lowQualScore                  :                                                                                                                                                                                                                                                                                                                                                            1111111111111111111111                                                                                                              111111111111111111111111111111111111                                                                                                                                                           
lowQualScore                  :                       11                             11           22            1                                                                                                                    11        11         11111111                    111        111          111           11                11111                    111111111           6666666666666666666666         11                               1111                                                                111111111111111111111111111111111111  11111                         111                                            11                             111111                            11         
lowQualScore                  :                       11                       6     00    6   3  88        6   9         5        9      3       5  5    3  5     77    5                5    5     5     66                  88 5  33        99 888     22222222    4  4        4   111        222   7 0  3 000 3   1 777 55    4   4  4    00000   8888 4     66    777777777 1     3   9999999999999999999999      0  00    9999    8888   99    999   0000   1   66 2 66 8 4 0          4          666 55 4    4    4     000000000000000000000000000000000000  22222    5 5 5  5 5   5   66  333  66         4         4 8       5    0 5   99  888 0 0 5   5     7        444444               5   1   66   00         
lowQualScore                  :                       ..                       .     ..    .   .  ..        .   .         .        .      .       .  .    .  .     ..    .                .    .     .     ..                  .. .  ..        .. ...     ........    .  .        .   ...        ...   . .  . ... .   . ... ..    .   .  .    .....   .... .     ..    ......... .     .   ......................      .  ..    ....    ....   ..    ...   ....   .   .. . .. . . .          .          ... .. .    .    .     ....................................  .....    . . .  . .   .   ..  ...  ..         .         . .       .    . .   ..  ... . . .   .     .        ......               .   .   ..   ..         
lowQualScore                  :                       00                       7     22    7   5  22        7   2         0        4      1       0  0    4  0     99    7                7    7     7     66                  33 7  66        00 888     55555555    0  0        0   888        777   3 1  6 000 6   3 000 99    0   0  0    00000   5555 0     11    888888888 9     1   2222222222222222222222      1  99    4444    9999   00    111   1111   8   11 7 11 3 4 7          0          222 55 0    0    0     000000000000000000000000000000000000  55555    0 0 0  0 0   0   99  888  99         4         4 9       0    5 0   22  888 2 4 0   0     1        444444               7   7   44   00         
consensus                     :           NGTATTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAC-TGCA-TTGACAT-AACTTACA-CACTTCACTGTTA-GAATCATTTATGAATTATATTCA-CA-TTATGAT-ACTAA--AAAT-ACGAGAGCCAAACGAA-TACA-CTCTG-CTCATATTTCCTCAATCAATACACTATA-CA-CAAACGAAANAA---GTTCA----C---TATA-TA-CAAACGAA-ATAA-TTTCTCAAA---CAA-AATT-A---C-AAATACT-GAGTCAA-CAG-TT-ATCC-----TAG----G-ACCGT--AAAA---------TTGAGAAAAGAA---AAT----GTAATG-AAAGTAAAATGTTNTACTC----ACCTC---AGAAGTCGT-GTCTG-TACTTTTAAA--ACT--TTA-AAGAATTATGAA-GCTCGTGCTA-G-T--T-GTAG-AGCA-CGGTTCGA-CGA-AG--NG------------AAACC--AA-CT-----CAGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAC-GACTAG-AGAG-GT---CCTAT-ACA-GGATAACTGAAACA------TACTATATACAAACA-CGTAACAC-TGTN-AATGTGACA
Reference ( gi|3 )            :           AGTATTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAT-TGCA-TTGACAA-AACTTACA-CACGTCACTGTTA-GAATCATTTATGAATCATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-CTCTG-CTCATATTTCCTCAATCAATACACTGTA-CA-GAAACGAAAGCA---GTTCA----C---TATA-TA-CAAACGAA-ATAA-TTTCTCAAA---CAA-AATT-A---C-AAATACT-GACTCAA-CAG-TT-ATCC-----TAG----G-ACCGT--AAAA---------TTGAGAAAAGAAGAAAATGAAAGTAATG-AAGGTAAAATGTTGCACTC----ACCTC---AGAGATCGT-GTCTG-TACTTTTAAA--ACT--TAA-AAGAATTATGAA-GCTCGTGCTA-G-T--T-GTAG-AGCA-CGGTT----AGA-AG--TG------------A---------CT-----CAGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAC-GACTAG-AGAT-GT---CCTAT-ACA-GGATAGCTGAAACA------TACTATATACAAACA-TGTAACAC-TGTC-AATGTGACA
gi|2                          :            GTATTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAC-TGCAATTGACAT-AACTTGCA-CACTTCACTGTTA-GAATCATTTATGAATTATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-CTCTG-CTCATATTTTCTCAATCAATACACTATA-CA-GAAACGAAACAA---GTTCAATTACATGTATA-TA-CAAACGAA-ATAA-TT-CTCAAA---CAA-AATT-A---C-AAATACT-GACTCAA-CAG-TT-ATCC-----TAA----G-ACCGT--AAAA---------TTGAGAAAAGAA----AT--------TGTAAAGTAAAATGTTGTACTC----ACCTC---AGAGGTCGT-GTCTG-TACTTTTAAA--ACT--TTA-AAGAATTATGAA-GCTCGTGCTA-G-T--T-GTAG-AGCA-CGGTT----CGA-AG--AG------------A---------CT-----CAGG-T-G-AA-T-AAA-TAC--AG---GT--ATC-AAGGG-TACCTTGAA-G-GGTGTTC-GACTAGAAGAG-GT---CCTAT-ACA-GGATACCTGAAACATACATGTACTATATACAAACA-TGTAACAC-TGTC-AATGTGA
gi|1                          : tatatacatatgTATTTTTATTTAACACCATTTTAGTTTACTCGAGAACTTAACCTGCA-TTGACAT-AACTTTCA-CAC-TTACTGT---AAATCATTTATGA-TCATATTCA-CA-TTATTATTACTGATAAAATGACAAGAGCCAA-CGA--TACATCTCTG-CTCATATTTCCTCAATCAATACACTA-A-CACGAACCGAAAACAAGTATGCA----C---TATA-TACCAAACGAACATAA-TTCGTCAAA---CAA-GTTTCA---CAAAATACTAGAGTCAA-CAG-TT-ATCC-----TAG----ATAACG---AAAAGGTTCTTTTCTGCGGA---AAGAAATTG---GTA----AAG--AAAAGATTGTA-TC----A-CTC----GAAGTCGTAGTCTG--ACTTTTAAAATATT--TAA-AAGAA-TATGAA-GCTCGTGGTA-GAT--T-GAAGAAACACCGGTT----CG--AG--AG------------G---------CT-----CAGGATGG-AA-TGGAA-TAC--AGA--GTCGATCGA--GG-TACCTTGAA-GAGGTGTAC-GACTAG-AGAA-GTTTCCTTATAACAGGGATAACTGAAATA------TACTATATACAAACACTGT-ACACATGTCAAATGT
gi|11                         :       acaataTATTTTTATT--ACACCATTTTAATTTACTCGAGA-CTTAAC-TGCA-TTGACATTAGCTTACA-CACTTCACTGTTAAGAATCATTTATGAATGATATTCA-CATTTATGAT-ACTAA--GTA--ACAAGAGCCAAACGAA-TACA-CTCTGCCTCATATTTCCT-AATCAATACACTATATCA-CAAAC-AAAACA---ATTCA----C---TATATTA-CA
gi|13                         :         taatatTTTTTATT--GCAC-ATTTTAGTTTATT-GAGA-CTTAAC--GCA-TTG-C-----TTTATAACACTTCACTGTTA-TAATCATTTATCAATTATATTCACCG-TTAT-AT-ACT
gi|10                         :           attggTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAC-TGCA-TTGACAT-AACTTACA-CACTTCACTGTTA-GAATCATTTATGAATCATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-ATCTA-CTCATAAGTCCCCAATTAATACATTATA-CA-CAAACGAAATAA---GTTCA----C---TATA-T--------AA-ATCA-TTTATCAAA---CAA-ATTT-A---C-AAATACT-
gi|4                          :                                          TCGAGA-TCTTAT-TGCA-TTGTCAGTAATTTATA-C-------CGTTA-GAATCGTT-ATGAAATATATTCA-CA-TTGTGAT-ACTAT--AAAT-ACAACAGCCAAACGAAATACA-CTCTA-TTCATATTTCCTCAATTGATACACTATA-CC-CAAACGAAAAAA---GTTCA----A---TGTA-TA-CAAACGAA-ATGA-GTTATCAAG---CAA-AATT-A---C-AAACACT-GAGTT---CAG-TT-ATCC-----TAG----G-ACCGT--AAAA---------TTAAGAAAAGA----AAT--------TG-AA----AAAT-----ACTC----AC--------AAATAG---------------AAA--A----TAAGAAAAATTATGAG-ACCCGTGCTG-G-T--T-GTTA-AACA-CGGTT----CGA-AG--AGGGAAAAAAACAAA---------CT-----CAGG-T-G-AA-T-AAG-CAC--AG---GT--ATCGGGTAG-TACCTTGAA-G-GATGTTA-GACTAA-AAAG-GT---CCTTT-ATA-AGATAATTCAAACA------TACTATATACAAACA-TGTAAAAC-TGTG-AATGTGGCA
