|10                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              AGAGGACCACAGGGAAGA---TTGGAGATTGTTCCAAATGTGTTTGCTCCTTT---------AAATAAA----TAAT--TTATTATTGTTATAA---TAA
gi|11                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  GACCCCAGGAAAGA---TTGGACATTGTTCCAAAGGTG--------TTTTTCCTCTTTAAATAAAGA------TATTATTATT
gi|12                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     CACAGGGGAGA---CTAGACATTGTTCCAACTCTGTTTCCTA-TTT---------AAATAAAAAC---ATTATTATT
gi|13                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             AGA---TTGGACATTGTTCCATGTGTG--------TTTCCTCTTT--GAATAAAGACTTTATTATTATTATT
gi|14                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                AAGACCACAGAGAAGAGTGTTGGACACTGTTCTAACTGTG--------TTT---------
gi|15                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            tTAAAGGACCTCAGGGAAGA---TTGGACAATGTTCTAACTGTG--------TTT---------tctctttcaa
gi|16                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            aTAAAGGACCACAGGGAAGA---TTGGACAATGTTCTAACTGTG--------TTT---------cctcttt
gi|17                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  tcaCACAGGGAAGA---TTGGAAATTGTTCCAACTGTG--------Tcct
gi|18                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           GAAGA---TTGGAGACTGTTCCAACTGTG--------TTT---------atcctct
gi|2                          :                                                                                                                                                                                                                                                                ACTACTGTAAAAAAATTAAA-T---------AAATAA---TAATAAATAATTAAAAGTATTTTTGTAATTCATAAATAACTGAATAAATA-ATTAAAAATAAATAA----------ATAAGCATGACCACTACTGAA----TAAATAAT----TAGACTTTGTATTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAAGGAATTCCATACGTTACACAAGACACAAAGTGATTTTACGCACGACTTTTCTATTTTTAGATATAGCATATCACAACCATTGCATCAGTTTAATCC-ACGCTAAGAGATTAGTGTCAAGTCTAGCATGTGTCTCCTTACTGTCTGCTCTTGTATTGACACGATACATAATCTCTAAGCGGATTAGGCAGCA---ACCGGATACACCGCAATTGCCTATTGATATGTCAGAGTTAATACCTTT-ATGTGACCGCAGTATGTCTAGGGTATACCGGATAGGAACACAATAGCC------------AAAAGGTAATCTCTTTAACGTCACCAGTATGTCTAGCGTTTGTTTATTTAGGCACGGAAGTGTATCAATG--ATGT--ATTAAAGTCTCAAACTTAACGACTGGACGTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATTGTCATGATTGGACTATTTAACTCGAGCAAAGTTAG--GTA-TTGGTATAAC--TGTCCACGGTGTGAATATTGGAGTTTTATAGCAAGAGGTAAA----TTATTTT-AAAATAAAATG-TTGTTGTTTTTTTTGTAGT-TTTTAGTATCGTAGATGTTGCCTTAATTGTATAACACGAATTTTATTGGGAAAATTGGATGTATTGAATTTTTATGGCAGGAGGTAAATATTTAATTTTAGAGGACCACAGGGAATA---TTGGA----GTTCCAGCTGTGTTTTTTC-TTT---------AAACAAGAACTTAATTATTATAATTATTACTA---TAATCATTATTGTTATTATTAATGATGAAATATGTTCTTTTTAGTATCATAAATGTTGCCTTAACTGTGTAACACGAATTTTACGGAAAATTA-------ATGGGTTCGATCCTAAAACCGGAAGTTGAAAA-TAATTGTTTCGAAGTAGGGCAAGTTATAT-TTTTTGAAAAGGTATGACCGATTACATTACGAAAAATATGGTTcctctttaaa
gi|20                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     CACAGGGAAGA---TTGGACATTGTTCCAACTATG--------T
gi|3                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ATAGCCCATTCATCAGCCAAAAGTTAATCTCCTTAACGTCGCAAATATGTCTAGCGTTTGTTTATTTAGGCACGGGATAGTAACAATG--GTGTGTATTCAAGTGTCAAACTTAACGACTGAACTTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATAGTCATGATTGGACTAAATAACTCGAGCAAAGTTAGATGTATTTGGTATATCTGTGTTCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACTTTA-TTTAAAAATAAAATGATTTTTGTTGTGGTT---GTATTTTAGTATCGTAGATGTTGCCTTAACTGTATAACAAGAATTTTATGGGGGAAATCGGGTGTATTGAATTTTTATAGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN---NNNNNNNNNNNNNNNNNNNNN--------NNN---------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTAATCATAATAATTACTATTAAAGATGAAATCTGTTCTTTTTAGTATCGTAAATGTTACCTTAACTGTGTAACAAGAATTTTACGGAAAATTAATGGGTTA-------GATCCTAAAACTGGAAGTTGAAAA-TAATTGTTTCGAAGTAGGGCAAGTTATATATTTTTGAAAAGGTATAACTGAGTACATTACGAAAAATATCGTTTC-CGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAAAATAA-----TTTTCGATTGATGTTAGAAATAAAAAATGGAAACCTTAGA
gi|4                          :                                                                                                                                                                                                                                                                  TACTGTAATAAA-TTANN-N---------NNNNNN---N--NNNN--NNNNN--------NNNNNNN----NNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNNNNNATAAGCATGAACACTACTGAA----TAA----TTAATTAGACTCTGTATTATAAATAACTTACATGTTTTTTCTCCAACGGCCAACACTCAAATGAATTCCCTACGTTACACAAGACACAAAGTAATTTTGCGCACGACTTTTCTATTTTTAGATATAGCATTTCACAACCATTGCATCTGTCAAACCC-ACGCTAAGATATTAGTGTCAAACCTAGAATGTGTCTCCTTACTGTCTGCTCTTGTATTGGCACGATACATAATCCCTAAGCGGATTAGGCAACACATGCCGGATAGACCACAATGGCCTATTGATATGTCAGAGTTAATACCTTT-ACGTGACCCCAGTATGTCTAGCGTCTAATGGATATGAACACAATAGCCCATTCATCAGCCAAAAGGTAATCTCCTTAACGTCGCCAGTATGTCTAGCGTTTGTTTATTTAGGCACGGAAGTGTAATAATGGTGTGT--ATTCAAGTGTCAAACTTAACGACTGGACGTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATAGTCATGATTGGACTAAATAACTCGAGCAAAGTTAGTTGTATTTGGTATATCTGTGTCCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACT
gi|5                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  TCATTATTATTATTATTAAAGATGAAATATGTTCTTTTTAGTATCGTAAATGTTGCCTTAACTGTGTAACACGAATTTTACGGAAAATTAATGGGTT-------CGATCCTAAAACCGGAAGTTAAAAAATAATTGTTTCGAAATAGGGCAAGTTATATATTTTTGAAAAAGTATGACCGAGTACATTACGAAAAATATGGTTCC-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAAAATATTTTTCGATTTATGTCAGAAATTAGAAATGAAAACTCTA
gi|6                          : ACTACTAAAATATAATAATAAATAATTAAAACTAACTGTAATAAATAACTGAATAAATAATTAAAACTTTAAT------GAACAAGTTACTGAATAAATAATTAAA------TATAGACTCTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTACTGTAATAAA-TTAAATAATAACTAATAAATGA---T--TAAA--ACTAA--------TTGTAAT----AAATAACTGAATAAATA-AATAAAACAAAGTAA----------ATGAAC
gi|7                          :                                       tAATAAAAAACTGAATCAATAATTAAAACTATAAT------GAACATATAACTGAATAAATAATTAAA------TATAAACTCTATAAATAACTTAAATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTTAT-----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTACTGTAATAAA-TT-AA-A---------ACATAA---T--TAAA--ACTAA--------CTGTAAT----AAATAACAGAAAAAAAATATTAAAAATAAATAA----------ATAAGCATGAACACTAATGAATAATTAA----T----TAGACTCTGTATTtataa
gi|8                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          aataaattaaaCTTAATANNNNNNNNNNNNNNNN---NNNNNNNNNNNNNNNNNNNNNAAGATGAAATATGTTTTTCTTAGTATCGTAAATGTTACCTTAACTGTGTAACACGAATTTTACGGAAAAT-------TTATGGGTTCGATCCTAA------AAGTTAAAAA-TAATTGTTTCGAAAT--GGCAAGTTATATATTTTTGAAAAGGTATGACTGAGTACATTACGACAAATATGGT
gi|9                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            ACCACAAGGGCCTATTGAAACGCCATAGTTAATACTTTTTACGTGATCCCCGTATGGCTAGCGTCTACCGGACATGAACACAATA
2 sequences could not be aligned to this reference sequence:
Unaligned ( gi|19 ): TTTTAAATATTCATTTTTGTTAGCATGAATATAAT
Unaligned ( gi|21 ): GCAGAGGGGTAAATGTCCATATATCACATAA






Alignments
lowQualScore                  :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111                                                      
