lowQualScore                  :                                                                                                                                                                                                                                                                                                              111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
lowQualScore                  :                                                                      8888888              3333                               2      111              33333333333333333333333                     2             33333333         2222222           22   111    666666                               22        222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222      1    222        1       77777777777777777          222      1  666666666   22    1  1        4                         2222               1  222     11  55555555555555555       222    1           9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999          6666666   1         11     22       333           33      1  222222222       11   333       2   444444444              222      1    33           44444      11  1          2         2  2   
lowQualScore                  :                                                            4   555   0000000       3      0000       33 66                   5    3 555   3       3  88888888888888888888888   99 4 4   4 8888   6    5        44444444   6     2222222        6  99   111    666666  8   6       99       6   99  99 6 2    666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666 7    7    111  7     3    7  22222222222222222          111      5  555555555   33    5  5        0                         3333            7  3  999     11  44444444444444444       888    3     2 2   4444444444444444444444444444444444444444444444444444444444444444444444444444444444444444444444          2222222   7         99     77       444           00      5  666666666       77   444       0   111111111         3    111      5    00           66666      88  7   2      0      2  0  0   
lowQualScore                  :                                                            .   ...   .......       .      ....       .. ..                   .    . ...   .       .  .......................   .. . .   . ....   .    .        ........   .     .......        .  ..   ...    ......  .   .       ..       .   ..  .. . .    .................................................................................................................................................................................................................................... .    .    ...  .     .    .  .................          ...      .  .........   ..    .  .        .                         ....            .  .  ...     ..  .................       ...    .     . .   ..............................................................................................          .......   .         ..     ..       ...           ..      .  .........       ..   ...       .   .........         .    ...      .    ..           .....      ..  .   .      .      .  .  .   
lowQualScore                  :                                                            4   333   3333333       3      6666       99 88                   8    1 999   6       6  66666666666666666666666   55 0 0   9 9999   7    0        11111111   7     0000000        7  22   777    888888  3   7       22       7   22  00 7 2    555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555 7    3    777  3     3    3  00000000000000000          555      0  000000000   00    5  5        0                         0000            3  3  000     22  55555555555555555       222    5     5 5   8888888888888888888888888888888888888888888888888888888888888888888888888888888888888888888888          5555555   0         00     55       000           55      5  555555555       55   555       0   555555555         0    000      0    00           00000      00  0   5      0      5  0  0   
consensus                     :                                                        AAAG-AAA-A-TAA--TCAC-AACGCCG-AAAATA--ACTCAACCG--G--TTTCATTTTCAATCTTCAA-GAGT-T-N-TGA-CAATCGC-TT-----------------------AGT--T-A-CACATG---TTATCAAC-AATTTTTT----CTA-TGA-CATCA---A-ANGCGCCAAA-TTA-TAT---TTGC-G---CTTTAAC-AAAGTTC--ATTGTGA-CGT--CATAA-TNTAACTGT-TATGC----CGTATTAT-CG-CG-GCAT--AT---CTGACTTTCTG-AACTGT-GC-ATGT-ACAAAAATATAC-------TAT-GT-ACAATA-TNATGGCAA---ATA-TAAAT-ATT-AT--TAAATAT--AATGA-GGAGGGGGGA----TCACGTTT-GT-ATNAACATA-TG--A--ATATAT--AANATAGTA-AC------TACG-GTGATA--N-ANAAAATTATAAT-AAATAAAA-AAATAAA-A--AAA-AA-AATT--GGGGGGGGGGAATTACGCCCTAC-CTCGCA-CAAATTACGAAAATATACAAA-ATGGNNNNNNNNNNNNNNNTTGATAATATAGAGGGCATGCATAA-ATTG-TACAA-TATT------AT-AAT--ATTAATGGG-GGAAAANAGGGGGGGGGG----GT-NTCACGN---TATTA---ACAATACGTAGACGA-NATTT---AAA-CATAA--TATGACA----GAT--GATTACCTGTAAAATAA-ATTCTGACCTACNNNNTATAATGCGGGGAAANGTTTCTGGAAAATAATATTTTCAAAGAAGTTTACAATTGATNNAGCNNTTTAGCGCCGGTNTTGTATCCTTCGATATAAACAAGCTTTCCTTNGTTCCANCGTTCTGTTTCCGTGGTATCTTTCCCAAAGAATTTNTAAAAGGNGAAAACGGGTAAGNTCCGGTATG
Reference ( gi|1 )            :                                                        AAAG-AAA-A-TAAGCCCACTAACGCCG-AAAATA--CATCAACCG--G--TTTCATTTTCAATCTTCAACGAGT-T-T-TGA-CAATCGC-TT-----------------------AGT--T-A-CACATG---TTA-CAAC-AATTTTTT----CTAATGA-CATCA---A-TTGCGCCAAA-TT--TAT---TTGCTGCCTCTTAAAC-AAAGTTC--ATTGTGA-CGT--CAATA-TATAACCGT-TA-GC----CGTATTAT-CG-TG-GCAT--AT---CTGACTT-CTG-A--TGT-GCAATGTTACGAAAATA-AC-------TAT-GTTACAATA-TAATGGCAA---ATA-TAAATTATT-ATCATAAGCA---AATGA-GGAGGGGGGAGTGTCCACGTTTTGT-ACTAACATA-TG--A--ATATAT-TAATAT-GTA-AC------TAAG-GTGATA--G-ATAAAACTATAATTAAATAAAA-AAATAAATAATAAAAAA-AATT--GGGGGGGGGGAATTACGCCCTACGCTCGCAACAATCTACGAAAATATACAAAGATGGTAAGTCATATATAAATTAATAGCA-AGAGGGCATGCATAA-ATTGGTACAA-TAT-------AT-AAT--CCTAATGGGTGGAAAAAAGGGGGGGGGG----GTCATCACGT---TATTA---ACAATACGTAAAGGATCGTTT---AAA-CATAAT-TATAACACA-GGAT--GAGTAC-TGTAAGATAACATTCTGACCTCCTAAG-ATATTGCGGGGAACAGTTTC--GAAAATAATATTTTCAAAGAAGTTTACAATTG-TGCAGCCATTTAGCGCCAGTTTAGTATCCT-CGA-A--AACAAGTTTTTCTTTGTTTCAACGTTCTGTTTCCGTGGTATCTTTC---A-GAATTTTGAATAGGGGAAAAC-GGTAAAGTT-GG-ATG
gi|2                          :                                                        AAAG-AAA-A-TAA--TCAC-AACGCCG-AAAAAA--C-TCAACCGCGG--TTTCATTTTCAATCTTCAA-GAGT-TAT-TGA-CAACCGCCTT-----------------------AGT--T-A-CACATT---GTATCAAC-AATTTTTT----CTA-TGA-CATTA---AATGGCGTCAA--TT--TATGATTTGC-GCTTTTTAACCCAAAGTTC--ATTGTGA-CGT--CATAA-TTTAAC-GT-TA----------ATTA--CG-CT-GCAT--AT---CTGACTTTCTG-GACTGTTGCCATGT-ACAAAAATATACAA-----TAT-GT-ACAATAATAATGGCAA---ATT-GAAA--ATT-AT--TAAATAT--AATAA-GGGAGGAGGA----TCATATTTGGTTATAAACATA-GGGAA--ATATAT--GATAT-GTA--C------CACG-GTGATA--G-ATAAAA--ATA-TTAA-TAAAA-AAATAAA-------------------AGGAGGGG---TACACC-TAC-TTGGCA-CAAATTACGAAA-TATACAAA-ATGG
gi|3                          :                  caaaatatatgtaaatatcacacaagtaatggtataatAAAG-AAA-A-TAA-TTCA--AACGCCG-AAAATA--ACTCAACCG--G--TTTCAATTTCAAACTTT--CAAGT-A-T--GA-CA-TCGC-TT-----------------------CAT----A-CAC-TG---TTATCAAC-AATTTCT--------AT-A-CATCC---A-ATGACCCAAA-TTA-TAT---TTGC-----CTTTAAC-AAA-TTC--CTT-T-A-CGT--CATAA-TATAACTCT----GC----C-TAT-ATACG-TG--CATTAAT---C-GACT--CTG-A--TGC----ATGT-ACAAAAATATAC-------AATAG--ACAATA-ATATGGCAA---A-A-TAAATAATTTAT--TAAATATAAAATGAAGGAGCGGGGA----TCACGTTT-G--ACTAACAT--TA--A--ATA-----AGCATAGTACAC------T--G-GT-ATA--TTAAAAAATTTTAA--AAATTAAA-AAAAAAAAAA-AAAAAA-AATT--GGGGGGGGTAAATTACGTCCTA--CTCAC--CAAATTACG-AAATATACAAA
gi|11                         :              taataaatccaaataatgtaaaatccacacagtaattataatAAAG-AAATA-TCAG------AATGCCA-AAAATA--ACTCAACCA--G--TTTCATTTTCAATCTTC-ATGAGT-T-A-TGA--AA-CGC-TTGA---------------------AGTGGT-A-TA-GTG---TTA-t
gi|13                         :                         aacaatgtaatccttgtataataattatgatAAAGCAAA-ACTAA--TCAC-AACGC-G-AAAATA--ACTCAACCG--G--TT-CATTTTCAATCTTCAA-GAGT-