gi|5                          :                                                                                           -GAATCATG-ATGAATTATATCCA-CA-TTATAAT-ACTAA--AAAT-ACGAGAGCCAAACAAA-TACA-CTCTA-CTCAT--TCCCTCAATTAAAACACTACA-CA-CATGCGAAACAA---GTTCG----C---TATA-TA-CAAACGAA-ATA----TCTCTAA---CAA-ACTT-A---C-AAATA---G--TCAA-CAG-TT-ATCC-----TAG----G-ACTGT--AAAA---------TTGAGAAAAGAA----ATC---GTAA-----AGTAGAATGTTTTACTC----ACCTA---AGAAGTCGT-GTCTG-TA-TTTTAAA--ACT--TTA-ACGAATTATGAA-GCTCTTGCCA-T-T--T-GTAG-AGCA-CGGTTCAA-AGAGAG--TG------------AAACCCTAAACT-----CGGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAT-GACTTG-AGATGGT---CATAT-ACA-GAATAACTGAAACA------TACTATGTACAAAAA-CATAACAA-TGTA-AAGGTGACg
gi|6                          :                                                                                           -GAATCATG-ATGAATTATATCCA-CA-TTATAAT-ACTAA--AAAT-ACGAGAGC-AAACAAA-TACA-CTCTA-CTCAT--TCCCTCAATTAAAACACTACA-CA-CATGCGAAACAA---GTTCG----C---TATA-TA-CAAACGAA-ATA----TCTCTAA---CAA-ACTT-A---C-AAATA---G--TCAA-CAG-TT-ATCC-----TAG----G-ACTGT--AAAA---------T-GAGAAAAGAA----ATC---GTAA-----AGTAGAATGTTTTACTC----ACCTA---AGAAGTCGT-GTCTG-TATTTT--AA--ACT--TTA-ACGAATTATGAA-GCTCTTGCCA-T-T--T-GTAG-AGCA-GGGTTCAA-AGAGAG--TG------------AAACCCTAAACT-----CGGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAT-GACTTG-AGATGGT---CATAT-ACA-GAATAACTGAAA-A------TACTATGTACAAAAA-CATAACAA-TGTA-AAGGTGAC
gi|15                         :                                                                                                                                                                                                                  A---GTTCA----C---TATA-TA-CA---GAA-ATTA-TTTCTCAAA---CAA-AA-----------ATACT-GAGTCAA-CAG-TT-ATCC-----TAG----G-A
gi|12                         :                                                                                                                                                                                                                                  acaTA-TA-GAAACGAA-ATAAAGTTCTCAGAAGGCAAGAATT-AGTAC-AAA-----GAGTAAG-CAG-TT-ATCC-----TAGCTAGG-ACCAT--AAAA---------TTAAAA
gi|8                          :                                                                                                                                                                                                                                     TA-TA-GAAACGAA-ATAAAGTTCTCAGAAGGCAAGAATT-AG--C-AAA-----GAGT-AA-CAGGTT-ATCCGTAGCTAG----G-ACCATTTAAAA---------TT-----------AAAATG----TGTT------TA---TCTCGTGATC----ACCTCGTTAGA-AT-GTCGGCTGGTACTTTTAAA--ATTGGTAA-AGAAGTTTTGAA-GC-CATGTTA-G-TGTT-GTC--AGCA-CGGTCCGC-AAG-AG--TG------------AAACC-----CTAAAATCAGG-T-G-A--T-AA--TACTTAGTCAGT---TCGAGGGG-TACTTTACA-GCGGTGTACAGACTAG-AGAG-GT---CTT-T-ACA-GATTAACTCAACCA------CAtgttttactcgatcacctcagaagtcgtgattgtacttttaaaactttaaagaattttgaagctcatgttagttgtacagcacggtc
gi|7                          :                                                                                                                                                                                                                                            AAACGAA-ATAA-TTTTTCAAA---CAA-AATT-A---C-AAATACT-GAGTCAAACAG-TTTATCC-----TAG----G-AACGT--AAAA---------T-GAGAAAAGAA----AT--------TGTAAAGTAAAATGTTGTACTC----ACCTC---AGAAGTCGT------------TTGAA--ATT--TTA-AAGAATTATGAAAGCTCGTGCTA-G-T--T-GTAG-AGCA-CGGTT----CGA-AG--AG------------A---------CT-----CAGG-T-G-AAGT-AAAATAC--AG---GT--ATCGAGGGG-TACCTTGAAAG-GGTGTAC-GACTCG-AGAG-GT---CCTAT-ACA-GGATAACTGAAACA------TACTATATACAAACA-TGTAACAC-TGTC-AATGTGACA
gi|9                          :                                                                                                                                                                                                                                                                  ---CAA-AATT-A---A-AAATACT-ATGTCAA-AAG-TT-ATCC-----TAG----G-ACCAC--AAGA---------TTGAAAACATAA----ATT---GTAATG-----TAAAATGTTTTACTC----CTCTG---AGAAATCGT-GTCTG-AATTTTGAAA--ATG--TTA-ACGAATTATCAA-ACTCGTGACA-A-T--T-GTAG-AGCA-CGGT
gi|12                         :                                                                                                                                                                                                                                                                                                                                                                        tcATA-AAATTAAAATGTTTTACTCGATCACCTC---AGAAGTCGT-GATTG-TACTTTTAAA--ACT--TTA-AAGAATTTTGAA-GCTCATGTTA-G-T--T-GTAC-AGCA-CGGTaccttgaaggctgtacgactagaaaggtcctatgcaggataactgaaacacgctatatgcaagcatgttacagtgtaaatgtaac
gi|14                         :                                                                                                                                                                                                                                                                                                                                                                                tatagaaacgaaataaagttctcagaaggcaagaattagtacaaagagtaagcagttatcctagctaggaccTATGAA---CCGTGCTATA-T--TCGAAG-AACA-CGGTTCGACAGA-AGAGTG------------AAACTAAAA-CT-----CAGG-T-GCAA-T-AAA-TAC--AG---GT--ATCGAGGGGTTACCTTGAA-G-GGc
gi|9                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  GG-TACCTTGAA-G-GCTGTAC-GACTAG-AAAG-GT---CCTAT-GCA-GGATAACTGAAACA------CGCTATATGCAAGCA-TGTTACAG-TGTA-AATGTAAC
2 sequences could not be aligned to this particular reference sequence:
Unaligned ( gi|16 ): AAGTGTAAGACTTTATGCTCTACAATAAGGCTATTGTGATGGTATGTTCAAGGGA
Unaligned ( gi|17 ): ATAACTTTCTGAAAATGTTTCCAGATTTTAAATACTGGGT






Alignments
lowQualScore                  :                                                                    1                                                                                                                                                                                   11        111                                                                   111111111                66666666666666666                                                                                                                66666666666666666666666666                           111                                                                           111111                                       
lowQualScore                  :                        99                       5      5    5      1  0           0      5         7              4  4    1  4     66    5  2             5    5     5                          0 5       66    1    4 4 9999  777    3  3        3    33        111   6    3 999 3   0 0 3       3   3  3    99999   7777 3     55    666666666 22    777      77777777777777777        1     8888     777    4    44     3 3   0    55  4  55     4       3          444 55 3    3    3     1  44444444444444444444444444      4 4 4  4 4   4   66  222  66         4         4 8       4      4   8   777     4   4              222222                5  0    5   66         
lowQualScore                  :                        ..                       .      .    .      .  .           .      .         .              .  .    .  .     ..    .  .             .    .     .                          . .       ..    .    . . ....  ...    .  .        .    ..        ...   .    . ... .   . . .       .   .  .    .....   .... .     ..    ......... ..    ...      .................        .     ....     ...    .    ..     . .   .    ..  .  ..     .       .          ... .. .    .    .     .  ..........................      . . .  . .   .   ..  ...  ..         .         . .       .      .   .   ...     .   .              ......                .  .    .   ..         