lowQualScore                  :     11                                                                   333333                           333333                                                                       99999999999999999999999999999999999999999999999999999999999999999999999                     33333333333      111111    11     22222222       1111                                 3333333333                     2222   333333333                                                                                                                                                        1                                                                                                                                                 1                                                                                                                                  11    11                                                                                                                                                                      3333333                          333333                                                                                                                                             33333333333333333333                                111                                                                                           8888888888888888                                                                                                     111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111                                                      
lowQualScore                  :     88                                                                   888888                           888888                      1                                                99999999999999999999999999999999999999999999999999999999999999999999999               8  0  88888888888      888888    11     99999999       7777               1 8               5555555555                     1111   333333333                                                                                                                                                        3           7               1                                                                  6                                                  0                           1                    2                1                                                                33    33                            0                                                    1                   9    3          3                                           3    0000000           7              444444                                                                                                                     555     2               33333333333333333333       8888 1  1              0 444                                                                                        0  0000000000000000         0  1            8               0             0                                             111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111         7                                            
lowQualScore                  :     ..                                                                   ......                           ......                      .                                                .......................................................................               .  .  ...........      ......    ..     ........       ....               . .               ..........                     ....   .........                                                                                                                                                        .           .               .                                                                  .                                                  .                           .                    .                .                                                                ..    ..                            .                                                    .                   .    .          .                                           .    .......           .              ......                                                                                                                     ...     .               ....................       .... .  .              . ...                                                                                        .  ................         .  .            .               .             .                                             ..................................................................................................................         .                                            
lowQualScore                  :     00                                                                   333333                           333333                      0                                                33333333333333333333333333333333333333333333333333333333333333333333333               0  8  22222222222      000000    00     00000000       0000               0 0               0000000000                     2222   555555555                                                                                                                                                        3           3               0                                                                  7                                                  0                           0                    5                0                                                                88    88                            2                                                    0                   8    2          2                                           2    0000000           3              333333                                                                                                                     444     4               11111111111111111111       0000 5  6              2 000                                                                                        8  0000000000000000         8  4            0               8             8                                             777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777         3                                            