gi|16                         :   tattataaataatccaaaatatatgtagaatatccacacaagtaatggataatAAAA-AGA-A-TAA--TCAC-AACGCCG-AAAATA--ACTCAACCG--G--TTGAGTTTTCACTCTTCAAAGA-----T-AGA-CAAatga
gi|14                         :                                          tatatttaaattatAAAG-AAA-A-TAA--TCAC-AACGCCG-AAAATA--ACTCAACCG--G--TTT
gi|19                         : atatatataatgcaaactatatgtaaatatccacaccagtaatggtatatataatAAAG-AAA---TA---TCA-TAACACC---AAATG--CATT-------G--TTTCATTTTCAATCTTCAA-GAGG-T-T-
gi|17                         :                                                    ataatAAG-AAA-A-TAA--TCA--AACGCCG-AAAATA---ATCAACCG--GTTTTTC-TTTTCAATCTTCAA-GAGT-T-TATGA-CAATCGC-TT-----------------------Aattattg
gi|12                         :                                                         AAG-AAA-A-TAA--TCA--AACGCCGGAAAATAATC-TCAACCG--GT-TTTCA-TTTCAATCTTCAA-AAGT-T-TATGATCAATCGC-TT-----------------------AGT--T-C-CATA
gi|22                         :                                            aagatatgaagatatcaccaatatggtatccagAACGCCG-AAAATA--ACTCAACCG--G--TTTC
gi|15                         :                                                                                cCTG-AAAATA--ACTCCACCG--G--TATCATTTTTAATCTTCAA-AAGT-T-A-TGG-CAATCGC-TT-----------------------AGC--T-A-CACATG---TT-------AATTTTTT----TTAGT
gi|18                         :                                                                                    -AAAATA--ACCCAACC------TTTCATTTTCAATCTT-GAGGATTAT-A-TGA-CAATTGC-AT-----------------------TGT--T-A-CAC--G---TTATCAAC-at
gi|9                          :                                                                                                 aACCG--G--TTTCTTGTTCAATCTTCAA-GAGT-T-A-TAA-CAATCGC-TT-----------------------AGT--TTA-CACAT----TTATCAAC-ATTTTTTT----CT--TGA-TATCA---A-ATGCGCCAAA-TT--TAT---TTGC-G---CTTTAAC-AGAGTTA--GTTGTGA-CGT--CATAA-TATAA
gi|8                          :                                                                                                   cCA--G--TTTCATTTTCAAACTTCAAC-AGT-T---------ATCGC-TT-----------------------AGT--T-A-CACATG---TTATCAAC-AATTGTTT----CT-ATGA-CATCA---A-ATACGCCAAA-TTA-TAT---TTG----CTCTTTAAC-AAAGTTC--ATTGTGA-CGT--CATAA-TATAACT-T-CATGC----CGTA--AT-CA-CGTGCCT--AC---CTGACTT-CTG-AACTGT-Gtgtt
gi|7                          :                                                                                                                  TTTAATCTTCAA-GAGT-T-A-TGA-CAATCGC-TTTATAGTTAATATAATATAGTAATAGT--T-A-CACATT---TTATCAAC-AGTTTTTTA---CTA-TGA-CATCA---A-AAGCGCCAGA-TTA-TAT---TTGCAG----TTTAAC-AAAGTTC--ATTGTGA-CAT--TATGA-TTTAA-TGT-TATGC----CGTAATAC-CGCTG-GC
gi|4                          :                                                                                                                                               TCGC-TT-----------------------AGTG-T-AGCAGTTGGTTTTA-TTACTAATTTTTTTTCTCTA-TGATCATAATGTG-TCGCGCAAAAATTAGTAT---TTGC-GC---TTACAC-ATAGTTCCAATTGTGATCGTTTCGCTAATGTAAC-GTATG-GTGTGGCGTA--AT-TA-CT-GCAT--ATATTCTGACTTTCTGGA--TGT-GCA-TGT-ATCAAAATA-ACCTACAATTAT-GTAATAAC--TCATGGCAACATATAATAAATTATT-AT-ATAA--A---AGGGA-GGAGGGGGGG--GTTCACG-TTTGT-ATCAACATACTG--ACCATATATATAAGATAGTT-ACCTCACATACGCGTAGTATCA-AGAAAATTATAATGAAACAAAATAAAT--ATACCAAACAATAATTCCGGGGGGGGGcaagtgtccaattttc
gi|6                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         TTAATAATATAAAAGGCATGCA--A-AT--GTACAAATTT-------AT-AAT-----AATGGG-GGAAAAAAGGGG-------------ATCATAG---TATTA----CAATAT---AACGACGGTTT---AA--CATAATATATGACA----GA---GATTAC-T-TAA--TAA-ATTCTGACTT--TACGTATAATGCGGGGAAAAGTTTC--GAAAATA--ATTTTCAAAGAAG-TTACAA-TG-TCGAG-CATTTAGCG-CAGTT--GTATCCT-CAATA--AAC-AGCTTTTCTTGGTTC--ACGTTCT-TTTCC-TAGTATCTTTTCCAA-GAATTTGTAAAAGGTAAAAAC-GGTAAGTTC-GGTATG
gi|5                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          TGATAATA-AGAGGGCATGCATAA-ATTG-TACAA-AATTT-----AT-AAT--ATTAATGGG-GGAAAA--GGGGGGCGGG----ATAGTAATG-----ATTA----CAATA-GTAGATGA-CATTT---AAAGCATAAA-TATGACA----GTTTTGATTACCTGTAAAATAA-ATTTTGACCTACGTAT-ATAATGCGGGGAAATGTTTCTGGAAAATAAT-TTTTCAAAGAA-TTTACAATTGATGTAGCATTTTAGCGCAGGTGTTGTATCCTTCGA-ATAAACA-GTTTTCTTTTGTTTCACCGTTCTGTTTC-GTGGTATCTTTC---AAGAATTTTTAAAAGGGGAAAACGGGTAAAGTTCGG-ATGa
gi|10                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         aATGCATAAGATTG-TACAA-TATTAATATTATTAAT--ATTAATGGG---AAAATAAGGGGGGGGGAAACGCCCACACAA---TAGTATGTACAGTA-GTAGGGGGAAATTTAACAAA-CATAA---ATGACAGATGGAT--a
gi|4                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          CAA-CAT-------AT-AATAAATTATTATATAAAAGGGAGGAGGGGGGG----GT--TCACGTTTGTATCA---AC-ATACtac

Unaligned ( gi|20 ): AATATATAATCCAAAATATATGTAAATATCCACACAATTAATGGTATA
Unaligned ( gi|21 ): TAGAATCCAAAATATATTTAAATATCCACACAAGTAATGGTATAA

lowQualScore                  :                                                                  111   11                                                                           33333333333333333333333                                  1111                      111111     11        222222                                         222222          2222222222  111      111            22        1   1         333333333     1     1111         1      1111111    11      222    2           3333        1 111        33333333333      1     1  3333333333333 1      222            22    111    1     222222222          11                 1    22     22         2           1    111111111111111         2               1    1        3333333333             1      1           4444444444    1     3333     2   1111  11    111   1     222  11    33333333      1          1          3333333                    33         2                    111      11        11111         2   333    11                                         44444                     2        2   1   
lowQualScore                  :                                                          4   44  000   11       3      3 3        33 66              2     2  2 666 3 2  3       3  88888888888888888888888  3 88  3   3  777                5555   5   5       66     666666     00 5      000000     77        77       5   77  5    1   222222   7   2  1111111111  111  99  111 1   7      00  8  8  0   0  0      333333333     0 2   4444 1       0 66   9999999    33      333    0           5555        0 777  1     00000000000   3  0  1  5  0000000000000 0  6   444 1    7   3 33    777    0     777777777 66  3    33       888       2    00     00         3           3    555555555555555  0      3            3  0  3 0     4  6666666666     7    2  0      0     2 2   8888888888    0     3333     7   7777  11    777   0     333  33    22222222      2 6        3          8888888              1     00         3           6  7     888 22   55        33333         3   888    44 0   0   1   77 1      6   6 6           33333      1       1      3     11 3   5   
lowQualScore                  :                                                          .   ..  ...   ..       .      . .        .. ..              .     .  . ... . .  .       .  .......................  . ..  .   .  ...                ....   .   .       ..     ......     .. .      ......     ..        ..       .   ..  .    .   ......   .   .  ..........  ...  ..  ... .   .      ..  .  .  .   .  .      .........     . .   .... .       . ..   .......    ..      ...    .           ....        . ...  .     ...........   .  .  .  .  ............. .  .   ... .    .   . ..    ...    .     ......... ..  .    ..       ...       .    ..     ..         .           .    ...............  .      .            .  .  . .     .  ..........     .    .  .      .     . .   ..........    .     ....     .   ....  ..    ...   .     ...  ..    ........      . .        .          .......              .     ..         .           .  .     ... ..   ..        .....         .   ...    .. .   .   .   .. .      .   . .           .....      .       .      .     .. .   .   