lowQualScore                  :                        22                       7      7    7      4  1           7      7         3              4  4    9  4     99    0  0             0    0     0                          9 0       99    0    4 4 4444  888    6  6        6    66        777   7    3 222 3   4 4 3       6   6  6    11111   7777 6     55    000000000 44    000      99999999999999999        0     5555     000    0    88     3 2   7    44  0  55     0       6          777 00 6    6    6     1  00000000000000000000000000      4 4 4  4 4   4   11  222  11         0         0 0       4      4   9   888     4   4              888888                0  4    0   00         
consensus                     :            NGTATTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAC-TGCA-TTGACA-TAACTTACACACTTCACTGTT-AGAATCATTTATGAATTATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-CTCTG-CTCATATTTCCTCAATCAATACACTATA-CACAAAC--GAAACAAGT-T-C----AC---TATA-TA-CAAACGAA-ATAA-TTTCTCAAA---CAA-AATT-A---C-AAATACT-GAGTCAA-CAG-TT-ATCC-----TAG----G-ACCGT--AAAA---------TTGAGAA---AAGAAATT----GTAAT-AAAGTAAAATGTTGTACTC----ACCTC---AGAA-GTCGT-GTCTGTACTTTTAAAAC-TT-TA--AAGAA-TTATGAA-GCTCGTGCTA-G-T--T-GTAG-AGCA-CGGTTCGA--GA-AG---NG--AAACC---AA--CTCAGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAC-GACTAG-AGA-GGT---CCTAT-ACA-GGATAACTGAAACA------TACTATATACAAACAC-GTAACAC-TGT-NAATGTGACA
Reference ( family-3450 )     :            NGTATTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAC-TGCA-TTGACA-TAACTTACACACTTCACTGTT-AGAATCATTTATGAATTATATTCA-CA-TTATGAT-ACTAA--AAAT-ACGAGAGCCAAACGAA-TACA-CTCTG-CTCATATTTCCTCAATCAATACACTATA-CACAAAC--GAAANAAGT-T-C----AC---TATA-TA-CAAACGAA-ATAA-TTTCTCAAA---CAA-AATT-A---C-AAATACT-GAGTCAA-CAG-TT-ATCC-----TAG----G-ACCGT--AAAA---------TTGAGAA---AAGAAAAT----GTAATGAAAGTAAAATGTTNTACTC----ACCTC---AGAA-GTCGT-GTCTGTACTTTTAAAAC-TT-TA--AAGAA-TTATGAA-GCTCGTGCTA-G-T--T-GTAG-AGCA-CGGTTCGAC-GA-AG---NG--AAACC---AA--CTCAGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAC-GACTAG-AGA-GGT---CCTAT-ACA-GGATAACTGAAACA------TACTATATACAAACAC-GTAACAC-TGT-NAATGTGACA
gi|1                          :              TATTTTTATTTAACACCATTTTAGTTTACTCGAGAACTTAACCTGCA-TTGACA-TAACTTTCACACTT-ACTGT---AAATCATTTATGA-TCATATTCA-CA-TTATTATTACTGATAAAATGACAAGAGCCAA-CGA--TACATCTCTG-CTCATATTTCCTCAATCAATACACTA-A-CACGAACCGAAAACAAGTATGC----AC---TATA-TACCAAACGAACATAA-TTCGTCAAA---CAA-GTTTCA---CAAAATACTAGAGTCAA-CAG-TT-ATCC-----TAG----ATAACG---AAAAGGTTCTTTTCTGCGGA---AAGAAATT----G--GT-AAAG-AAAAGATTGTA-TC----A-CTC----GAA-GTCGTAGTCTG-ACTTTTAAAATATT-TA--AAAGA-ATATGAA-GCTCGTGGTA-GAT--T-GAAGAAACACCGGTTCGA--GA-GG-------------------CTCAGGATGG-AA-TGGAA-TAC--AGA--GTCGATCGA--GG-TACCTTGAA-GAGGTGTAC-GACTAG-AGA-AGTTTCCTTATAACAGGGATAACTGAAATA------TACTATATACAAACACTGT-ACACATGTCAAATGT
gi|10                         :           acaataTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAC-TGCA-TTGACA-TAACTTACACACTTCACTGTT-AGAATCATTTATGAATCATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-ATCTA-CTCATAAGTCCCCAATTAATACATTATA-CACAAAC--GAAATAAGT-T-C----AC---TATA-T--------AA-ATCA-TTTATCAAA---CAA-ATTT-A---C-AAATACT-
gi|11                         :              TATTTTTATT--ACACCATTTTAATTTACTCGAGA-CTTAAC-TGCA-TTGACATTAGCTTACACACTTCACTGTTAAGAATCATTTATGAATGATATTCA-CATTTATGAT-ACTAA--GTA--ACAAGAGCCAAACGAA-TACA-CTCTGCCTCATATTTCCT-AATCAATACACTATATCACAAAC--AAAACAA-T-T-C----AC---TATATTA-CA
gi|12                         :                                                                                                                                                                                                                               taatatTA-TA-GAAACGAA-ATAAAGTTCTCAGAAGGCAAGAATT-AGTAC-AAA-----GAGTAAG-CAG-TT-ATCC-----TAGCTAGG-ACCAT--AAAA---------TT-------------------------------AAAATGTTTTACTCGATCACCTC---AGAA-GTCGT-GATTGTACTTTTAAAAC-TT-TA--AAGAA-TTTTGAA-GCTCATGTTA-G-T--T-GTAC-AGCA-CGGT
gi|13                         :                TTTTTATT--GCAC-ATTTTAGTTTATT-GAGA-CTTAAC--GCA-TTGCTT-TA---TA-ACACTTCACTGTT-ATAATCATTTATCAATTATATTCACCG-TTAT-AT-ACTc
gi|14                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                  attggTATGAA---CCGTGCTATA-T--TCGAAG-AACA-CGGTTCGACAGA-AG---AGTGAAACT---AAAACTCAGG-T-GCAA-T-AAA-TAC--AG---GT--ATCGAGGGGTTACCTTGAA-G-GG
gi|15                         :                                                                                                                                                                                                                ACAAGT-T-C----AC---TATA-TA-CA---GAA-ATTA-TTTCTCAAA---CAA-AA-----------ATACT-GAGTCAA-CAG-TT-ATCC-----TAG----G-A
gi|2                          :             GTATTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAC-TGCAATTGACA-TAACTTGCACACTTCACTGTT-AGAATCATTTATGAATTATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-CTCTG-CTCATATTTTCTCAATCAATACACTATA-CAGAAAC--GAAACAAGT-T-CAATTACATGTATA-TA-CAAACGAA-ATAA--TTCTCAAA---CAA-AATT-A---C-AAATACT-GACTCAA-CAG-TT-ATCC-----TAA----G-ACCGT--AAAA---------TTGAGAA---AAGAAATT----GT----AAAGTAAAATGTTGTACTC----ACCTC---AGAG-GTCGT-GTCTGTACTTTTAAAAC-TT-TA--AAGAA-TTATGAA-GCTCGTGCTA-G-T--T-GTAG-AGCA-CGGTT---C-GA-AG---AG-----------A--CTCAGG-T-G-AA-T-AAA-TAC--AG---GT--ATC-AAGGG-TACCTTGAA-G-GGTGTTC-GACTAGAAGA-GGT---CCTAT-ACA-GGATACCTGAAACATACATGTACTATATACAAACAT-GTAACAC-TGT-CAATGTGA