consensus                     : ACTACTAAAATATAATAATAAATAATTAAAACTAACTGTAATAAATAACTGAATAAATAATTAAAACTATAAT------GAACAAATAACTGAATAAATAATTAAA------TATAGACTCTATAAATAACTTANATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTTAT-----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTACTGTAATAAA-TTAAA-A---------AAATAA---T--TAAA--ACTAA--------CTGTAAT----AAATAACTGAATAAANA-ATTAAAAATAAATAA----------ATAAGCATGAACACTACTGAA----TAA----T----TAGACTCTGTATTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAATGAATTCCCTACGTTACACAAGACACAAAGTGATTTTGCGCACGACTTTTCTATTTTTAGATATAGCATTTCACAACCATTGCATCAGTCAAACCC-ACGCTAAGAGATTAGTGTCAAGCCTAGNATGTGTCTCCTTACTGTCTGCTCTTGTATTGACACGATACATAATCTCTAAGCGGATTAGGCAACACATGCCGGATACACCACAATGGCCTATTGATATGTCAGAGTTAATACCTTT-ACGTGACCCCAGTATGTCTAGCGTCTANCGGATATGAACACAATAGCCCATTCATCAGCCAAAAGNTAATCTCCTTAACGTCGCCAGTATGTCTAGCGTTTGTTTATTTAGGCACGGAAGTGTAACAATG--GTGT--ATTCAAGTGTCAAACTTAACGACTGGACGTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATAGTCATGATTGGACTANATAACTCGAGCAAAGTTAGTTGTATTTGGTATATCTGTGTCCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACTTTA-TTT-AAAATAAAATGATTTTTGTTGTTGTT---GT-TTTTAGTATCGTAGATGTTGCCTTAACTGTATAACACGAATTTTATGGGGAAAATCGGATGTATTGAATTTTTATAGCAGGAGGTAAATATTTAATTTTAGAGGACCACAGGGAAGA---TTGGACATTGTTCCAACTGTG--------TTT---------AAATAAAGACTTAATTATTATTATTATTACTA---TAATCATTATTATTATTATTAAAGATGAAATATGTTCTTTTTAGTATCGTAAATGTTACCTTAACTGTGTAACACGAATTTTACGGAAAATTAATGGGTTATGGGTTCGATCCTAAAACCGGAAGTTGAAAA-TAATTGTTTCGAAATAGGGCAAGTTATATATTTTTGAAAAGGTATGACCGAGTACATTACGAAAAATATGGTTCC-CGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAAACTAAAATATTTTTCGATTTATGTCAGAAATAAAAAATGAAAACCTTAGA
Reference ( family-761 )      : ACTACTAAAATATAATAATAAATAATTAAAACTAACTGTAATAAATAACTGAATAAATAATTAAAACTATAAT------GAACAAATAACTGAATAAATAATTAAA------TATAGACTCTATAAATAACTTANATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTTAT-----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTACTGTAATAAA-TTAAA-A---------AAATAA---T--TAAA--ACTAA--------CTGTAAT----AAATAACTGAATAAANA-ATTAAAAATAAATAA----------ATAAGCATGAACACTACTGAA----TAA----T----TAGACTCTGTATTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAATGAATTCCCTACGTTACACAAGACACAAAGTGATTTTGCGCACGACTTTTCTATTTTTAGATATAGCATTTCACAACCATTGCATCAGTCAAACCC-ACGCTAAGAGATTAGTGTCAAGCCTAGNATGTGTCTCCTTACTGTCTGCTCTTGTATTGACACGATACATAATCTCTAAGCGGATTAGGCAACACATGCCGGATACACCACAATGGCCTATTGATATGTCAGAGTTAATACCTTT-ACGTGACCCCAGTATGTCTAGCGTCTANCGGATATGAACACAATAGCCCATTCATCAGCCAAAAGNTAATCTCCTTAACGTCGCCAGTATGTCTAGCGTTTGTTTATTTAGGCACGGAAGTGTAACAATG--GTGT--ATTCAAGTGTCAAACTTAACGACTGGACGTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATAGTCATGATTGGACTANATAACTCGAGCAAAGTTAGTTGTATTTGGTATATCTGTGTCCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACTTTA-TTT-AAAATAAAATGATTTTTGTTGTTGTT---GT-TTTTAGTATCGTAGATGTTGCCTTAACTGTATAACACGAATTTTATGGGGAAAATCGGATGTATTGAATTTTTATAGCAGGAGGTAAATATTTAATTTTAGAGGACCACAGGGAAGA---TTGGACATTGTTCCAACTGTG--------TTT---------AAATAAAGACTTAATTATTATTATTATTACTA---TAATCATTATTATTATTATTAAAGATGAAATATGTTCTTTTTAGTATCGTAAATGTTACCTTAACTGTGTAACACGAATTTTACGGAAAATTAATGGGTTATGGGTTCGATCCTAAAACCGGAAGTTGAAAA-TAATTGTTTCGAAATAGGGCAAGTTATATATTTTTGAAAAGGTATGACCGAGTACATTACGAAAAATATGGTTCC-CGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAAACTAAAATATTTTTCGATTTATGTCAGAAATAAAAAATGAAAACCTTAGA
gi|1                          : ACTA--AAAATATAATAATAAATAATTAAAACTAACTGTAATAAATAACTGAATAAATAATTAAAAAAATAATAATTATGGACAAATAACTGAATAAATAATTAAACGTAAATATAGACTCTATAAATAACTTATATGTTTCTTCTCCAACAGCCAACACTCAAATGAACGCCCTACATTTAT-----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAACTACTGTAATAAA-TTAAA-A---------AAAAAAAAAT--TAAA--CTTAA--------CTGTGAT----AAATAACTGAGTAAACA-ATTAAAAATAAATAA----------ATAAGCATGAACACTACTGAA----TAA----T----TAGACTCTGTATTATAAATAACTTACATGTTTCTTCTCCAACTGCCAACACTCAAATAAATTCCCTACGTTACACAAGACACAAAGTGGTTTTGCGCACGATTTTTCTATTTTTAGATATAGCATTTCACAACCATTGCATCAGTCAAACCCCACGCTAAGAGA-------CAAGCCTAGTATGTGTCTTCATACTGTCTGCCATTTTATTGACACGATACATAATCTCTAAGCGGATTAGGCAACACATGCTGGATACACCACAATGGCCTATTGATATGTCAGAGTTAAAACCTTT-ACGTGACCCCAGTATGTGTAGCGTCTGACGGATATGAACACAATAGCCCATTCATCAGCCCAAAGTTAATCTCCATAATGTCGCCAGTATGTCTAGCGTTTGTTTATTTAGACACGGAAGTTAAACAATG--GTGT--ATTCAAGTGTCAAACTTAGCGACTGGACATCTTAACAATAGATTAATGGGTCCTTTGTTGTAAATAGTCATGATTGGACTATATAACTCAAGCAAAGTTAGTTATATTTGGTATATCTGTGTCCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACTT---------AATAAAATGATTTTTGTTGTTGTT----T-TTTTAGTATCGTAGATGTTGCCTTAACTGTATAACACGAATTTTATGGGGAAAATCGGATGTATTGCATTTTTATAGCAAGAGGTAAATATTTAATTTTAGAGCAACACAGGGAAGA---TTGGAGATAGTTCCAGCTGTG--------TTT---------AAATAAAGTCTTAATTATTATTATTATTACTG---TTGTCATTATTATTGTTATTAAAGATGAAATATGTTCTTTTTAGTATCATAAATGTTACCTTATCTGTGTAACATGAATTTTACGGAA---------------------ATCCTAAAACTGGAAGTTGAAAA-TAATGGTTTCGAAATAGGGCAAGTTATATATTTTTGAAAAGGTATGACTGAGTACATTACTAAAAATATGGTTCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTGCAATATTTTTCAATTTATGTCAGAAATAAAAAATGAAAACCTTAGA
gi|10                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              AGAGGACCACAGGGAAGA---TTGGAGATTGTTCCAAATGTGTTTGCTCCTTT---------AAATAAA----TAAT--TTATTATTGTTATAA---TAA
gi|11                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  GACCCCAGGAAAGA---TTGGACATTGTTCCAAAGGTG--------TTTTTCCTCTTTAAATAAAGA------TATTATTATT
gi|12                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     CACAGGGGAGA---CTAGACATTGTTCCAACTCTGTTTCCTA-TTT---------AAATAAAAAC---ATTATTATT
gi|13                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             AGA---TTGGACATTGTTCCATGTGTG--------TTTCCTCTTT--GAATAAAGACTTTATTATTATTATT
gi|14                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                AAGACCACAGAGAAGAGTGTTGGACACTGTTCTAACTGTG--------TTT---------
gi|15                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            tTAAAGGACCTCAGGGAAGA---TTGGACAATGTTCTAACTGTG--------TTT---------tctctttcaa
gi|16                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            aTAAAGGACCACAGGGAAGA---TTGGACAATGTTCTAACTGTG--------TTT---------cctcttt
gi|17                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  tcaCACAGGGAAGA---TTGGAAATTGTTCCAACTGTG--------Tcct
gi|18                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           GAAGA---TTGGAGACTGTTCCAACTGTG--------TTT---------atcctct
gi|2                          :                                                                                                                                                                                                                                                                ACTACTGTAAAAAAATTAAA-T---------AAATAA---TAATAAATAATTAAAAGTATTTTTGTAATTCATAAATAACTGAATAAATA-ATTAAAAATAAATAA----------ATAAGCATGACCACTACTGAA----TAAATAAT----TAGACTTTGTATTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAAGGAATTCCATACGTTACACAAGACACAAAGTGATTTTACGCACGACTTTTCTATTTTTAGATATAGCATATCACAACCATTGCATCAGTTTAATCC-ACGCTAAGAGATTAGTGTCAAGTCTAGCATGTGTCTCCTTACTGTCTGCTCTTGTATTGACACGATACATAATCTCTAAGCGGATTAGGCAGCA---ACCGGATACACCGCAATTGCCTATTGATATGTCAGAGTTAATACCTTT-ATGTGACCGCAGTATGTCTAGGGTATACCGGATAGGAACACAATAGCC------------AAAAGGTAATCTCTTTAACGTCACCAGTATGTCTAGCGTTTGTTTATTTAGGCACGGAAGTGTATCAATG--ATGT--ATTAAAGTCTCAAACTTAACGACTGGACGTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATTGTCATGATTGGACTATTTAACTCGAGCAAAGTTAG--GTA-TTGGTATAAC--TGTCCACGGTGTGAATATTGGAGTTTTATAGCAAGAGGTAAA----TTATTTT-AAAATAAAATG-TTGTTGTTTTTTTTGTAGT-TTTTAGTATCGTAGATGTTGCCTTAATTGTATAACACGAATTTTATTGGGAAAATTGGATGTATTGAATTTTTATGGCAGGAGGTAAATATTTAATTTTAGAGGACCACAGGGAATA---TTGGA----GTTCCAGCTGTGTTTTTTC-TTT---------AAACAAGAACTTAATTATTATAATTATTACTA---TAATCATTATTGTTATTATTAATGATGAAATATGTTCTTTTTAGTATCATAAATGTTGCCTTAACTGTGTAACACGAATTTTACGGAAAATTA-------ATGGGTTCGATCCTAAAACCGGAAGTTGAAAA-TAATTGTTTCGAAGTAGGGCAAGTTATAT-TTTTTGAAAAGGTATGACCGATTACATTACGAAAAATATGGTTcctctttaaa