lowQualScore                  :                                                          0   88  333   00       1      1 1        77 33              9     9  9 666 8 9  1       3  88888888888888888888888  6 66  6   6  000                6666   0   7       77     444444     77 7      111111     99        99       7   99  7    0   111111   3   5  5555555555  777  22  777 7   3      66  0  0  0   0  8      000000000     0 5   8888 0       0 55   8888888    88      555    0           0000        0 000  0     22222222222   2  0  0  5  0000000000000 0  5   888 0    0   2 22    555    0     000000000 22  5    88       777       0    00     77         7           3    000000000000000  7      7            2  0  2 0     0  8888888888     0    5  0      8     5 5   0000000000    8     0000     5   8888  00    555   0     222  88    00000000      0 7        3          0000000              0     33         7           7  3     000 00   00        33333         7   000    77 7   7   0   33 0      7   7 7           33333      0       0      3     77 0   5   
consensus                     :                                                      AAAG-AAAA-TAA--TCAC-AACGCCG-AAAATA-A-CTCAACCG--G--TTTCATTTTCAATC-TTCAA-GA-G-T-TAT-GA-CAATCGC-TT-----------------------AG-T--TA-CACATG---TTATCAACAATTTTTT----CTA-TGA-CATCAAA-TGCGCC------AAATTA-T-ATTTGC-GC---TTTAA--CAAAGTTC--ATTGTGA-CGT--CA-TAATATAAC---TGTTATGCCGTA-TATCGC-G-GC---AT--AT---CTGACTTTCTGAACTG-TG-CA-TGT-ACGAAAATA---TACAA-TATGT-ACAAT-A--TNATGGCAA-ATATAA-AN-A--TTAT--TAAATAT--AATGGAGGAGGGGGGAGT--TCACGTTT-G--TACTAACATA-TG--A----ATATAT-AATATAGTA-AC------TACG-GTGATAT-GANAAAATTATAAT-AAAT---AAAA-AAATA-A--A----AAAAAAAATT--GGGGGGGGGGAATTACGCCCTAC-CTCGCA-CAAATTACG-AAATATACAAA-ATGGTAAGTCATATATAAATTAATAATA-AGAGGGCATGCATAA-ATTG-TACAANATT-A-------TAATATTAATGGG-GGAAAAAAGGGGGGGGGG----GTCGT-CACGNTATTA---ACAATA-GTA-GANGAC-GTTT---AAA-CATAA-T-AT--GACA---GAT--GATTACCTGTAAAATAA-ATTCTGACCT-CTAAGTATAATGCGGGGAAAAGTTTC--GAAAATAAT-TTTTCAAAGAAGTTTACAATTGGTGNAGCA-TTTAGCGCAGGT-TTGTATCCT-CGA-A-AAACAAGTTTTTCTTTGTTTCAACGTTCTGTTTCCGTGGTATCTTTC---AAGAATTTTTAAAAGGGGAAAAC-GGTAAAGTTCGGTATG
Reference ( family-3078 )     :                                                      AAAG-AAAA-TAA--TCAC-AACGCCG-AAAATA-A-CTCAACCG--G--TTTCATTTTCAATC-TTCAA-GA-G-T-TNT-GA-CAATCGC-TT-----------------------AG-T--TA-CACATG---TTATCAACAATTTTTT----CTA-TGA-CATCAAA-NGCGCC------AAATTA-T-ATTTGC-GC---TTTAA--CAAAGTTC--ATTGTGA-CGT--CA-TAATNTAAC---TGTTATGCCGTATTATCGC-G-GC---AT--AT---CTGACTTTCTGAACTG-TG-CA-TGT-ACAAAAATA---TAC---TATGT-ACAAT-A--TNATGGCAA-ATATAA-AT-A--TTAT--TAAATAT--AATG-AGGAGGGGGGA----TCACGTTT-G--TATNAACATA-TG--A----ATATAT-AANATAGTA-AC------TACG-GTGATA--NANAAAATTATAAT-AAAT---AAAA-AAATA-A--A----AAAAAAAATT--GGGGGGGGGGAATTACGCCCTAC-CTCGCA-CAAATTACGAAAATATACAAA-ATGGNNNNNNNNNNNNNNNTTGATAATATAGAGGGCATGCATAA-ATTG-TACAATATT-A-------TAATATTAATGGG-GGAAAANAGGGGGGGGGG----GTN-T-CACGNTATTA---ACAATACGTA-GACGAN-ATTT---AAA-CATAA-T-AT--GACA---GAT--GATTACCTGTAAAATAA-ATTCTGACCTACNNNNTATAATGCGGGGAAANGTTTCTGGAAAATAATATTTTCAAAGAAGTTTACAATTGATNNAGCNNTTTAGCGCCGGTNTTGTATCCTTCGATATAAACAAGCTTTCCTTNGTTCCANCGTTCTGTTTCCGTGGTATCTTTCCCAAAGAATTTNTAAAAGGNGAAAACGGGTAAGNTCCGGTATG
gi|1                          :                                                      AAAG-AAAA-TAAGCCCACTAACGCCG-AAAATA-C-ATCAACCG--G--TTTCATTTTCAATC-TTCAACGA-G-T-TTT-GA-CAATCGC-TT-----------------------AG-T--TA-CACATG---TTA-CAACAATTTTTT----CTAATGA-CATCAAT-TGCGCC------AAATT--T-ATTTGCTGCCTCTTAAA--CAAAGTTC--ATTGTGA-CGT--CA-ATATATAAC---CGTTA-GCCGTATTATCGT-G-GC---AT--AT---CTGACTT-CTGA--TG-TG-CAATGTTACGAAAATA----AC---TATGTTACAAT-A--TAATGGCAA-ATATAA-ATTA--TTATCATAAGCA---AATG-AGGAGGGGGGAGTGTCCACGTTTTG--TACTAACATA-TG--A----ATATATTAATAT-GTA-AC------TAAG-GTGATA--GATAAAACTATAATTAAAT---AAAA-AAATA-A--ATAATAAAAAAAATT--GGGGGGGGGGAATTACGCCCTACGCTCGCAACAATCTACGAAAATATACAAAGATGGTAAGTCATATATAAATTAATAGCA-AGAGGGCATGCATAA-ATTGGTACAATAT--A-------TAATCCTAATGGGTGGAAAAAAGGGGGGGGGG----GTCAT-CACGTTATTA---ACAATACGTA-AAGGATCGTTT---AAA-CATAA-TTAT--AACACAGGAT--GAGTAC-TGTAAGATAACATTCTGACCTCCTAAG-ATATTGCGGGGAACAGTTTC--GAAAATAATATTTTCAAAGAAGTTTACAATTG-TGCAGCCATTTAGCGCCAGTTTAGTATCCT-CGA---AAACAAGTTTTTCTTTGTTTCAACGTTCTGTTTCCGTGGTATCTTTC----AGAATTTTGAATAGGGGAAAAC-GGTAAAGT
gi|10                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ATGCATAAGATTG-TACAATATT-AATATTATTAATATTAAT--G-GGAAAATAAGGGGGGGGGAAACGCC-CACACAATAGTATGTACAGTA-GTAGGGGGAA-ATTTAACAAA-CATAA---AT--GACA---GATG-GATTACtggatg
gi|11                         :                                                      AAAG-AAA--TA---TCAG-AATGCCA-AAAATA-A-CTCAACCA--G--TTTCATTTTCAATC-TTCAT-GA-G-T-TAT-GA--AA-CGC-TTGA---------------------AG-TGGTA-TA-GTG---TTA
gi|12                         :                        aacaatgtaatccttgtataataattatgatAAG-AAAA-TAA--TCA--AACGCCGGAAAATA-ATCTCAACCG--GT-TTTCA-TTTCAATC-TTCAA-AA-GTT-TAT-GATCAATCGC-TT-----------------------AG-T--TC-CATA
gi|13                         :                     aagatatgaagatatcaccaatatggtatccagAAAGCAAAACTAA--TCAC-AACGC-G-AAAATA-A-CTCAACCG--G--TT-CATTTTCAATC-TTCAA-GA-G---TAT-GA-
gi|14                         : tattataaataatccaaaatatatgtagaatatccacacaagtaatggataatAAAG-AAAA-TAA--TCAC-AACGCCG-AAAATA-A-CTCAACCG--G--TTT
gi|15                         :                       atatatataatgcaaactatatgtaaatatccacaccagtaatggtatatataatCTG-AAAATA-A-CTCCACCG--G--TATCATTTTTAATC-TTCAA-AA-G-T-TAT-GG-CAATCGC-TT-----------------------AG-C--TA-CACATG---TT------AATTTTTT----TTA-
gi|16                         :                                                      AAAA-AGAA-TAA--TCAC-AACGCCG-AAAATA-A-CTCAACCG--G--TTGAGTTTTCACTC-TTCAA--A-G-A-TA--GA-CAAgtat
gi|17                         :                                         tatatttaaattatAAG-AAAA-TAA--TCA--AACGCCG-AAAATA-A--TCAACCG--GTTTTTC-TTTTCAATC-TTCAA-GA-GTT-TAT-GA-CAATCGC-TT-----------------------A
gi|18                         :                                                                                 -AAAATA-A-CCCAACC------TTTCATTTTCAATC-TTGAG-GA-T-TATAT-GA-CAATTGC-AT-----------------------TG-T--TA-CAC--G---TTATCAAC
gi|19                         :                                                     aAAAG-AAA--TA---TCAT-AACACC---AAATGCA-TT--------G--TTTCATTTTCAATC-TTCAA-GAGG-T-TAT-
gi|2                          :                                                 ataatAAAG-AAAA-TAA--TCAC-AACGCCG-AAAA-A-A-CTCAACCGCGG--TTTCATTTTCAATC-TTCAA-GA-G-T-TATTGA-CAACCGCCTT-----------------------AG-T--TA-CACATT---GTATCAACAATTTTTT----CTA-TGA-CATTAAATGGCGTC------AATTTA-TGATTTGC-GCTT-TTTAACCCAAAGTTC--ATTGTGA-CGT--CA-TAATTTAAC----GTTA------ATTA-CGC-T-GC---AT--AT---CTGACTTTCTGGACTGTTGCCA-TGT-ACAAAAATA---TACAA-TATGT-ACAATAA--TAATGGCAA-AT-TGA-AA-A--TTAT--TAAATAT--AATA-AGGGAGGAGGA----TCATATTT-GGTTATAAACATA-GGGAA----ATATAT-GATAT-GT--AC------CACG-GTGATA--GATAAAA--AT-AT-TAAT---AAAA-AAATA-A--A----A-----------GGAGGGG------TACA-CCTAC-TTGGCA-CAAATTACG-AAATATACAAA-ATGGtattg