gi|3                          : tatatacatatgGTATTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAT-TGCA-TTGACA-AAACTTACACACGTCACTGTT-AGAATCATTTATGAATCATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-CTCTG-CTCATATTTCCTCAATCAATACACTGTA-CAGAAAC--GAAAGCAGT-T-C----AC---TATA-TA-CAAACGAA-ATAA-TTTCTCAAA---CAA-AATT-A---C-AAATACT-GACTCAA-CAG-TT-ATCC-----TAG----G-ACCGT--AAAA---------TTGAGAAAAGAAGAAAATGAAAGTAATGAAGGTAAAATGTTGCACTC----ACCTC---AGAG-ATCGT-GTCTGTACTTTTAAAAC-TT-AA--AAGAA-TTATGAA-GCTCGTGCTA-G-T--T-GTAG-AGCA-CGGTT--A--GA-AG---TG-----------A--CTCAGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAC-GACTAG-AGA-TGT---CCTAT-ACA-GGATAGCTGAAACA------TACTATATACAAACAT-GTAACAC-TGT-CAATGTGACA
gi|4                          :                                          aTCGAGA-TCTTAT-TGCA-TTGTCAGTAATTTATAC-------CGTT-AGAATCGTT-ATGAAATATATTCA-CA-TTGTGAT-ACTAT--AAAT-ACAACAGCCAAACGAAATACA-CTCTA-TTCATATTTCCTCAATTGATACACTATA-CCCAAAC--GAAAAAAGT-T-C----AA---TGTA-TA-CAAACGAA-ATGA-GTTATCAAG---CAA-AATT-A---C-AAACACT-GAGTT---CAG-TT-ATCC-----TAG----G-ACCGT--AAAA---------TTAAGAA---AAGAAATT----G----------AAAA----ATACTC----AC--------AA-ATAG--------------AAAA-----TAAGAAAAA-TTATGAG-ACCCGTGCTG-G-T--T-GTTA-AACA-CGGTTCGAA-GA-GGGAAAA--AAACA---AA--CTCAGG-T-G-AA-T-AAG-CAC--AG---GT--ATCGGGTAG-TACCTTGAA-G-GATGTTA-GACTAA-AAA-GGT---CCTTT-ATA-AGATAATTCAAACA------TACTATATACAAACAT-GTAAAAC-TGT-GAATGTGGCA
gi|5                          :                                                                                            GAATCATG-ATGAATTATATCCA-CA-TTATAAT-ACTAA--AAAT-ACGAGAGCCAAACAAA-TACA-CTCTA-CTC--ATTCCCTCAATTAAAACACTACA-CACATGC--GAAACAAGT-T-C----GC---TATA-TA-CAAACGAA-ATA----TCTCTAA---CAA-ACTT-A---C-AAAT-----AGTCAA-CAG-TT-ATCC-----TAG----G-ACTGT--AAAA---------TTGAGAA---AAGAAATC----GT----AAAGTAGAATGTTTTACTC----ACCTA---AGAA-GTCGT-GTCTGTA-TTTTAAAAC-TT-TA--ACGAA-TTATGAA-GCTCTTGCCA-T-T--T-GTAG-AGCA-CGGTTCAAA-GAGAG---TG--AAACCCTAAA--CTCGGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAT-GACTTG-AGATGGT---CATAT-ACA-GAATAACTGAAACA------TACTATGTACAAAAAC-ATAACAA-TGT-AAAGGTGACg
gi|6                          :                                                                                            GAATCATG-ATGAATTATATCCA-CA-TTATAAT-ACTAA--AAAT-ACGAGAGC-AAACAAA-TACA-CTCTA-CTCAT--TCCCTCAATTAAAACACTACA-CACATGC--GAAACAAGT-T-C----GC---TATA-TA-CAAACGAA-ATA----TCTCTAA---CAA-ACTT-A---C-AAATA-----GTCAA-CAG-TT-ATCC-----TAG----G-ACTGT--AAAA---------T-GAGAA---AAGAAATC----GTAA----AGTAGAATGTTTTACTC----ACCTA---AGAA-GTCGT-GTCTGTATTTT--AAAC-TT-TA--ACGAA-TTATGAA-GCTCTTGCCA-T-T--T-GTAG-AGCA-GGGTTCAAA-GAGAG---TG--AAACCCTAAA--CTCGGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAT-GACTTG-AGATGGT---CATAT-ACA-GAATAACTGAAA-A------TACTATGTACAAAAAC-ATAACAA-TGT-AAAGGTGAC
gi|7                          :                                                                                                                                                                                                                                            AAACGAA-ATAA-TTTTTCAAA---CAA-AATT-A---C-AAATACT-GAGTCAAACAG-TTTATCC-----TAG----G-AACGT--AAAA---------T-GAGAA---AAGAAATT----GTAA----AGTAAAATGTTGTACTC----ACCTC---AGAA-GTCGT-----------TTGAAAT-TT-TA--AAGAA-TTATGAAAGCTCGTGCTA-G-T--T-GTAG-AGCA-CGGTTCGA-----AG---AG--A-----------CTCAGG-T-G-AAGT-AAAATAC--AG---GT--ATCGAGGGG-TACCTTGAAAG-GGTGTAC-GACTCG-AGA-GGT---CCTAT-ACA-GGATAACTGAAACA------TACTATATACAAACAT-GTAACAC-TGT-CAATGTGACA
gi|8                          :                                                                                                                                                                                                                                     TA-TA-GAAACGAA-ATAAAGTTCTCAGAAGGCAAGAATT-AG--C-AAA-----GAGT-AA-CAGGTT-ATCCGTAGCTAG----G-ACCATTTAAAA---------TT-----------AAAAT----GTGTT-----TA---TCTCGTGATC----ACCTCGTTAGAATGTCG--GCTGGTACTTTTAAAAT-TGGTA--AAGAAGTTTTGAA-GC-CATGTTA-G-TGTT-GTC--AGCA-CGGTCCG-C-AAGAG---TG--AAACCCTAAA--ATCAGG-T-G-A--T-AA--TACTTAGTCAGT---TCGAGGGG-TACTTTACA-GCGGTGTACAGACTAG-AGA-GGT---CTT-T-ACA-GATTAACTCAACCA------CA
gi|9                          :                                                                                                                                                                                                                                                                  ---CAA-AATT-A---A-AAATACT-ATGTCAA-AAG-TT-ATCC-----TAG----G-ACCAC--AAGA---------TTGAAAA---CATAAATT----GTAATG----TAAAATGTTTTACTC----CTCTG---AGAA-ATCGT-GTCTGAATTTTGAAAAT-GT-TA--ACGAA-TTATCAA-ACTCGTGACA-A-T--T-GTAG-AGCA-CGGT
gi|9                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   tcGG-TACCTTGAA-G-GCTGTAC-GACTAG-AAA-GGT---CCTAT-GCA-GGATAACTGAAACA------CGCTATATGCAAGCAT-GTTACAG-TGT-AAATGTAACaccttgaaggctgtacgactagaaaggtcctatgcaggataactgaaacacgctatatgcaagcatgttacagtgtaaatgtaac
2 sequences could not be aligned to this reference sequence:
Unaligned ( gi|16 ): AAGTGTAAGACTTTATGCTCTACAATAAGGCTATTGTGATGGTATGTTCAAGGGA
Unaligned ( gi|17 ): ATAACTTTCTGAAAATGTTTCCAGATTTTAAATACTGGGT






Alignments
lowQualScore                  :                                                                    1                                                                                                                                                                                   11        111                                                                   111111111                       44444444                                                                                                                66666666666666666666666666666                           111                                                                           111111                                       