gi|20                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     CACAGGGAAGA---TTGGACATTGTTCCAACTATG--------T
gi|3                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ATAGCCCATTCATCAGCCAAAAGTTAATCTCCTTAACGTCGCAAATATGTCTAGCGTTTGTTTATTTAGGCACGGGATAGTAACAATG--GTGTGTATTCAAGTGTCAAACTTAACGACTGAACTTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATAGTCATGATTGGACTAAATAACTCGAGCAAAGTTAGATGTATTTGGTATATCTGTGTTCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACTTTA-TTTAAAAATAAAATGATTTTTGTTGTGGTT---GTATTTTAGTATCGTAGATGTTGCCTTAACTGTATAACAAGAATTTTATGGGGGAAATCGGGTGTATTGAATTTTTATAGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN---NNNNNNNNNNNNNNNNNNNNN--------NNN---------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTAATCATAATAATTACTATTAAAGATGAAATCTGTTCTTTTTAGTATCGTAAATGTTACCTTAACTGTGTAACAAGAATTTTACGGAAAATTAATGGGTTA-------GATCCTAAAACTGGAAGTTGAAAA-TAATTGTTTCGAAGTAGGGCAAGTTATATATTTTTGAAAAGGTATAACTGAGTACATTACGAAAAATATCGTTTC-CGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAAAATAA-----TTTTCGATTGATGTTAGAAATAAAAAATGGAAACCTTAGA
gi|4                          :                                                                                                                                                                                                                                                                  TACTGTAATAAA-TTANN-N---------NNNNNN---N--NNNN--NNNNN--------NNNNNNN----NNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNNNNNATAAGCATGAACACTACTGAA----TAA----TTAATTAGACTCTGTATTATAAATAACTTACATGTTTTTTCTCCAACGGCCAACACTCAAATGAATTCCCTACGTTACACAAGACACAAAGTAATTTTGCGCACGACTTTTCTATTTTTAGATATAGCATTTCACAACCATTGCATCTGTCAAACCC-ACGCTAAGATATTAGTGTCAAACCTAGAATGTGTCTCCTTACTGTCTGCTCTTGTATTGGCACGATACATAATCCCTAAGCGGATTAGGCAACACATGCCGGATAGACCACAATGGCCTATTGATATGTCAGAGTTAATACCTTT-ACGTGACCCCAGTATGTCTAGCGTCTAATGGATATGAACACAATAGCCCATTCATCAGCCAAAAGGTAATCTCCTTAACGTCGCCAGTATGTCTAGCGTTTGTTTATTTAGGCACGGAAGTGTAATAATGGTGTGT--ATTCAAGTGTCAAACTTAACGACTGGACGTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATAGTCATGATTGGACTAAATAACTCGAGCAAAGTTAGTTGTATTTGGTATATCTGTGTCCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACT
gi|5                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  TCATTATTATTATTATTAAAGATGAAATATGTTCTTTTTAGTATCGTAAATGTTGCCTTAACTGTGTAACACGAATTTTACGGAAAATTAATGGGTT-------CGATCCTAAAACCGGAAGTTAAAAAATAATTGTTTCGAAATAGGGCAAGTTATATATTTTTGAAAAAGTATGACCGAGTACATTACGAAAAATATGGTTCC-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAAAATATTTTTCGATTTATGTCAGAAATTAGAAATGAAAACTCTA
gi|6                          : ACTACTAAAATATAATAATAAATAATTAAAACTAACTGTAATAAATAACTGAATAAATAATTAAAACTTTAAT------GAACAAGTTACTGAATAAATAATTAAA------TATAGACTCTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTACTGTAATAAA-TTAAATAATAACTAATAAATGA---T--TAAA--ACTAA--------TTGTAAT----AAATAACTGAATAAATA-AATAAAACAAAGTAA----------ATGAAC
gi|7                          :                                       tAATAAAAAACTGAATCAATAATTAAAACTATAAT------GAACATATAACTGAATAAATAATTAAA------TATAAACTCTATAAATAACTTAAATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTTAT-----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTACTGTAATAAA-TT-AA-A---------ACATAA---T--TAAA--ACTAA--------CTGTAAT----AAATAACAGAAAAAAAATATTAAAAATAAATAA----------ATAAGCATGAACACTAATGAATAATTAA----T----TAGACTCTGTATTtataa
gi|8                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          aataaattaaaCTTAATANNNNNNNNNNNNNNNN---NNNNNNNNNNNNNNNNNNNNNAAGATGAAATATGTTTTTCTTAGTATCGTAAATGTTACCTTAACTGTGTAACACGAATTTTACGGAAAAT-------TTATGGGTTCGATCCTAA------AAGTTAAAAA-TAATTGTTTCGAAAT--GGCAAGTTATATATTTTTGAAAAGGTATGACTGAGTACATTACGACAAATATGGT
gi|9                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            ACCACAAGGGCCTATTGAAACGCCATAGTTAATACTTTTTACGTGATCCCCGTATGGCTAGCGTCTACCGGACATGAACACAATA


blockSeqs                     :     CT                                                                   .                                .                           C                                                NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN               A     TAATAACTAAT      TAA       TA     AAGTATTT       TCAT               T T               NNNNNNNNNN                     TAAT   ATAAT                                                                                                                                                            .           T               C                                                                  C                                                  T                           C                    C                G                                                                GT    GT                                                                                 T                   A    T          T                                           T    TATTTT            A              GTAGT                                                                                                                      GTG     G               TTTTTCCTCTTT               GACT A  T                NNT                                                                                           TAATGGGTTA                  C            A                                                                           CGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN          A
blockSeqs                     :                                                                          .                                .                           A                                                NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN                    .     T                N         .      .              .                  N .               .                              .      TTAAT                                                                                                                                                            .           T               A                                                                  .                                                  .                           A                    C                T                                                                .     .                                                                                  A                   T    T          T                                           T    TATTTA            .              GTA                                                                                                                        .       C               TTTGCTCCTTT                AACT T  T                .                                                                                             TAATGGGTT                   T            .                                                                           NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN          .