gi|22                         :                                  caaaatatatgtaaatatcacacaagtaatggtataatC-AACGCCG-AAAATA-A-CTCAACCG--G--TTTC
gi|3                          :                                                      AAAG-AAAA-TAAT-TCA--AACGCCG-AAAATA-A-CTCAACCG--G--TTTCAATTTCAAACTTTCAA-G------TAT-GA-C-ATCGC-TTC----------------------A-----TA-CAC-TG---TTATCAACAA---TTT----CTA-T-A-CATCCAA-TGACCC------AAATTA-T-ATTTGC--C---TTTAA--CAAA-TTC--CTT-T-A-CGT--CA-TAATATAAC------TCTGCC-TA-TAT-AC-GTGC---ATTAAT---C-GAC--TCTGA-----TG-CA-TGT-ACAAAAATA---TAC---AATAG-ACAAT-A--ATATGGCAA-A-ATAA-AT-AATTTAT--TAAATATAAAATGAAGGAGCGGGGA----TCACGTTT-G---ACTAACAT--TA--A----ATA----AGCATAGTACAC------T--G-GT-ATAT-TAAAAAATTTTAA--AAATTAAAAAA-AAAAA-A--A----AAAAAAAATT--GGGGGGGGTAAATTACGTCCTA--CTCAC--CAAATTACG-AAATATACAAA-
gi|4                          :                                                                                                    taataaatccaaataatgtaaaatccacacagtaattataatTCGC-TT-----------------------AG-TG-TAGCAGTTGGTTTTATTACTAATTTTTTTTCTCTA-TGATCAT--AA-TGTGTCGCGCAAAAATTAGT-ATTTGC-GC---TTACA--CATAGTTCCAATTGTGATCGTTTCGCTAATGTAACGTATGGTGTGGCGTA--ATTAC-T-GC---AT--ATATTCTGACTTTCTGGA-TG-TG-CA-TGT-ATCAAAATAACCTACAATTATGT-A--AT-AACTCATGGCAACATATAATAA-A--TTAT--TATATAA--AAGGGAGGAGGGGGGGGT--TCACGTTT-G--TATCAACATACTG--ACCATATATAT-AAGATAGTT-ACCTCACATACGCGTAGTATCAAGAAAATTATAATGAAAC---AAAATAAATATACCA----AACAATAATTCCGGGGGGGGGt
gi|5                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              TGATAATA-AGAGGGCATGCATAA-ATTG-TACAAAATTTA-------TAATATTAATGGG-GGAAAA--GGGGGGCGGG----ATAGT-AATG--ATTA----CAATA-GTA-GATGAC-ATTT---AAAGCATAAAT-AT--GACA---GTTTTGATTACCTGTAAAATAA-ATTTTGACCTACGTA-TATAATGCGGGGAAATGTTTCTGGAAAATAAT-TTTTCAAAGAA-TTTACAATTGATGTAGCATTTTAGCGCAGGTGTTGTATCCTTCGA-ATAAAC-AGTTTTCTTTTGTTTCACCGTTCTGTTT-CGTGGTATCTTTC---AAGAATTTTTAAAAGGGGAAAACGGGTAAAGTTCGG-ATG
gi|6                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            aTTAATAATATAAAAGGCATGCA--A-AT-G-TACAAATTT-A-------TAATA---ATGGG-GGAAAAAAGGGG------------A-T-CATAGTATTA----CAATA--TA--ACGAC-GGTT---TAA-CATAA-T-ATATGACA---GA---GATTACTT----AATAA-ATTCTGACTT--TACGTATAATGCGGGGAAAAGTTTC--GAAAATAAT--TTTCAAAGAAGTT-ACAAT--GTCGAGCA-TTTAGCGCAG---TTGTATCCT-CAATA--AACA-GCTTTTCTTGGTTC--ACGTTCT-TTTCC-TAGTATCTTTTCCAA-GAATTTGTAAAAGGTAAAAAC-GGTAAGTT-CGGTATGa
gi|7                          :                                                                                                               TTTAATC-TTCAA-GA-G-T-TAT-GA-CAATCGC-TTTATAGTTAATATAATATAGTAATAG-T--TA-CACATT---TTATCAACAGTTTTTTA---CTA-TGA-CATCAAA-AGCGCC------AGATTA-T-ATTTGC-AG---TTTAA--CAAAGTTC--ATTGTGA-CAT--TA-TGATTTAA----TGTTATGCCGTAATACCGCTG-GCCAAGT--GT---CCAATTTTCa
gi|8                          :                                                                                                 CA--G--TTTCATTTTCAAAC-TTCAA-CA-G-T-T--------ATCGC-TT-----------------------AG-T--TA-CACATG---TTATCAACAATTGTTT----CTA-TGA-CATCAAA-TACGCC------AAATTA-T-ATTTGC-TC---TTTAA--CAAAGTTC--ATTGTGA-CGT--CA-TAATATAAC---T-TCATGCCGTA--ATCAC-GTGC---CT--AC---CTGAC-TTCTGAACTG-TG-
gi|9                          :                                                                                               ACCG--G--TTTCTTGTTCAATC-TTCAA-GA-G-T-TAT-AA-CAATCGC-TT-----------------------AGTT--TA-CACAT----TTATCAACATTTTTTT----CT--TGA-TATCAAA-TGCGCC------AAATT--T-ATTTGC-GC---TTTAA--CAGAGTTA--GTTGTGA-CGT--CA-TAATATAA----TGTT

Unaligned ( gi|20 ): AATATATAATCCAAAATATATGTAAATATCCACACAATTAATGGTATA
Unaligned ( gi|21 ): TAGAATCCAAAATATATTTAAATATCCACACAAGTAATGGTATAA

lowQualScore                  :                                                                  111   11                                                                           33333333333333333333333                                  1111                      111111     11        111111                                           222222           11     111  111      111            22      111   1         2222     1   11     1111         1      1111111    11      222    1          33333        1 111        33333333333      1     1  3333333333333 1      222            22    111    1     222222222          11                 1    22     22            1        1                            1               1    1        3333333333             1      11          222222222    1     3333     11  11    1     111   1     222  11    33333333      1          1          3333333                    11        22           11       22      1     1       111  1       1  222    11                            11          11                        1            1   
lowQualScore                  :                                                          4   44  000   11       3      3 3        33 66              2     2  2 666   2  3       3  88888888888888888888888  3 88  3   3  777                5555   5   5         5    666666     00 5      222222   77   77       77       5   77  5    0   222222   7   2 6 44  1  888  111  99  111 1   7      00   8  111   0  4      0000  3  0 3 33 2   4444 1       0 66   6666666    33      333    0          22222        0 777  1     00000000000   3  0  0  5  0000000000000 0  6   555 1    7   3 33    777    0     777777777 66  3    33       888       2    00     00            3        3                            3            3  0  3 0     1  6666666666     7    2  0      33      55  333333333    0     3333     22  66 1  0     777   0     333  33    22222222      2 6        3          0000000                    88        00           44       22   1  3     3       999  3       3  000    44              6        6    33          88 7                      3   7        5   
lowQualScore                  :                                                          .   ..  ...   ..       .      . .        .. ..              .     .  . ...   .  .       .  .......................  . ..  .   .  ...                ....   .   .         .    ......     .. .      ......   ..   ..       ..       .   ..  .    .   ......   .   . . ..  .  ...  ...  ..  ... .   .      ..   .  ...   .  .      ....  .  . . .. .   .... .       . ..   .......    ..      ...    .          .....        . ...  .     ...........   .  .  .  .  ............. .  .   ... .    .   . ..    ...    .     ......... ..  .    ..       ...       .    ..     ..            .        .                            .            .  .  . .     .  ..........     .    .  .      ..      ..  .........    .     ....     ..  .. .  .     ...   .     ...  ..    ........      . .        .          .......                    ..        ..           ..       ..   .  .     .       ...  .       .  ...    ..              .        .    ..          .. .                      .   .        .   