lowQualScore                  :                        99                       5      5    5      1  0           0      5         7              4  4    1  4     66    5                5    5     5                          0 5       66         4 4 9999  777    3  3        3    33        111   6    3 999 3   0 0 3       3   3  3    99999   7777 3     55    666666666 22       8888     777 99999999 0        1     8888     777    4    44     3 3   0    55  4  55     4       3          444 55 3    3    3      11111111111111111111111111111      4 4 4  4 4   4   66  222  66         4         4 8       4      4   8   777     4   4              222222                5  0    5   66         
lowQualScore                  :                        ..                       .      .    .      .  .           .      .         .              .  .    .  .     ..    .                .    .     .                          . .       ..         . . ....  ...    .  .        .    ..        ...   .    . ... .   . . .       .   .  .    .....   .... .     ..    ......... ..       ....     ... ........ .        .     ....     ...    .    ..     . .   .    ..  .  ..     .       .          ... .. .    .    .      .............................      . . .  . .   .   ..  ...  ..         .         . .       .      .   .   ...     .   .              ......                .  .    .   ..         
lowQualScore                  :                        22                       7      7    7      4  1           7      7         3              4  4    9  4     99    0                0    0     0                          9 0       99         4 4 4444  888    6  6        6    66        777   7    3 222 3   4 4 3       6   6  6    11111   7777 6     55    000000000 44       5555     000 77777777 7        6     5555     000    0    88     3 2   7    44  0  55     0       6          777 00 6    6    6      22222222222222222222222222222      4 4 4  4 4   4   11  222  11         0         0 0       4      4   9   888     4   4              888888                0  4    0   00         
consensus                     :            NGTATTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAC-TGCA-TTGACA-TAACTTACACACTTCACTGTT-AGAATCATTTATGAATTATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-CTCTG-CTCATATTTCCTCAATCAATACACTATA-CACAAAC--GAAACAAGT-T-C----AC---TATA-TA-CAAACGAA-ATAA-TTTCTCAAA---CAA-AATT-A---C-AAATACT-GAGTCAA-CAG-TT-ATCC-----TAG----G-ACCGT--AAAA---------TTGAGAAAAG----AAATT---GTAAT-AAAGTAAAATGTTGTACTC----ACCTC---AGAA-GTCGT-GTCTGTACTTTTAAAAC-TT-TA--AAGAA-TTATGAA-GCTCGTGCTA-G-T--T-GTAG-AGCA-CGGTTC-G-A--GA-AGNG----AAACC---AA--CTCAGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAC-GACTAG-AGA-GGT---CCTAT-ACA-GGATAACTGAAACA------TACTATATACAAACAC-GTAACAC-TGT-NAATGTGACA
Reference ( family-3450 )     :            NGTATTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAC-TGCA-TTGACA-TAACTTACACACTTCACTGTT-AGAATCATTTATGAATTATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-CTCTG-CTCATATTTCCTCAATCAATACACTATA-CACAAAC--GAAACAAGT-T-C----AC---TATA-TA-CAAACGAA-ATAA-TTTCTCAAA---CAA-AATT-A---C-AAATACT-GAGTCAA-CAG-TT-ATCC-----TAG----G-ACCGT--AAAA---------TTGAGAAAAG----AAATT---GTAAT-AAAGTAAAATGTTGTACTC----ACCTC---AGAA-GTCGT-GTCTGTACTTTTAAAAC-TT-TA--AAGAA-TTATGAA-GCTCGTGCTA-G-T--T-GTAG-AGCA-CGGTTC-G-A--GA-AGNG----AAACC---AA--CTCAGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAC-GACTAG-AGA-GGT---CCTAT-ACA-GGATAACTGAAACA------TACTATATACAAACAC-GTAACAC-TGT-NAATGTGACA
gi|1                          :              TATTTTTATTTAACACCATTTTAGTTTACTCGAGAACTTAACCTGCA-TTGACA-TAACTTTCACACTT-ACTGT---AAATCATTTATGA-TCATATTCA-CA-TTATTATTACTGATAAAATGACAAGAGCCAA-CGA--TACATCTCTG-CTCATATTTCCTCAATCAATACACTA-A-CACGAACCGAAAACAAGTATGC----AC---TATA-TACCAAACGAACATAA-TTCGTCAAA---CAA-GTTTCA---CAAAATACTAGAGTCAA-CAG-TT-ATCC-----TAG----ATAACG---AAAAGGTTCTTTTCTGCGGAAAG----AAATT---G--GT-AAAG-AAAAGATTGTA-TC----A-CTC----GAA-GTCGTAGTCTG-ACTTTTAAAATATT-TA--AAAGA-ATATGAA-GCTCGTGGTA-GAT--T-GAAGAAACACCGGTTC-G-A--GA-GG------------------CTCAGGATGG-AA-TGGAA-TAC--AGA--GTCGATCGA--GG-TACCTTGAA-GAGGTGTAC-GACTAG-AGA-AGTTTCCTTATAACAGGGATAACTGAAATA------TACTATATACAAACACTGT-ACACATGTCAAATGT
gi|10                         :           acaataTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAC-TGCA-TTGACA-TAACTTACACACTTCACTGTT-AGAATCATTTATGAATCATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-ATCTA-CTCATAAGTCCCCAATTAATACATTATA-CACAAAC--GAAATAAGT-T-C----AC---TATA-T--------AA-ATCA-TTTATCAAA---CAA-ATTT-A---C-AAATACT-
gi|11                         :              TATTTTTATT--ACACCATTTTAATTTACTCGAGA-CTTAAC-TGCA-TTGACATTAGCTTACACACTTCACTGTTAAGAATCATTTATGAATGATATTCA-CATTTATGAT-ACTAA--GTA--ACAAGAGCCAAACGAA-TACA-CTCTGCCTCATATTTCCT-AATCAATACACTATATCACAAAC--AAAACAA-T-T-C----AC---TATATTA-CA
gi|12                         :                                                                                                                                                                                                                               taatatTA-TA-GAAACGAA-ATAAAGTTCTCAGAAGGCAAGAATT-AGTAC-AAA-----GAGTAAG-CAG-TT-ATCC-----TAGCTAGG-ACCAT--AAAA---------TT-------------------------------AAAATGTTTTACTCGATCACCTC---AGAA-GTCGT-GATTGTACTTTTAAAAC-TT-TA--AAGAA-TTTTGAA-GCTCATGTTA-G-T--T-GTAC-AGCA-CGGT