blockSeqs                     :                                                                                                                                                                                                                                                                              .     N                T         .      .              .                  T .               .                              .      T                                                                                                                                                                                                                                                                                                                  .                           C                    .                G                                                                .     .                                                                                  A                   .    .          .                                           .                                                                                                                                                                .       C               TTTCCTATTT                 NNNN A  T                .                                                                                             TAATGGGTT                   C            .                                                                                                                                                                                                       
blockSeqs                     :                                                                                                                                                                                                                                                                              .     A                T         .      .              .                  A .               .                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     .       C               TTTCCTCTTT                 AAC  N  T                .                                                                                             TTATGGGTT                   .            .                                                                                                                                                                                                       
blockSeqs                     :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                .       C               TTTTTTCTTT                 GA   A  N                                                                                                                                                                                                                                                                                                                                                               
blockSeqs                     :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                .       C               TTT                        .    .  A                                                                                                                                                                                                                                                                                                                                                               
blockSeqs                     :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                .       C               TTT                             .  .                                                                                                                                                                                                                                                                                                                                                               
blockSeqs                     :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                .       A               TTT                                                                                                                                                                                                                                                                                                                                                                                                
blockSeqs                     :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                .       G               TTT                                                                                                                                                                                                                                                                                                                                                                                                
blockSeqs                     :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                .       C               NNN                                                                                                                                                                                                                                                                                                                                                                                                
blockSeqs                     :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                .       N                                                                                                                                                                                                                                                                                                                                                                                                                  
blockSeqs                     :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                .       .                                                                                                                                                                                                                                                                                                                                                                                                                  


blockSeqCons                  :                                                                                                                                                                                                                                                                                                     T*****                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               TAATGGGTT*******