lowQualScore                  :                                                          0   88  333   00       1      1 1        77 33              9     9  9 666   9  1       3  88888888888888888888888  6 66  6   6  000                6666   0   7         7    444444     77 7      333333   99   99       99       7   99  7    6   111111   3   5 7 00  0  333  777  22  777 7   3      66   0  000   0  2      8888  2  0 2 22 5   8888 0       0 55   8888888    88      555    5          55555        0 000  2     22222222222   2  0  8  5  0000000000000 0  5   888 0    0   2 22    555    0     000000000 22  5    88       777       0    00     77            3        3                            3            2  0  2 0     0  8888888888     0    5  0      22      00  000000000    8     0000     55  55 0  0     555   0     222  88    00000000      0 7        3          7777777                    33        77           00       33   0  3     3       000  3       3  333    77              7        7    33          33 3                      3   3        5   
consensus                     :                                                      AAAG-AAAA-TAA--TCAC-AACGCCG-AAAATA-A-CTCAACCG--G--TTTCATTTTCAATC-TTCAA-GA-G-T-TAT-GA-CAATCGC-TT-----------------------AG-T--TA-CACATG---TTATCAACAATTTTTT----CTA-TGA-CATCAAATG-CGCC------AAATTA-T-ATTTGC-GC---TTT--AAC--AAAGTTC--ATTGTGA-CGT--CA-TAATATAAC---TGTTATGCCGT-AT-ATCGC-G-GC---AT--AT---CTGACTTTCTGAACTGT-GC-A-TGT-ACGAAAATA---TACAAT-ATGT-ACAAT-A--TNATGGCAA-ATATAA-AN-A--TTAT--TAAATAT--AATGAAGGAGGGGGGAGT--TCACGTTT-G--TACTAACATA-TG--A----ATATAT-AATATAGTA-AC------TACG-GTGATAT-GANAAAATTATAAT-AAAT---AAAA-AAATA-A--A----AAAAAAAATT--GGGGGGGGGGAATTACGCCCTAC-CTCGCA-CAAATTACGAAA-TATACAAA-ATGGTAAGTCATATATAAATTAATAATA-AGAGGGCATGCATAA-ATTG-TACAANATT-A-------TAATATTAATGGG-GGAAAA-AAGGGGGGGGGGATCGT---CACGNTATTA---ACAATA-GTA-GANGA-CGTTT---AAA-CATAA-T-AT--GACA---GAT--GATTACCTGTAAAATAA-ATTCTGACCT--TANGTATAATGCGGGGAAAAGTTTC--GAAAATAAT-TTTTCAAAGAAGTTTACAATT-GTGNAG-CATTT-AGCGCAGGT-TT-GTATCCT-CGAA-AAACAAGTTTTTCTTTGTTTCAACGTTCTGTTTCCGTGGTATCTTT--CAAGAATTTTTAAAAGGGGAAAAC-GGTAAAGTTCGGTATG
Reference ( family-3078 )     :                                                      AAAG-AAAA-TAA--TCAC-AACGCCG-AAAATA-A-CTCAACCG--G--TTTCATTTTCAATC-TTCAA-GA-G-T-TAT-GA-CAATCGC-TT-----------------------AG-T--TA-CACATG---TTATCAACAATTTTTT----CTA-TGA-CATCAAATG-CGCC------AAATTA-T-ATTTGC-GC---TTT--AAC--AAAGTTC--ATTGTGA-CGT--CA-TAATATAAC---TGTTATGCCGT-AT-ATCGC-G-GC---AT--AT---CTGACTTTCTGAACTGT-GC-A-TGT-ACGAAAATA---TACAAT-ATGT-ACAAT-A--TNATGGCAA-ATATAA-AN-A--TTAT--TAAATAT--AATGGAGGAGGGGGGAGT--TCACGTTT-G--TACTAACATA-TG--A----ATATAT-AATATAGTA-AC------TACG-GTGATAT-GANAAAATTATAAT-AAAT---AAAA-AAATA-A--A----AAAAAAAATT--GGGGGGGGGGAATTACGCCCTAC-CTCGCA-CAAATTACGAAA-TATACAAA-ATGGTAAGTCATATATAAATTAATAATA-AGAGGGCATGCATAA-ATTG-TACAANATT-A-------TAATATTAATGGG-GGAAAA-AAGGGGGGGGGGGTCGT---CACGNTATTA---ACAATA-GTA-GANGA-CGTTT---AAA-CATAA-T-AT--GACA---GAT--GATTACCTGTAAAATAA-ATTCTGACCTC-TAAGTATAATGCGGGGAAAAGTTTC--GAAAATAAT-TTTTCAAAGAAGTTTACAATTGGTGNAG-CATTT-AGCGCAGGT-TT-GTATCCT-CGAA-AAACAAGTTTTTCTTTGTTTCAACGTTCTGTTTCCGTGGTATCTTT--CAAGAATTTTTAAAAGGGGAAAAC-GGTAAAGTTCGGTATG
gi|1                          :                                                      AAAG-AAAA-TAAGCCCACTAACGCCG-AAAATA-C-ATCAACCG--G--TTTCATTTTCAATC-TTCAACGA-G-T-TTT-GA-CAATCGC-TT-----------------------AG-T--TA-CACATG---TTA-CAACAATTTTTT----CTAATGA-CATCAATTG-CGCC------AAATT--T-ATTTGCTGCCTCTTA--AAC--AAAGTTC--ATTGTGA-CGT--CA-ATATATAAC---CGTTA-GCCGT-ATTATCGT-G-GC---AT--AT---CTGACTT-CTGA--TGT-GC-AATGTTACGAAAATA----AC--T-ATGTTACAAT-A--TAATGGCAA-ATATAA-ATTA--TTATCATAAGCA---AATG-AGGAGGGGGGAGTGTCCACGTTTTG--TACTAACATA-TG--A----ATATATTAATAT-GTA-AC------TAAG-GTGATA--GATAAAACTATAATTAAAT---AAAA-AAATA-A--ATAATAAAAAAAATT--GGGGGGGGGGAATTACGCCCTACGCTCGCAACAATCTACGAAAATATACAAAGATGGTAAGTCATATATAAATTAATAGCA-AGAGGGCATGCATAA-ATTGGTACAATAT--A-------TAATCCTAATGGGTGGAAAA-AAGGGGGGGGGGGTCAT---CACGTTATTA---ACAATACGTA-AAGGATCGTTT---AAA-CATAA-TTAT--AACACAGGAT--GAGTAC-TGTAAGATAACATTCTGACCTCCTAAG-ATATTGCGGGGAACAGTTTC--GAAAATAATATTTTCAAAGAAGTTTACAATT-GTGCAGCCATTT-AGCGCCAGT-TTAGTATCCT-CG-A-AAACAAGTTTTTCTTTGTTTCAACGTTCTGTTTCCGTGGTATCTTT--C-AGAATTTTGAATAGGGGAAAAC-GGTAAAGTT
gi|10                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 ATGCATAAGATTG-TACAATATT-AATATTATTAATATTAAT--G-GGAAAATAAGGGGGGGGGAAACGCCCACACAATAGTATGTACAGTA-GTAGGGGGA-AATTTAACAAA-CATAA---AT--GACA---GATG-GATTACggatg
gi|11                         :                                                      AAAG-AAA--TA---TCAG-AATGCCA-AAAATA-A-CTCAACCA--G--TTTCATTTTCAATC-TTCAT-GA-G-T-TAT-GA--AA-CGC-TTGA---------------------AG-TGGTA-TA-GTG---TTA
gi|12                         :                        aacaatgtaatccttgtataataattatgatAAG-AAAA-TAA--TCA--AACGCCGGAAAATA-ATCTCAACCG--GT-TTTCA-TTTCAATC-TTCAA-AA-GTT-TAT-GATCAATCGC-TT-----------------------AG-T--TC-CATA
gi|13                         :                     aagatatgaagatatcaccaatatggtatccagAAAGCAAAACTAA--TCAC-AACGC-G-AAAATA-A-CTCAACCG--G--TT-CATTTTCAATC-TTCAA-GA-G---TAT-GA-
gi|14                         : tattataaataatccaaaatatatgtagaatatccacacaagtaatggataatAAAG-AAAA-TAA--TCAC-AACGCCG-AAAATA-A-CTCAACCG--G--TTT
gi|15                         :                       atatatataatgcaaactatatgtaaatatccacaccagtaatggtatatataatCTG-AAAATA-A-CTCCACCG--G--TATCATTTTTAATC-TTCAA-AA-G-T-TAT-GG-CAATCGC-TT-----------------------AG-C--TA-CACATG---TT------AATTTTTT----TTA-
gi|16                         :                                                      AAAA-AGAA-TAA--TCAC-AACGCCG-AAAATA-A-CTCAACCG--G--TTGAGTTTTCACTC-TTCAA--A-G-A-TA--GA-CAAgtat
gi|17                         :                                         tatatttaaattatAAG-AAAA-TAA--TCA--AACGCCG-AAAATA-A--TCAACCG--GTTTTTC-TTTTCAATC-TTCAA-GA-GTT-TAT-GA-CAATCGC-TT-----------------------A
gi|18                         :                                                                                 -AAAATA-A-CCCAACC------TTTCATTTTCAATC-TTGAG-GA-T-TATAT-GA-CAATTGC-AT-----------------------TG-T--TA-CAC--G---TTATCAAC
gi|19                         :                                                     aAAAG-AAA--TA---TCAT-AACACC---AAATGCA-TT--------G--TTTCATTTTCAATC-TTCAA-GAGG-T-TAT-
gi|2                          :                                                 ataatAAAG-AAAA-TAA--TCAC-AACGCCG-AAAA-A-A-CTCAACCGCGG--TTTCATTTTCAATC-TTCAA-GA-G-T-TATTGA-CAACCGCCTT-----------------------AG-T--TA-CACATT---GTATCAACAATTTTTT----CTA-TGA-CATTAAATGGCGTC------AATTTA-TGATTTGC-GC---TTTTTAACCCAAAGTTC--ATTGTGA-CGT--CA-TAATTTAAC----GTTA-------AT-TACGC-T-GC---AT--AT---CTGACTTTCTGGACTGTTGCCA-TGT-ACAAAAATA---TACAAT-ATGT-ACAATAA--TAATGGCAA-AT-TGA-AA-A--TTAT--TAAATAT--AATAAGGGAGGAGGA-----TCATATTT-GGTTATAAACATA-GGGAA----ATATAT-GATAT-GT--AC------CACG-GTGATA--GATAAAA--AT-AT-TAAT---AAAA-AAATA-A--A----A-----------GGAGGGG------TACA-CCTAC-TTGGCA-CAAATTACGAAA-TATACAAA-ATGGtattg