gi|13                         :                TTTTTATT--GCAC-ATTTTAGTTTATT-GAGA-CTTAAC--GCA-TTGCTT-TA---TA-ACACTTCACTGTT-ATAATCATTTATCAATTATATTCACCG-TTAT-AT-ACTc
gi|14                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                  attggTATGAA---CCGTGCTATA-T--TCGAAG-AACA-CGGTTC-G-ACAGA-AGAGTG--AAACT---AAAACTCAGG-T-GCAA-T-AAA-TAC--AG---GT--ATCGAGGGGTTACCTTGAA-G-GG
gi|15                         :                                                                                                                                                                                                                ACAAGT-T-C----AC---TATA-TA-CA---GAA-ATTA-TTTCTCAAA---CAA-AA-----------ATACT-GAGTCAA-CAG-TT-ATCC-----TAG----G-A
gi|2                          :             GTATTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAC-TGCAATTGACA-TAACTTGCACACTTCACTGTT-AGAATCATTTATGAATTATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-CTCTG-CTCATATTTTCTCAATCAATACACTATA-CAGAAAC--GAAACAAGT-T-CAATTACATGTATA-TA-CAAACGAA-ATAA--TTCTCAAA---CAA-AATT-A---C-AAATACT-GACTCAA-CAG-TT-ATCC-----TAA----G-ACCGT--AAAA---------TTGAGAAAAG----AAATT---G---T-AAAGTAAAATGTTGTACTC----ACCTC---AGAG-GTCGT-GTCTGTACTTTTAAAAC-TT-TA--AAGAA-TTATGAA-GCTCGTGCTA-G-T--T-GTAG-AGCA-CGGTTC------GA-AGAG-------------A--CTCAGG-T-G-AA-T-AAA-TAC--AG---GT--ATC-AAGGG-TACCTTGAA-G-GGTGTTC-GACTAGAAGA-GGT---CCTAT-ACA-GGATACCTGAAACATACATGTACTATATACAAACAT-GTAACAC-TGT-CAATGTGA
gi|3                          : tatatacatatgGTATTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAT-TGCA-TTGACA-AAACTTACACACGTCACTGTT-AGAATCATTTATGAATCATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-CTCTG-CTCATATTTCCTCAATCAATACACTGTA-CAGAAAC--GAAAGCAGT-T-C----AC---TATA-TA-CAAACGAA-ATAA-TTTCTCAAA---CAA-AATT-A---C-AAATACT-GACTCAA-CAG-TT-ATCC-----TAG----G-ACCGT--AAAA---------TTGAGAAAAGAAGAAAATGAAAGTAATGAAGGTAAAATGTTGCACTC----ACCTC---AGAG-ATCGT-GTCTGTACTTTTAAAAC-TT-AA--AAGAA-TTATGAA-GCTCGTGCTA-G-T--T-GTAG-AGCA-CGGTT----A--GA-AGTG-------------A--CTCAGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAC-GACTAG-AGA-TGT---CCTAT-ACA-GGATAGCTGAAACA------TACTATATACAAACAT-GTAACAC-TGT-CAATGTGACA
gi|4                          :                                          aTCGAGA-TCTTAT-TGCA-TTGTCAGTAATTTATAC-------CGTT-AGAATCGTT-ATGAAATATATTCA-CA-TTGTGAT-ACTAT--AAAT-ACAACAGCCAAACGAAATACA-CTCTA-TTCATATTTCCTCAATTGATACACTATA-CCCAAAC--GAAAAAAGT-T-C----AA---TGTA-TA-CAAACGAA-ATGA-GTTATCAAG---CAA-AATT-A---C-AAACACT-GAGTT---CAG-TT-ATCC-----TAG----G-ACCGT--AAAA---------TTAAGAAAAG----AAATT---G----------AAAA----ATACTC----AC--------AA-ATAG--------------AAAA-----TAAGAAAAA-TTATGAG-ACCCGTGCTG-G-T--T-GTTA-AACA-CGGTTC-G-A--AG-AGGGAAAAAAACA---AA--CTCAGG-T-G-AA-T-AAG-CAC--AG---GT--ATCGGGTAG-TACCTTGAA-G-GATGTTA-GACTAA-AAA-GGT---CCTTT-ATA-AGATAATTCAAACA------TACTATATACAAACAT-GTAAAAC-TGT-GAATGTGGCA
gi|5                          :                                                                                            GAATCATG-ATGAATTATATCCA-CA-TTATAAT-ACTAA--AAAT-ACGAGAGCCAAACAAA-TACA-CTCTA-CTC--ATTCCCTCAATTAAAACACTACA-CACATGC--GAAACAAGT-T-C----GC---TATA-TA-CAAACGAA-ATA----TCTCTAA---CAA-ACTT-A---C-AAAT-----AGTCAA-CAG-TT-ATCC-----TAG----G-ACTGT--AAAA---------TTGAGAAAAG----AAATC---G---T-AAAGTAGAATGTTTTACTC----ACCTA---AGAA-GTCGT-GTCTGTA-TTTTAAAAC-TT-TA--ACGAA-TTATGAA-GCTCTTGCCA-T-T--T-GTAG-AGCA-CGGTTCAA-A--GAGAGTG----AAACCCTAAA--CTCGGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAT-GACTTG-AGATGGT---CATAT-ACA-GAATAACTGAAACA------TACTATGTACAAAAAC-ATAACAA-TGT-AAAGGTGACg
gi|6                          :                                                                                            GAATCATG-ATGAATTATATCCA-CA-TTATAAT-ACTAA--AAAT-ACGAGAGC-AAACAAA-TACA-CTCTA-CTCAT--TCCCTCAATTAAAACACTACA-CACATGC--GAAACAAGT-T-C----GC---TATA-TA-CAAACGAA-ATA----TCTCTAA---CAA-ACTT-A---C-AAATA-----GTCAA-CAG-TT-ATCC-----TAG----G-ACTGT--AAAA---------T-GAGAAAAG----AAATC---GTAA----AGTAGAATGTTTTACTC----ACCTA---AGAA-GTCGT-GTCTGTATTTT--AAAC-TT-TA--ACGAA-TTATGAA-GCTCTTGCCA-T-T--T-GTAG-AGCA-GGGTTC-A-AA-GAGAGTG----AAACCCTAAA--CTCGGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAT-GACTTG-AGATGGT---CATAT-ACA-GAATAACTGAAA-A------TACTATGTACAAAAAC-ATAACAA-TGT-AAAGGTGAC
gi|7                          :                                                                                                                                                                                                                                            AAACGAA-ATAA-TTTTTCAAA---CAA-AATT-A---C-AAATACT-GAGTCAAACAG-TTTATCC-----TAG----G-AACGT--AAAA---------T-GAGAAAAG----AAATT---GTAA----AGTAAAATGTTGTACTC----ACCTC---AGAA-GTCGT-----------TTGAAAT-TT-TA--AAGAA-TTATGAAAGCTCGTGCTA-G-T--T-GTAG-AGCA-CGGTTC-G-A-----AGAG----A-----------CTCAGG-T-G-AAGT-AAAATAC--AG---GT--ATCGAGGGG-TACCTTGAAAG-GGTGTAC-GACTCG-AGA-GGT---CCTAT-ACA-GGATAACTGAAACA------TACTATATACAAACAT-GTAACAC-TGT-CAATGTGACA
gi|8                          :                                                                                                                                                                                                                                     TA-TA-GAAACGAA-ATAAAGTTCTCAGAAGGCAAGAATT-AG--C-AAA-----GAGT-AA-CAGGTT-ATCCGTAGCTAG----G-ACCATTTAAAA---------TT---AAAA---------T---GTGTT-----TA---TCTCGTGATC----ACCTCGTTAGAATGTCG--GCTGGTACTTTTAAAAT-TGGTA--AAGAAGTTTTGAA-GC-CATGTTA-G-TGTT-GTC--AGCA-CGGTCC-GCA--AG-AGTG----AAACCCTAAA--ATCAGG-T-G-A--T-AA--TACTTAGTCAGT---TCGAGGGG-TACTTTACA-GCGGTGTACAGACTAG-AGA-GGT---CTT-T-ACA-GATTAACTCAACCA------CA