originalCons                  : ACTACTAAAATATAATAATAAATAATTAAAACTAACTGTAATAAATAACTGAATAAATAATTAAAACTATAAT------GAACAAATAACTGAATAAATAATTAAA------TATAGACTCTATAAATAACTTANATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTTAT-----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTACTGTAATAAA-TTAAA-A---------AAATAA---T--TAAA--ACTAA--------CTGTAAT----AAATAACTGAATAAANA-ATTAAAAATAAATAA----------ATAAGCATGAACACTACTGAA----TAA----T----TAGACTCTGTATTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAATGAATTCCCTACGTTACACAAGACACAAAGTGATTTTGCGCACGACTTTTCTATTTTTAGATATAGCATTTCACAACCATTGCATCAGTCAAACCC-ACGCTAAGAGATTAGTGTCAAGCCTAGNATGTGTCTCCTTACTGTCTGCTCTTGTATTGACACGATACATAATCTCTAAGCGGATTAGGCAACACATGCCGGATACACCACAATGGCCTATTGATATGTCAGAGTTAATACCTTT-ACGTGACCCCAGTATGTCTAGCGTCTANCGGATATGAACACAATAGCCCATTCATCAGCCAAAAGNTAATCTCCTTAACGTCGCCAGTATGTCTAGCGTTTGTTTATTTAGGCACGGAAGTGTAACAATG--GTGT--ATTCAAGTGTCAAACTTAACGACTGGACGTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATAGTCATGATTGGACTANATAACTCGAGCAAAGTTAGTTGTATTTGGTATATCTGTGTCCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACTTTA-TTT-AAAATAAAATGATTTTTGTTGTTGTT---GT-TTTTAGTATCGTAGATGTTGCCTTAACTGTATAACACGAATTTTATGGGGAAAATCGGATGTATTGAATTTTTATAGCAGGAGGTAAATATTTAATTTTAGAGGACCACAGGGAAGA---TTGGACATTGTTCCAACTGTG--------TTT---------AAATAAAGACTTAATTATTATTATTATTACTA---TAATCATTATTATTATTATTAAAGATGAAATATGTTCTTTTTAGTATCGTAAATGTTACCTTAACTGTGTAACACGAATTTTACGGAAAATTAATGGGTTATGGGTTCGATCCTAAAACCGGAAGTTGAAAA-TAATTGTTTCGAAATAGGGCAAGTTATATATTTTTGAAAAGGTATGACCGAGTACATTACGAAAAATATGGTTCC-CGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAAACTAAAATATTTTTCGATTTATGTCAGAAATAAAAAATGAAAACCTTAGA
finalCons                     : ACTACTAAAATATAATAATAAATAATTAAAACTAACTGTAATAAATAACTGAATAAATAATTAAAACTATAAT------GAACAAATAACTGAATAAATAATTAAA------TATAGACTCTATAAATAACTTANATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTTAT-----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTACTGTAATAAA-TTAAA-A---------AAATAAT-----TAAA--ACTAA--------CTGTAAT----AAATAACTGAATAAANA-ATTAAAAATAAATAA----------ATAAGCATGAACACTACTGAA----TAA----T----TAGACTCTGTATTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAATGAATTCCCTACGTTACACAAGACACAAAGTGATTTTGCGCACGACTTTTCTATTTTTAGATATAGCATTTCACAACCATTGCATCAGTCAAACCC-ACGCTAAGAGATTAGTGTCAAGCCTAGNATGTGTCTCCTTACTGTCTGCTCTTGTATTGACACGATACATAATCTCTAAGCGGATTAGGCAACACATGCCGGATACACCACAATGGCCTATTGATATGTCAGAGTTAATACCTTT-ACGTGACCCCAGTATGTCTAGCGTCTANCGGATATGAACACAATAGCCCATTCATCAGCCAAAAGNTAATCTCCTTAACGTCGCCAGTATGTCTAGCGTTTGTTTATTTAGGCACGGAAGTGTAACAATG--GTGT--ATTCAAGTGTCAAACTTAACGACTGGACGTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATAGTCATGATTGGACTANATAACTCGAGCAAAGTTAGTTGTATTTGGTATATCTGTGTCCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACTTTA-TTT-AAAATAAAATGATTTTTGTTGTTGTT---GT-TTTTAGTATCGTAGATGTTGCCTTAACTGTATAACACGAATTTTATGGGGAAAATCGGATGTATTGAATTTTTATAGCAGGAGGTAAATATTTAATTTTAGAGGACCACAGGGAAGA---TTGGACATTGTTCCAACTGTG--------TTT---------AAATAAAGACTTAATTATTATTATTATTACTA---TAATCATTATTATTATTATTAAAGATGAAATATGTTCTTTTTAGTATCGTAAATGTTACCTTAACTGTGTAACACGAATTTTACGGAAAATTAATGGGTT-------CGATCCTAAAACCGGAAGTTGAAAA-TAATTGTTTCGAAATAGGGCAAGTTATATATTTTTGAAAAGGTATGACCGAGTACATTACGAAAAATATGGTTCC-CGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAAACTAAAATATTTTTCGATTTATGTCAGAAATAAAAAATGAAAACCTTAGA
2 sequences could not be aligned to this reference sequence:
Unaligned ( gi|19 ): TTTTAAATATTCATTTTTGTTAGCATGAATATAAT
Unaligned ( gi|21 ): GCAGAGGGGTAAATGTCCATATATCACATAA






Alignments
lowQualScore                  :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111                                                      
lowQualScore                  :     11                                                                   333333                           333333                                                                       99999999999999999999999999999999999999999999999999999999999999999999999                     33333333333      111111    11     22222222       1111                                 3333333333                     2222   333333333                                                                                                                                                        1                                                                                                                                                 1                                                                                                                                  11    11                                                                                                                                                                      333333                            333                                                                                                                                             22222222   333333333                                111                                                                                                                                                                                                         111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111                                                      
lowQualScore                  :     88                                                                   888888                           888888                      1                                                99999999999999999999999999999999999999999999999999999999999999999999999               8  0  88888888888      888888    11     99999999       7777               1 8               5555555555                     1111   333333333                                                                                                                                                        3           7               1                                                                  6                                                  0                           1                    2                1                                                                33    33                            0                                                    1                   9      3           2                                         3   000000           7              6 666                                                                                                                     555     2               11111111   888888888       8888 1  1              0 444                                                                                        0   1                0  1       8                    0             0                                             111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111         7                                            