gi|22                         :                                  caaaatatatgtaaatatcacacaagtaatggtataatC-AACGCCG-AAAATA-A-CTCAACCG--G--TTTC
gi|3                          :                                                      AAAG-AAAA-TAAT-TCA--AACGCCG-AAAATA-A-CTCAACCG--G--TTTCAATTTCAAACTTTCAA-G------TAT-GA-C-ATCGC-TTC----------------------A-----TA-CAC-TG---TTATCAACAA---TTT----CTA-T-A-CATCCAATG-ACCC------AAATTA-T-ATTTGC--C---TTT--AAC--AAA-TTC--CTT-T-A-CGT--CA-TAATATAAC------TCTGCC-T-AT-AT-AC-GTGC---ATTAAT---C-GAC--TCTGA----T-GC-A-TGT-ACAAAAATA---TACAAT-A-G--ACAAT-A--ATATGGCAA-A-ATAA-AT-AATTTAT--TAAATATAAAATGAAGGAGCGGGGA----TCACGTTT-G---ACTAACAT--TA--A----ATA----AGCATAGTACAC------T--G-GT-ATAT-TAAAAAATTTTAA--AAATTAAAAAA-AAAAA-A--A----AAAAAAAATT--GGGGGGGGTAAATTACGTCCTA--CTCAC--CAAATTACGAAA-TATACAAA-
gi|4                          :                                                                                                    taataaatccaaataatgtaaaatccacacagtaattataatTCGC-TT-----------------------AG-TG-TAGCAGTTGGTTTTATTACTAATTTTTTTTCTCTA-TGATCAT--AATG-TGTCGCGCAAAAATTAGT-ATTTGC-GC---TTA--CAC--ATAGTTCCAATTGTGATCGTTTCGCTAATGTAACGTATGGTGTGGCGT-A--ATTAC-T-GC---AT--ATATTCTGACTTTCTGGA-TGT-GC-A-TGT-ATCAAAATAACCTACAATTATGT-A--AT-AACTCATGGCAACATATAATAA-A--TTAT--TATATAA--AAGGGAGGAGGGGGGGGT--TCACGTTT-G--TATCAACATACTG--ACCATATATAT-AAGATAGTT-ACCTCACATACGCGTAGTATCAAGAAAATTATAATGAAAC---AAAATAAATATACCA----AACAATAATTCCGGGGGGGGGt
gi|5                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 TGATAATA-AGAGGGCATGCATAA-ATTG-TACAAAATTTA-------TAATATTAATGGG-GGAAAA---GGGGGGCGGGATAGT---AATG--ATTA----CAATA-GTA-GATGA-CATTT---AAAGCATAAAT-AT--GACA---GTTTTGATTACCTGTAAAATAA-ATTTTGACCTA-CGTATATAATGCGGGGAAATGTTTCTGGAAAATAAT-TTTTCAAAGAA-TTTACAATTGATGTAG-CATTTTAGCGCAGGTGTT-GTATCCTTCGAATAAACA-GTTTTCTTTTGTTTCACCGTTCTGTTTC-GTGGTATCTTT--CAAGAATTTTTAAAAGGGGAAAACGGGTAAAGTTCGG-ATG
gi|6                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               aTTAATAATATAAAAGGCATGCA--A-AT-G-TACAAATTT-A-------TAATA---ATGGG-GGAAAA-AAGGGGA---------T---CATAGTATTA----CAATA--TA--ACGA-CGGTT---TAA-CATAA-T-ATATGACA---GA---GATTACTT----AATAA-ATTCTGACTT--TACGTATAATGCGGGGAAAAGTTTC--GAAAATAA--TTTTCAAAGAAG-TTACAAT--GTCGAG-CATTT-AGCGCAG---TT-GTATCCT-CAAT-AAAC-AGCTTTTCTTGGTTC--ACGTTCT-TTTCC-TAGTATCTTTTCCAAGAATTTGTAAAAGGTAAAAAC-GGT-AAGTTCGGTATGa
gi|7                          :                                                                                                               TTTAATC-TTCAA-GA-G-T-TAT-GA-CAATCGC-TTTATAGTTAATATAATATAGTAATAG-T--TA-CACATT---TTATCAACAGTTTTTTA---CTA-TGA-CATCAAAAG-CGCC------AGATTA-T-ATTTGC-AG---TTT--AAC--AAAGTTC--ATTGTGA-CAT--TA-TGATTTAA----TGTTATGCCGTAAT-ACCGCTG-GCCAAGT--GT---CCAATTTTCa
gi|8                          :                                                                                                 CA--G--TTTCATTTTCAAAC-TTCAA-CA-G-T-TAT--------CGC-TT-----------------------AG-T--TA-CACATG---TTATCAACAATTGTTT----CTA-TGA-CATCAAATA-CGCC------AAATTA-T-ATTTGC-TC---TTT--AAC--AAAGTTC--ATTGTGA-CGT--CA-TAATATAAC---T-TCATGCCGT-A--ATCAC-GTGC---CT--AC---CTGAC-TTCTGAACTGT-G
gi|9                          :                                                                                               ACCG--G--TTTCTTGTTCAATC-TTCAA-GA-G-T-TAT-AA-CAATCGC-TT-----------------------AGTT--TA-CACAT----TTATCAACATTTTTTT----CT--TGA-TATCAAATG-CGCC------AAATT--T-ATTTGC-GC---TTT--AAC--AGAGTTA--GTTGTGA-CGT--CA-TAATATAA----TGTT

Unaligned ( gi|20 ): AATATATAATCCAAAATATATGTAAATATCCACACAATTAATGGTATA
Unaligned ( gi|21 ): TAGAATCCAAAATATATTTAAATATCCACACAAGTAATGGTATAA

lowQualScore                  :                                                                  111   11                                                                           33333333333333333333333                                  1111                      111111     11        111111                                           222222           11     111  111      111            22      111   1         2222     1   11     1111         1      1111111    11      222               33333        1 111        33333333333      1     1  3333333333333 1      222            22    111    1     222222222          11                 1    22     22            1        1                            1               1  11          333333333             1      11          111111111    1     3333     11  11    1     111   1     22  11    33333333                 1          222       11                 11        22           11         1     1     1       111  1       1  222    11                            11          11                        1            1   
lowQualScore                  :                                                          4   44  000   11       3      3 3        33 66              2     2  2 666   2  3       3  88888888888888888888888  3 88  3   3  777                5555   5   5         5    666666     00 5      222222   77   77       77       5   77  5    0   222222   7   2 6 44  1  888  111  99  111 1   7      00   8  111   0  4      0000  3  0 3 33 2   4444 1       0 66   6666666    33      333     7         22222        0 777  1     00000000000   3  0  0  5  0000000000000 0  6   555 1    7   3 33    777    0     777777777 66  3    33       888       2    00     00            3        3                            3            3  0  33      1 3 333333333     7    2  0      33      55  999999999    0     3333     22  66 1  0     777   0     33  33    22222222     2  6        3          555 1 7   88                 88        00           44      7  3  1  3     3       999  3       3  000    44              6        6    33          88 7                      3   7        5   
lowQualScore                  :                                                          .   ..  ...   ..       .      . .        .. ..              .     .  . ...   .  .       .  .......................  . ..  .   .  ...                ....   .   .         .    ......     .. .      ......   ..   ..       ..       .   ..  .    .   ......   .   . . ..  .  ...  ...  ..  ... .   .      ..   .  ...   .  .      ....  .  . . .. .   .... .       . ..   .......    ..      ...     .         .....        . ...  .     ...........   .  .  .  .  ............. .  .   ... .    .   . ..    ...    .     ......... ..  .    ..       ...       .    ..     ..            .        .                            .            .  .  ..      . . .........     .    .  .      ..      ..  .........    .     ....     ..  .. .  .     ...   .     ..  ..    ........     .  .        .          ... . .   ..                 ..        ..           ..      .  .  .  .     .       ...  .       .  ...    ..              .        .    ..          .. .                      .   .        .   