gi|9                          :                                                                                                                                                                                                                                                                  ---CAA-AATT-A---A-AAATACT-ATGTCAA-AAG-TT-ATCC-----TAG----G-ACCAC--AAGA---------TTGAAAACAT----AAATT---GTAAT----GTAAAATGTTTTACTC----CTCTG---AGAA-ATCGT-GTCTGAATTTTGAAAAT-GT-TA--ACGAA-TTATCAA-ACTCGTGACA-A-T--T-GTAG-AGCA-CGGT
gi|9                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    tcGG-TACCTTGAA-G-GCTGTAC-GACTAG-AAA-GGT---CCTAT-GCA-GGATAACTGAAACA------CGCTATATGCAAGCAT-GTTACAG-TGT-AAATGTAACaccttgaaggctgtacgactagaaaggtcctatgcaggataactgaaacacgctatatgcaagcatgttacagtgtaaatgtaac
2 sequences could not be aligned to this reference sequence:
Unaligned ( gi|16 ): AAGTGTAAGACTTTATGCTCTACAATAAGGCTATTGTGATGGTATGTTCAAGGGA
Unaligned ( gi|17 ): ATAACTTTCTGAAAATGTTTCCAGATTTTAAATACTGGGT






Alignments
lowQualScore                  :                                                                    1                                                                                                                                                                                   11        111                                                                   111111111                       44444444                                                                                                                66666666666666666666666666666                           111                                                                           111111                                       
lowQualScore                  :                        99                       5      5    5      1  0           0      5         7              4  4    1  4     66    5                5    5     5                          0 5       66         4 4 9999  777    3  3        3    33        111   6    3 999 3   0 0 3       3   3  3    99999   7777 3     55    666666666 22       8888     777 99999999 0        1     8888     777    4    44     3 3   0    55  4  55     4       3          444 55 3    3    3      11111111111111111111111111111      4 4 4  4 4   4   66  222  66         4         4 8       4      4   8   777     4   4              222222                5  0    5   66         
lowQualScore                  :                        ..                       .      .    .      .  .           .      .         .              .  .    .  .     ..    .                .    .     .                          . .       ..         . . ....  ...    .  .        .    ..        ...   .    . ... .   . . .       .   .  .    .....   .... .     ..    ......... ..       ....     ... ........ .        .     ....     ...    .    ..     . .   .    ..  .  ..     .       .          ... .. .    .    .      .............................      . . .  . .   .   ..  ...  ..         .         . .       .      .   .   ...     .   .              ......                .  .    .   ..         
lowQualScore                  :                        22                       7      7    7      4  1           7      7         3              4  4    9  4     99    0                0    0     0                          9 0       99         4 4 4444  888    6  6        6    66        777   7    3 222 3   4 4 3       6   6  6    11111   7777 6     55    000000000 44       5555     000 77777777 7        6     5555     000    0    88     3 2   7    44  0  55     0       6          777 00 6    6    6      22222222222222222222222222222      4 4 4  4 4   4   11  222  11         0         0 0       4      4   9   888     4   4              888888                0  4    0   00         
consensus                     :            NGTATTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAC-TGCA-TTGACA-TAACTTACACACTTCACTGTT-AGAATCATTTATGAATTATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-CTCTG-CTCATATTTCCTCAATCAATACACTATA-CACAAAC--GAAACAAGT-T-C----AC---TATA-TA-CAAACGAA-ATAA-TTTCTCAAA---CAA-AATT-A---C-AAATACT-GAGTCAA-CAG-TT-ATCC-----TAG----G-ACCGT--AAAA---------TTGAGAAAAG----AAATT---GTAAT-AAAGTAAAATGTTGTACTC----ACCTC---AGAA-GTCGT-GTCTGTACTTTTAAAAC-TT-TA--AAGAA-TTATGAA-GCTCGTGCTA-G-T--T-GTAG-AGCA-CGGTTC-G-A--GA-AGNG----AAACC---AA--CTCAGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAC-GACTAG-AGA-GGT---CCTAT-ACA-GGATAACTGAAACA------TACTATATACAAACAC-GTAACAC-TGT-NAATGTGACA
Reference ( family-3450 )     :            NGTATTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAC-TGCA-TTGACA-TAACTTACACACTTCACTGTT-AGAATCATTTATGAATTATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-CTCTG-CTCATATTTCCTCAATCAATACACTATA-CACAAAC--GAAACAAGT-T-C----AC---TATA-TA-CAAACGAA-ATAA-TTTCTCAAA---CAA-AATT-A---C-AAATACT-GAGTCAA-CAG-TT-ATCC-----TAG----G-ACCGT--AAAA---------TTGAGAAAAG----AAATT---GTAAT-AAAGTAAAATGTTGTACTC----ACCTC---AGAA-GTCGT-GTCTGTACTTTTAAAAC-TT-TA--AAGAA-TTATGAA-GCTCGTGCTA-G-T--T-GTAG-AGCA-CGGTTC-G-A--GA-AGNG----AAACC---AA--CTCAGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAC-GACTAG-AGA-GGT---CCTAT-ACA-GGATAACTGAAACA------TACTATATACAAACAC-GTAACAC-TGT-NAATGTGACA