lowQualScore                  :     ..                                                                   ......                           ......                      .                                                .......................................................................               .  .  ...........      ......    ..     ........       ....               . .               ..........                     ....   .........                                                                                                                                                        .           .               .                                                                  .                                                  .                           .                    .                .                                                                ..    ..                            .                                                    .                   .      .           .                                         .   ......           .              . ...                                                                                                                     ...     .               ........   .........       .... .  .              . ...                                                                                        .   .                .  .       .                    .             .                                             ..................................................................................................................         .                                            
lowQualScore                  :     00                                                                   333333                           333333                      0                                                33333333333333333333333333333333333333333333333333333333333333333333333               0  8  22222222222      000000    00     00000000       0000               0 0               0000000000                     2222   555555555                                                                                                                                                        3           3               0                                                                  7                                                  0                           0                    5                0                                                                88    88                            2                                                    0                   8      2           5                                         2   000000           3              7 777                                                                                                                     444     4               22222222   222222222       0000 5  6              2 000                                                                                        8   0                8  4       0                    8             8                                             777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777         3                                            
consensus                     : ACTACTAAAATATAATAATAAATAATTAAAACTAACTGTAATAAATAACTGAATAAATAATTAAAACTATAAT------GAACAAATAACTGAATAAATAATTAAA------TATAGACTCTATAAATAACTTANATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTTAT-----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTACTGTAATAAA-TTAAA-A---------AAATAA---T--TAAA--ACTAA--------CTGTAAT----AAATAACTGAATAAANA-ATTAAAAATAAATAA----------ATAAGCATGAACACTACTGAA----TAA----T----TAGACTCTGTATTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAATGAATTCCCTACGTTACACAAGACACAAAGTGATTTTGCGCACGACTTTTCTATTTTTAGATATAGCATTTCACAACCATTGCATCAGTCAAACCC-ACGCTAAGAGATTAGTGTCAAGCCTAGNATGTGTCTCCTTACTGTCTGCTCTTGTATTGACACGATACATAATCTCTAAGCGGATTAGGCAACACATGCCGGATACACCACAATGGCCTATTGATATGTCAGAGTTAATACCTTT-ACGTGACCCCAGTATGTCTAGCGTCTANCGGATATGAACACAATAGCCCATTCATCAGCCAAAAGNTAATCTCCTTAACGTCGCCAGTATGTCTAGCGTTTGTTTATTTAGGCACGGAAGTGTAACAATG--GTGT--ATTCAAGTGTCAAACTTAACGACTGGACGTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATAGTCATGATTGGACTANATAACTCGAGCAAAGTTAGTTGTATTTGGTATATCTGTGTCCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACTTTATTT-AAAATAAAATGATTTTTGTTGTTGTTGTA--TTTTAGTATCGTAGATGTTGCCTTAACTGTATAACACGAATTTTATGGGGAAAATCGGATGTATTGAATTTTTATAGCAGGAGGTAAATATTTAATTTTAGAGGACCACAGGGAAGA---TTGGACATTGTTCCAACTGTG--------TTT---------AAATAAAGACTTAATTATTATTATTATTACTA---TAATCATTATTATTATTATTAAAGATGAAATATGTTCTTTTTAGTATCGTAAATGTTACCTTAACTGTGTAACACGAATTTTACGGAAAATTAATGGGTTCGATCCTAAAACCGGAAGTT-GAAAATAATTGTTTCGAAATAGGGCAAGTTATATATTTTTGAAAAGGTATGACCGAGTACATTACGAAAAATATGGTTCC-CGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAAACTAAAATATTTTTCGATTTATGTCAGAAATAAAAAATGAAAACCTTAGA
Reference ( family-761 )      : ACTACTAAAATATAATAATAAATAATTAAAACTAACTGTAATAAATAACTGAATAAATAATTAAAACTATAAT------GAACAAATAACTGAATAAATAATTAAA------TATAGACTCTATAAATAACTTANATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTTAT-----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTACTGTAATAAA-TTAAA-A---------AAATAA---T--TAAA--ACTAA--------CTGTAAT----AAATAACTGAATAAANA-ATTAAAAATAAATAA----------ATAAGCATGAACACTACTGAA----TAA----T----TAGACTCTGTATTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAATGAATTCCCTACGTTACACAAGACACAAAGTGATTTTGCGCACGACTTTTCTATTTTTAGATATAGCATTTCACAACCATTGCATCAGTCAAACCC-ACGCTAAGAGATTAGTGTCAAGCCTAGNATGTGTCTCCTTACTGTCTGCTCTTGTATTGACACGATACATAATCTCTAAGCGGATTAGGCAACACATGCCGGATACACCACAATGGCCTATTGATATGTCAGAGTTAATACCTTT-ACGTGACCCCAGTATGTCTAGCGTCTANCGGATATGAACACAATAGCCCATTCATCAGCCAAAAGNTAATCTCCTTAACGTCGCCAGTATGTCTAGCGTTTGTTTATTTAGGCACGGAAGTGTAACAATG--GTGT--ATTCAAGTGTCAAACTTAACGACTGGACGTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATAGTCATGATTGGACTANATAACTCGAGCAAAGTTAGTTGTATTTGGTATATCTGTGTCCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACTTTATTT-AAAATAAAATGATTTTTGTTGTTGTTGT---TTTTAGTATCGTAGATGTTGCCTTAACTGTATAACACGAATTTTATGGGGAAAATCGGATGTATTGAATTTTTATAGCAGGAGGTAAATATTTAATTTTAGAGGACCACAGGGAAGA---TTGGACATTGTTCCAACTGTG--------TTT---------AAATAAAGACTTAATTATTATTATTATTACTA---TAATCATTATTATTATTATTAAAGATGAAATATGTTCTTTTTAGTATCGTAAATGTTACCTTAACTGTGTAACACGAATTTTACGGAAAATTAATGGGTTCGATCCTAAAACCGGAAGTT-GAAAATAATTGTTTCGAAATAGGGCAAGTTATATATTTTTGAAAAGGTATGACCGAGTACATTACGAAAAATATGGTTCC-CGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAAACTAAAATATTTTTCGATTTATGTCAGAAATAAAAAATGAAAACCTTAGA
gi|1                          : ACTA--AAAATATAATAATAAATAATTAAAACTAACTGTAATAAATAACTGAATAAATAATTAAAAAAATAATAATTATGGACAAATAACTGAATAAATAATTAAACGTAAATATAGACTCTATAAATAACTTATATGTTTCTTCTCCAACAGCCAACACTCAAATGAACGCCCTACATTTAT-----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAACTACTGTAATAAA-TTAAA-A---------AAAAAAAAAT--TAAA--CTTAA--------CTGTGAT----AAATAACTGAGTAAACA-ATTAAAAATAAATAA----------ATAAGCATGAACACTACTGAA----TAA----T----TAGACTCTGTATTATAAATAACTTACATGTTTCTTCTCCAACTGCCAACACTCAAATAAATTCCCTACGTTACACAAGACACAAAGTGGTTTTGCGCACGATTTTTCTATTTTTAGATATAGCATTTCACAACCATTGCATCAGTCAAACCCCACGCTAAGAGA-------CAAGCCTAGTATGTGTCTTCATACTGTCTGCCATTTTATTGACACGATACATAATCTCTAAGCGGATTAGGCAACACATGCTGGATACACCACAATGGCCTATTGATATGTCAGAGTTAAAACCTTT-ACGTGACCCCAGTATGTGTAGCGTCTGACGGATATGAACACAATAGCCCATTCATCAGCCCAAAGTTAATCTCCATAATGTCGCCAGTATGTCTAGCGTTTGTTTATTTAGACACGGAAGTTAAACAATG--GTGT--ATTCAAGTGTCAAACTTAGCGACTGGACATCTTAACAATAGATTAATGGGTCCTTTGTTGTAAATAGTCATGATTGGACTATATAACTCAAGCAAAGTTAGTTATATTTGGTATATCTGTGTCCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACTT--------AATAAAATGATTTTTGTTGTTGTT-T---TTTTAGTATCGTAGATGTTGCCTTAACTGTATAACACGAATTTTATGGGGAAAATCGGATGTATTGCATTTTTATAGCAAGAGGTAAATATTTAATTTTAGAGCAACACAGGGAAGA---TTGGAGATAGTTCCAGCTGTG--------TTT---------AAATAAAGTCTTAATTATTATTATTATTACTG---TTGTCATTATTATTGTTATTAAAGATGAAATATGTTCTTTTTAGTATCATAAATGTTACCTTATCTGTGTAACATGAATTTTACGGAA--------------ATCCTAAAACTGGAAGTT-GAAAATAATGGTTTCGAAATAGGGCAAGTTATATATTTTTGAAAAGGTATGACTGAGTACATTACTAAAAATATGGTTCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTGCAATATTTTTCAATTTATGTCAGAAATAAAAAATGAAAACCTTAGA