lowQualScore                  :                                                          0   88  333   00       1      1 1        77 33              9     9  9 666   9  1       3  88888888888888888888888  6 66  6   6  000                6666   0   7         7    444444     77 7      333333   99   99       99       7   99  7    6   111111   3   5 7 00  0  333  777  22  777 7   3      66   0  000   0  2      8888  2  0 2 22 5   8888 0       0 55   8888888    88      555     0         55555        0 000  2     22222222222   2  0  8  5  0000000000000 0  5   888 0    0   2 22    555    0     000000000 22  5    88       777       0    00     77            3        3                            3            2  0  22      0 2 555555555     0    5  0      22      00  555555555    8     0000     55  55 0  0     555   0     22  88    00000000     5  7        3          777 0 3   33                 33        77           00      3  3  0  3     3       000  3       3  333    77              7        7    33          33 3                      3   3        5   
consensus                     :                                                      AAAG-AAAA-TAA--TCAC-AACGCCG-AAAATA-A-CTCAACCG--G--TTTCATTTTCAATC-TTCAA-GA-G-T-TAT-GA-CAATCGC-TT-----------------------AG-T--TA-CACATG---TTATCAACAATTTTTT----CTA-TGA-CATCAAATG-CGCC------AAATTA-T-ATTTGC-GC---TTT--AAC--AAAGTTC--ATTGTGA-CGT--CA-TAATATAAC---TGTTATGCCGT-AT-ATCGC-G-GC---AT--AT---CTGACTTTCTGAACTGT-GC-A-TGT-ACGAAAATA---TACAAT-ATGT-ACAAT-A--TNATGGCAA-ATATAA-AN-A--TTAT--TAAATAT--AATGAAGGAGGGGGGAGT--TCACGTTT-G--TACTAACATA-TG--A----ATATAT-AATATAGTA-AC------TACG-GTGATAT-GANAAAATTATAAT-AAAT---AAAA-AAATA-A--A----AAAAAAAATT--GGGGGGGGGGAATTACGCCCTAC-CTCGCA-CAAATTACGAAA-TATACAAA-ATGGTAAGTCATATATAAATTAATAATA-AGAGGGCATGCATAA-ATT-GTACAANATT-A-------TAATATTAATGGG-GGAAAA-AAGGGGGGGGGGATCGT---CACGNTATTA---ACAATA-GTA-GANGA-CGTTT---AAA-CATAA-TAT--GACA---GAT--GATTACCTGTAAAATAA-ATTCTGACCT--TACGTATA--ATGCGGGGAAAAGTTTC--GAAAATAAT-TTTTCAAAGAAGTTTACAATTG-TGNAG-CATTT-AGCGCAGGT-TT-GTATCCT-CGAA-AAACAAGTTTTTCTTTGTTTCAACGTTCTGTTTCCGTGGTATCTTT--CAAGAATTTTTAAAAGGGGAAAAC-GGTAAAGTTCGGTATG
Reference ( family-3078 )     :                                                      AAAG-AAAA-TAA--TCAC-AACGCCG-AAAATA-A-CTCAACCG--G--TTTCATTTTCAATC-TTCAA-GA-G-T-TAT-GA-CAATCGC-TT-----------------------AG-T--TA-CACATG---TTATCAACAATTTTTT----CTA-TGA-CATCAAATG-CGCC------AAATTA-T-ATTTGC-GC---TTT--AAC--AAAGTTC--ATTGTGA-CGT--CA-TAATATAAC---TGTTATGCCGT-AT-ATCGC-G-GC---AT--AT---CTGACTTTCTGAACTGT-GC-A-TGT-ACGAAAATA---TACAAT-ATGT-ACAAT-A--TNATGGCAA-ATATAA-AN-A--TTAT--TAAATAT--AATGAAGGAGGGGGGAGT--TCACGTTT-G--TACTAACATA-TG--A----ATATAT-AATATAGTA-AC------TACG-GTGATAT-GANAAAATTATAAT-AAAT---AAAA-AAATA-A--A----AAAAAAAATT--GGGGGGGGGGAATTACGCCCTAC-CTCGCA-CAAATTACGAAA-TATACAAA-ATGGTAAGTCATATATAAATTAATAATA-AGAGGGCATGCATAA-ATT-GTACAANATT-A-------TAATATTAATGGG-GGAAAA-AAGGGGGGGGGGATCGT---CACGNTATTA---ACAATA-GTA-GANGA-CGTTT---AAA-CATAA-TAT--GACA---GAT--GATTACCTGTAAAATAA-ATTCTGACCT--TANGTATA--ATGCGGGGAAAAGTTTC--GAAAATAAT-TTTTCAAAGAAGTTTACAATTG-TGNAG-CATTT-AGCGCAGGT-TT-GTATCCT-CGAA-AAACAAGTTTTTCTTTGTTTCAACGTTCTGTTTCCGTGGTATCTTT--CAAGAATTTTTAAAAGGGGAAAAC-GGTAAAGTTCGGTATG
gi|1                          :                                                      AAAG-AAAA-TAAGCCCACTAACGCCG-AAAATA-C-ATCAACCG--G--TTTCATTTTCAATC-TTCAACGA-G-T-TTT-GA-CAATCGC-TT-----------------------AG-T--TA-CACATG---TTA-CAACAATTTTTT----CTAATGA-CATCAATTG-CGCC------AAATT--T-ATTTGCTGCCTCTTA--AAC--AAAGTTC--ATTGTGA-CGT--CA-ATATATAAC---CGTTA-GCCGT-ATTATCGT-G-GC---AT--AT---CTGACTT-CTGA--TGT-GC-AATGTTACGAAAATA----AC--T-ATGTTACAAT-A--TAATGGCAA-ATATAA-ATTA--TTATCATAAGCA---AATGA-GGAGGGGGGAGTGTCCACGTTTTG--TACTAACATA-TG--A----ATATATTAATAT-GTA-AC------TAAG-GTGATA--GATAAAACTATAATTAAAT---AAAA-AAATA-A--ATAATAAAAAAAATT--GGGGGGGGGGAATTACGCCCTACGCTCGCAACAATCTACGAAAATATACAAAGATGGTAAGTCATATATAAATTAATAGCA-AGAGGGCATGCATAA-ATTGGTACAATA-T-A-------TAATCCTAATGGGTGGAAAA-AAGGGGGGGGGGGTCAT---CACGTTATTA---ACAATACGTA-AAGGATCGTTT---AAA-CATAATTAT--AACACAGGAT--GAGTA-CTGTAAGATAACATTCTGACCTCCTAAG-ATA--TTGCGGGGAACAGTTTC--GAAAATAATATTTTCAAAGAAGTTTACAATTG-TGCAGCCATTT-AGCGCCAGT-TTAGTATCCT-CG-A-AAACAAGTTTTTCTTTGTTTCAACGTTCTGTTTCCGTGGTATCTTT--C-AGAATTTTGAATAGGGGAAAAC-GGTAAAGTT
gi|10                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 ATGCATAAGATT-GTACAATATT-AATATTATTAATATTAAT--G-GGAAAATAAGGGGGGGGGAAACGCCCACACAATAGTATGTACAGTA-GTAGGGGGA-AATTTAACAAA-CATAA--AT--GACA---GATG-GATTACggatg
gi|11                         :                                                      AAAG-AAA--TA---TCAG-AATGCCA-AAAATA-A-CTCAACCA--G--TTTCATTTTCAATC-TTCAT-GA-G-T-TAT-GA--AA-CGC-TTGA---------------------AG-TGGTA-TA-GTG---TTA
gi|12                         :                        aacaatgtaatccttgtataataattatgatAAG-AAAA-TAA--TCA--AACGCCGGAAAATA-ATCTCAACCG--GT-TTTCA-TTTCAATC-TTCAA-AA-GTT-TAT-GATCAATCGC-TT-----------------------AG-T--TC-CATA
gi|13                         :                     aagatatgaagatatcaccaatatggtatccagAAAGCAAAACTAA--TCAC-AACGC-G-AAAATA-A-CTCAACCG--G--TT-CATTTTCAATC-TTCAA-GA-G---TAT-GA-
gi|14                         : tattataaataatccaaaatatatgtagaatatccacacaagtaatggataatAAAG-AAAA-TAA--TCAC-AACGCCG-AAAATA-A-CTCAACCG--G--TTT
gi|15                         :                       atatatataatgcaaactatatgtaaatatccacaccagtaatggtatatataatCTG-AAAATA-A-CTCCACCG--G--TATCATTTTTAATC-TTCAA-AA-G-T-TAT-GG-CAATCGC-TT-----------------------AG-C--TA-CACATG---TT------AATTTTTT----TTA-
gi|16                         :                                                      AAAA-AGAA-TAA--TCAC-AACGCCG-AAAATA-A-CTCAACCG--G--TTGAGTTTTCACTC-TTCAA--A-G-A-TA--GA-CAAgtat
gi|17                         :                                         tatatttaaattatAAG-AAAA-TAA--TCA--AACGCCG-AAAATA-A--TCAACCG--GTTTTTC-TTTTCAATC-TTCAA-GA-GTT-TAT-GA-CAATCGC-TT-----------------------A
gi|18                         :                                                                                 -AAAATA-A-CCCAACC------TTTCATTTTCAATC-TTGAG-GA-T-TATAT-GA-CAATTGC-AT-----------------------TG-T--TA-CAC--G---TTATCAAC
gi|19                         :                                                     aAAAG-AAA--TA---TCAT-AACACC---AAATGCA-TT--------G--TTTCATTTTCAATC-TTCAA-GAGG-T-TAT-
gi|2                          :                                                 ataatAAAG-AAAA-TAA--TCAC-AACGCCG-AAAA-A-A-CTCAACCGCGG--TTTCATTTTCAATC-TTCAA-GA-G-T-TATTGA-CAACCGCCTT-----------------------AG-T--TA-CACATT---GTATCAACAATTTTTT----CTA-TGA-CATTAAATGGCGTC------AATTTA-TGATTTGC-GC---TTTTTAACCCAAAGTTC--ATTGTGA-CGT--CA-TAATTTAAC----GTTA-------AT-TACGC-T-GC---AT--AT---CTGACTTTCTGGACTGTTGCCA-TGT-ACAAAAATA---TACAAT-ATGT-ACAATAA--TAATGGCAA-AT-TGA-AA-A--TTAT--TAAATAT--AATAAGGGAGGAGGA-----TCATATTT-GGTTATAAACATA-GGGAA----ATATAT-GATAT-GT--AC------CACG-GTGATA--GATAAAA--AT-AT-TAAT---AAAA-AAATA-A--A----A-----------GGAGGGG------TACA-CCTAC-TTGGCA-CAAATTACGAAA-TATACAAA-ATGGtattg
gi|22                         :                                  caaaatatatgtaaatatcacacaagtaatggtataatC-AACGCCG-AAAATA-A-CTCAACCG--G--TTTC
gi|3                          :                                                      AAAG-AAAA-TAAT-TCA--AACGCCG-AAAATA-A-CTCAACCG--G--TTTCAATTTCAAACTTTCAA-G------TAT-GA-C-ATCGC-TTC----------------------A-----TA-CAC-TG---TTATCAACAA---TTT----CTA-T-A-CATCCAATG-ACCC------AAATTA-T-ATTTGC--C---TTT--AAC--AAA-TTC--CTT-T-A-CGT--CA-TAATATAAC------TCTGCC-T-AT-AT-AC-GTGC---ATTAAT---C-GAC--TCTGA----T-GC-A-TGT-ACAAAAATA---TACAAT-A-G--ACAAT-A--ATATGGCAA-A-ATAA-AT-AATTTAT--TAAATATAAAATGAAGGAGCGGGGA----TCACGTTT-G---ACTAACAT--TA--A----ATA----AGCATAGTACAC------T--G-GT-ATAT-TAAAAAATTTTAA--AAATTAAAAAA-AAAAA-A--A----AAAAAAAATT--GGGGGGGGTAAATTACGTCCTA--CTCAC--CAAATTACGAAA-TATACAAA-
gi|4                          :                                                                                                    taataaatccaaataatgtaaaatccacacagtaattataatTCGC-TT-----------------------AG-TG-TAGCAGTTGGTTTTATTACTAATTTTTTTTCTCTA-TGATCAT--AATG-TGTCGCGCAAAAATTAGT-ATTTGC-GC---TTA--CAC--ATAGTTCCAATTGTGATCGTTTCGCTAATGTAACGTATGGTGTGGCGT-A--ATTAC-T-GC---AT--ATATTCTGACTTTCTGGA-TGT-GC-A-TGT-ATCAAAATAACCTACAATTATGT-A--AT-AACTCATGGCAACATATAATAA-A--TTAT--TATATAA--AAGGGAGGAGGGGGGGGT--TCACGTTT-G--TATCAACATACTG--ACCATATATAT-AAGATAGTT-ACCTCACATACGCGTAGTATCAAGAAAATTATAATGAAAC---AAAATAAATATACCA----AACAATAATTCCGGGGGGGGGt
gi|5                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 TGATAATA-AGAGGGCATGCATAA-ATT-GTACAAAATTTA-------TAATATTAATGGG-GGAAAA---GGGGGGCGGGATAGT---AATG--ATTA----CAATA-GTA-GATGA-CATTT---AAAGCATAAATAT--GACA---GTTTTGATTACCTGTAAAATAA-ATTTTGACCT---ACGTATATAATGCGGGGAAATGTTTCTGGAAAATAAT-TTTTCAAAGAA-TTTACAATTGATGTAG-CATTTTAGCGCAGGTGTT-GTATCCTTCGAATAAACA-GTTTTCTTTTGTTTCACCGTTCTGTTTC-GTGGTATCTTT--CAAGAATTTTTAAAAGGGGAAAACGGGTAAAGTTCGG-ATG
gi|6                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               aTTAATAATATAAAAGGCATGCA--A-AT--GTACAAATTT-A-------TAATA---ATGGG-GGAAAA-AAGGGGA---------T---CATAGTATTA----CAATA--TA--ACGA-CGGTT---TAA-CATAA-TATATGACA---GA---GATTACTT----AATAA-ATTCTGACTT--TACGTATA--ATGCGGGGAAAAGTTTC--GAAAATAA--TTTTCAAAGAAG-TTACAA-TG-TCGAG-CATTT-AGCGCAG---TT-GTATCCT-CAAT-AAAC-AGCTTTTCTTGGTTC--ACGTTCT-TTTCC-TAGTATCTTTTCCAAGAATTTGTAAAAGGTAAAAAC-GGT-AAGTTCGGTATGa
gi|7                          :                                                                                                               TTTAATC-TTCAA-GA-G-T-TAT-GA-CAATCGC-TTTATAGTTAATATAATATAGTAATAG-T--TA-CACATT---TTATCAACAGTTTTTTA---CTA-TGA-CATCAAAAG-CGCC------AGATTA-T-ATTTGC-AG---TTT--AAC--AAAGTTC--ATTGTGA-CAT--TA-TGATTTAA----TGTTATGCCGTAAT-ACCGCTG-GCCAAGT--GT---CCAATTTTCa
gi|8                          :                                                                                                 CA--G--TTTCATTTTCAAAC-TTCAA-CA-G-T-TAT--------CGC-TT-----------------------AG-T--TA-CACATG---TTATCAACAATTGTTT----CTA-TGA-CATCAAATA-CGCC------AAATTA-T-ATTTGC-TC---TTT--AAC--AAAGTTC--ATTGTGA-CGT--CA-TAATATAAC---T-TCATGCCGT-A--ATCAC-GTGC---CT--AC---CTGAC-TTCTGAACTGT-G
gi|9                          :                                                                                               ACCG--G--TTTCTTGTTCAATC-TTCAA-GA-G-T-TAT-AA-CAATCGC-TT-----------------------AGTT--TA-CACAT----TTATCAACATTTTTTT----CT--TGA-TATCAAATG-CGCC------AAATT--T-ATTTGC-GC---TTT--AAC--AGAGTTA--GTTGTGA-CGT--CA-TAATATAA----TGTT