gi|10                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            AGAGGACCACAGGGAAGA---TTGGAGATTGTTCCAAATGTGTTTGCTCCTTT---------AAATAAA----TAAT--TTATTATTGTTATAA---TAA
gi|11                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                GACCCCAGGAAAGA---TTGGACATTGTTCCAAAGGTG--------TTTTTCCTCTTTAAATAAAGA------TATTATTATT
gi|12                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   CACAGGGGAGA---CTAGACATTGTTCCAACTCTGTTTCCTA-TTT---------AAATAAAAAC---ATTATTATT
gi|13                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           AGA---TTGGACATTGTTCCATGTGTG--------TTTCCTCTTT--GAATAAAGACTTTATTATTATTATT
gi|14                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              AAGACCACAGAGAAGAGTGTTGGACACTGTTCTAACTGTG--------TTT---------
gi|15                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          tTAAAGGACCTCAGGGAAGA---TTGGACAATGTTCTAACTGTG--------TTT---------tctctttcaa
gi|16                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          aTAAAGGACCACAGGGAAGA---TTGGACAATGTTCTAACTGTG--------TTT---------cctcttt
gi|17                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                tcaCACAGGGAAGA---TTGGAAATTGTTCCAACTGTG--------Tcct
gi|18                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         GAAGA---TTGGAGACTGTTCCAACTGTG--------TTT---------atcctct
gi|2                          :                                                                                                                                                                                                                                                                ACTACTGTAAAAAAATTAAA-T---------AAATAA---TAATAAATAATTAAAAGTATTTTTGTAATTCATAAATAACTGAATAAATA-ATTAAAAATAAATAA----------ATAAGCATGACCACTACTGAA----TAAATAAT----TAGACTTTGTATTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAAGGAATTCCATACGTTACACAAGACACAAAGTGATTTTACGCACGACTTTTCTATTTTTAGATATAGCATATCACAACCATTGCATCAGTTTAATCC-ACGCTAAGAGATTAGTGTCAAGTCTAGCATGTGTCTCCTTACTGTCTGCTCTTGTATTGACACGATACATAATCTCTAAGCGGATTAGGCAGCA---ACCGGATACACCGCAATTGCCTATTGATATGTCAGAGTTAATACCTTT-ATGTGACCGCAGTATGTCTAGGGTATACCGGATAGGAACACAATAGCC------------AAAAGGTAATCTCTTTAACGTCACCAGTATGTCTAGCGTTTGTTTATTTAGGCACGGAAGTGTATCAATG--ATGT--ATTAAAGTCTCAAACTTAACGACTGGACGTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATTGTCATGATTGGACTATTTAACTCGAGCAAAGTTAG--GTATT-GGTATAACTGT--CCACGGTGTGAATATTGGAGTTTTATAGCAAGAGGTAAAT----TATTTTAAAATAAAATG-TTGTTGTTTTTTTTGTAGTTTTTAGTATCGTAGATGTTGCCTTAATTGTATAACACGAATTTTATTGGGAAAATTGGATGTATTGAATTTTTATGGCAGGAGGTAAATATTTAATTTTAGAGGACCACAGGGAATA---TTGGA----GTTCCAGCTGTG--------TTTTTTCTTT--AAACAAGAACTTAATTATTATAATTATTACTA---TAATCATTATTGTTATTATTAATGATGAAATATGTTCTTTTTAGTATCATAAATGTTGCCTTAACTGTGTAACACGAATTTTACGGAAAATTAATGGGTTCGATCCTAAAACCGGAAGTT-GAAAATAATTGTTTCGAAGTAGGGCAAGTTATAT-TTTTTGAAAAGGTATGACCGATTACATTACGAAAAATATGGTTcctctttaaa
gi|20                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   CACAGGGAAGA---TTGGACATTGTTCCAACTATG--------T
gi|3                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ATAGCCCATTCATCAGCCAAAAGTTAATCTCCTTAACGTCGCAAATATGTCTAGCGTTTGTTTATTTAGGCACGGGATAGTAACAATG--GTGTGTATTCAAGTGTCAAACTTAACGACTGAACTTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATAGTCATGATTGGACTAAATAACTCGAGCAAAGTTAGATGTATTTGGTATATCTGTGTTCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACTTTATTTAAAAATAAAATGATTTTTGTTGTGGTTGTA--TTTTAGTATCGTAGATGTTGCCTTAACTGTATAACAAGAATTTTATGGGGGAAATCGGGTGTATTGAATTTTTATAGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN---NNNNNNNNNNNNNNNNNNNNN--------NNN---------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTAATCATAATAATTACTATTAAAGATGAAATCTGTTCTTTTTAGTATCGTAAATGTTACCTTAACTGTGTAACAAGAATTTTACGGAAAATTAATGGGTTAGATCCTAAAACTGGAAGTT-GAAAATAATTGTTTCGAAGTAGGGCAAGTTATATATTTTTGAAAAGGTATAACTGAGTACATTACGAAAAATATCGTTTC-CGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAAAATAA-----TTTTCGATTGATGTTAGAAATAAAAAATGGAAACCTTAGA
gi|4                          :                                                                                                                                                                                                                                                                  TACTGTAATAAA-TTANN-N---------NNNNNN---N--NNNN--NNNNN--------NNNNNNN----NNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNNNNNATAAGCATGAACACTACTGAA----TAA----TTAATTAGACTCTGTATTATAAATAACTTACATGTTTTTTCTCCAACGGCCAACACTCAAATGAATTCCCTACGTTACACAAGACACAAAGTAATTTTGCGCACGACTTTTCTATTTTTAGATATAGCATTTCACAACCATTGCATCTGTCAAACCC-ACGCTAAGATATTAGTGTCAAACCTAGAATGTGTCTCCTTACTGTCTGCTCTTGTATTGGCACGATACATAATCCCTAAGCGGATTAGGCAACACATGCCGGATAGACCACAATGGCCTATTGATATGTCAGAGTTAATACCTTT-ACGTGACCCCAGTATGTCTAGCGTCTAATGGATATGAACACAATAGCCCATTCATCAGCCAAAAGGTAATCTCCTTAACGTCGCCAGTATGTCTAGCGTTTGTTTATTTAGGCACGGAAGTGTAATAATGGTGTGT--ATTCAAGTGTCAAACTTAACGACTGGACGTCTTAACAATAGATTAATGGGTCCTTTGTTGTACATAGTCATGATTGGACTAAATAACTCGAGCAAAGTTAGTTGTATTTGGTATATCTGTGTCCACGGTGTGTGTATTGGAGTTTTATAGCAAGAGGTAAATACT
gi|5                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                TCATTATTATTATTATTAAAGATGAAATATGTTCTTTTTAGTATCGTAAATGTTGCCTTAACTGTGTAACACGAATTTTACGGAAAATTAATGGGTTCGATCCTAAAACCGGAAGTTAAAAAATAATTGTTTCGAAATAGGGCAAGTTATATATTTTTGAAAAAGTATGACCGAGTACATTACGAAAAATATGGTTCC-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAAAATATTTTTCGATTTATGTCAGAAATTAGAAATGAAAACTCTA
gi|6                          : ACTACTAAAATATAATAATAAATAATTAAAACTAACTGTAATAAATAACTGAATAAATAATTAAAACTTTAAT------GAACAAGTTACTGAATAAATAATTAAA------TATAGACTCTATAAATAACTTACATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTACTGTAATAAA-TTAAATAATAACTAATAAATGA---T--TAAA--ACTAA--------TTGTAAT----AAATAACTGAATAAATA-AATAAAACAAAGTAA----------ATGAAC
gi|7                          :                                       tAATAAAAAACTGAATCAATAATTAAAACTATAAT------GAACATATAACTGAATAAATAATTAAA------TATAAACTCTATAAATAACTTAAATGTTTCTTCTCCAACGGCCAACACTCAAATGAACGCCCTACGTTTAT-----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTACTGTAATAAA-TT-AA-A---------ACATAA---T--TAAA--ACTAA--------CTGTAAT----AAATAACAGAAAAAAAATATTAAAAATAAATAA----------ATAAGCATGAACACTAATGAATAATTAA----T----TAGACTCTGTATTtataa
gi|8                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        aataaattaaaCTTAATANNNNNNNNNNNNNNNN---NNNNNNNNNNNNNNNNNNNNNAAGATGAAATATGTTTTTCTTAGTATCGTAAATGTTACCTTAACTGTGTAACACGAATTTTACGGAAAATTTATGGGTTCGATCCTAA------AAGTT-AAAAATAATTGTTTCGAAAT--GGCAAGTTATATATTTTTGAAAAGGTATGACTGAGTACATTACGACAAATATGGT
gi|9                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            ACCACAAGGGCCTATTGAAACGCCATAGTTAATACTTTTTACGTGATCCCCGTATGGCTAGCGTCTACCGGACATGAACACAATA
2 sequences could not be aligned to this reference sequence:
Unaligned ( gi|19 ): TTTTAAATATTCATTTTTGTTAGCATGAATATAAT
Unaligned ( gi|21 ): GCAGAGGGGTAAATGTCCATATATCACATAA