gi|1                          :              TATTTTTATTTAACACCATTTTAGTTTACTCGAGAACTTAACCTGCA-TTGACA-TAACTTTCACACTT-ACTGT---AAATCATTTATGA-TCATATTCA-CA-TTATTATTACTGATAAAATGACAAGAGCCAA-CGA--TACATCTCTG-CTCATATTTCCTCAATCAATACACTA-A-CACGAACCGAAAACAAGTATGC----AC---TATA-TACCAAACGAACATAA-TTCGTCAAA---CAA-GTTTCA---CAAAATACTAGAGTCAA-CAG-TT-ATCC-----TAG----ATAACG---AAAAGGTTCTTTTCTGCGGAAAG----AAATT---G--GT-AAAG-AAAAGATTGTA-TC----A-CTC----GAA-GTCGTAGTCTG-ACTTTTAAAATATT-TA--AAAGA-ATATGAA-GCTCGTGGTA-GAT--T-GAAGAAACACCGGTTC-G-A--GA-GG------------------CTCAGGATGG-AA-TGGAA-TAC--AGA--GTCGATCGA--GG-TACCTTGAA-GAGGTGTAC-GACTAG-AGA-AGTTTCCTTATAACAGGGATAACTGAAATA------TACTATATACAAACACTGT-ACACATGTCAAATGT
gi|10                         :           acaataTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAC-TGCA-TTGACA-TAACTTACACACTTCACTGTT-AGAATCATTTATGAATCATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-ATCTA-CTCATAAGTCCCCAATTAATACATTATA-CACAAAC--GAAATAAGT-T-C----AC---TATA-T--------AA-ATCA-TTTATCAAA---CAA-ATTT-A---C-AAATACT-
gi|11                         :              TATTTTTATT--ACACCATTTTAATTTACTCGAGA-CTTAAC-TGCA-TTGACATTAGCTTACACACTTCACTGTTAAGAATCATTTATGAATGATATTCA-CATTTATGAT-ACTAA--GTA--ACAAGAGCCAAACGAA-TACA-CTCTGCCTCATATTTCCT-AATCAATACACTATATCACAAAC--AAAACAA-T-T-C----AC---TATATTA-CA
gi|12                         :                                                                                                                                                                                                                               taatatTA-TA-GAAACGAA-ATAAAGTTCTCAGAAGGCAAGAATT-AGTAC-AAA-----GAGTAAG-CAG-TT-ATCC-----TAGCTAGG-ACCAT--AAAA---------TT-------------------------------AAAATGTTTTACTCGATCACCTC---AGAA-GTCGT-GATTGTACTTTTAAAAC-TT-TA--AAGAA-TTTTGAA-GCTCATGTTA-G-T--T-GTAC-AGCA-CGGT
gi|13                         :                TTTTTATT--GCAC-ATTTTAGTTTATT-GAGA-CTTAAC--GCA-TTGCTT-TA---TA-ACACTTCACTGTT-ATAATCATTTATCAATTATATTCACCG-TTAT-AT-ACTc
gi|14                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                  attggTATGAA---CCGTGCTATA-T--TCGAAG-AACA-CGGTTC-G-ACAGA-AGAGTG--AAACT---AAAACTCAGG-T-GCAA-T-AAA-TAC--AG---GT--ATCGAGGGGTTACCTTGAA-G-GG
gi|15                         :                                                                                                                                                                                                                ACAAGT-T-C----AC---TATA-TA-CA---GAA-ATTA-TTTCTCAAA---CAA-AA-----------ATACT-GAGTCAA-CAG-TT-ATCC-----TAG----G-A
gi|2                          :             GTATTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAC-TGCAATTGACA-TAACTTGCACACTTCACTGTT-AGAATCATTTATGAATTATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-CTCTG-CTCATATTTTCTCAATCAATACACTATA-CAGAAAC--GAAACAAGT-T-CAATTACATGTATA-TA-CAAACGAA-ATAA--TTCTCAAA---CAA-AATT-A---C-AAATACT-GACTCAA-CAG-TT-ATCC-----TAA----G-ACCGT--AAAA---------TTGAGAAAAG----AAATT---G---T-AAAGTAAAATGTTGTACTC----ACCTC---AGAG-GTCGT-GTCTGTACTTTTAAAAC-TT-TA--AAGAA-TTATGAA-GCTCGTGCTA-G-T--T-GTAG-AGCA-CGGTTC------GA-AGAG-------------A--CTCAGG-T-G-AA-T-AAA-TAC--AG---GT--ATC-AAGGG-TACCTTGAA-G-GGTGTTC-GACTAGAAGA-GGT---CCTAT-ACA-GGATACCTGAAACATACATGTACTATATACAAACAT-GTAACAC-TGT-CAATGTGA
gi|3                          : tatatacatatgGTATTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAT-TGCA-TTGACA-AAACTTACACACGTCACTGTT-AGAATCATTTATGAATCATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-CTCTG-CTCATATTTCCTCAATCAATACACTGTA-CAGAAAC--GAAAGCAGT-T-C----AC---TATA-TA-CAAACGAA-ATAA-TTTCTCAAA---CAA-AATT-A---C-AAATACT-GACTCAA-CAG-TT-ATCC-----TAG----G-ACCGT--AAAA---------TTGAGAAAAGAAGAAAATGAAAGTAATGAAGGTAAAATGTTGCACTC----ACCTC---AGAG-ATCGT-GTCTGTACTTTTAAAAC-TT-AA--AAGAA-TTATGAA-GCTCGTGCTA-G-T--T-GTAG-AGCA-CGGTT----A--GA-AGTG-------------A--CTCAGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAC-GACTAG-AGA-TGT---CCTAT-ACA-GGATAGCTGAAACA------TACTATATACAAACAT-GTAACAC-TGT-CAATGTGACA
gi|4                          :                                          aTCGAGA-TCTTAT-TGCA-TTGTCAGTAATTTATAC-------CGTT-AGAATCGTT-ATGAAATATATTCA-CA-TTGTGAT-ACTAT--AAAT-ACAACAGCCAAACGAAATACA-CTCTA-TTCATATTTCCTCAATTGATACACTATA-CCCAAAC--GAAAAAAGT-T-C----AA---TGTA-TA-CAAACGAA-ATGA-GTTATCAAG---CAA-AATT-A---C-AAACACT-GAGTT---CAG-TT-ATCC-----TAG----G-ACCGT--AAAA---------TTAAGAAAAG----AAATT---G----------AAAA----ATACTC----AC--------AA-ATAG--------------AAAA-----TAAGAAAAA-TTATGAG-ACCCGTGCTG-G-T--T-GTTA-AACA-CGGTTC-G-A--AG-AGGGAAAAAAACA---AA--CTCAGG-T-G-AA-T-AAG-CAC--AG---GT--ATCGGGTAG-TACCTTGAA-G-GATGTTA-GACTAA-AAA-GGT---CCTTT-ATA-AGATAATTCAAACA------TACTATATACAAACAT-GTAAAAC-TGT-GAATGTGGCA
gi|5                          :                                                                                            GAATCATG-ATGAATTATATCCA-CA-TTATAAT-ACTAA--AAAT-ACGAGAGCCAAACAAA-TACA-CTCTA-CTC--ATTCCCTCAATTAAAACACTACA-CACATGC--GAAACAAGT-T-C----GC---TATA-TA-CAAACGAA-ATA----TCTCTAA---CAA-ACTT-A---C-AAAT-----AGTCAA-CAG-TT-ATCC-----TAG----G-ACTGT--AAAA---------TTGAGAAAAG----AAATC---G---T-AAAGTAGAATGTTTTACTC----ACCTA---AGAA-GTCGT-GTCTGTA-TTTTAAAAC-TT-TA--ACGAA-TTATGAA-GCTCTTGCCA-T-T--T-GTAG-AGCA-CGGTTCAA-A--GAGAGTG----AAACCCTAAA--CTCGGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAT-GACTTG-AGATGGT---CATAT-ACA-GAATAACTGAAACA------TACTATGTACAAAAAC-ATAACAA-TGT-AAAGGTGACg
gi|6                          :                                                                                            GAATCATG-ATGAATTATATCCA-CA-TTATAAT-ACTAA--AAAT-ACGAGAGC-AAACAAA-TACA-CTCTA-CTCAT--TCCCTCAATTAAAACACTACA-CACATGC--GAAACAAGT-T-C----GC---TATA-TA-CAAACGAA-ATA----TCTCTAA---CAA-ACTT-A---C-AAATA-----GTCAA-CAG-TT-ATCC-----TAG----G-ACTGT--AAAA---------T-GAGAAAAG----AAATC---GTAA----AGTAGAATGTTTTACTC----ACCTA---AGAA-GTCGT-GTCTGTATTTT--AAAC-TT-TA--ACGAA-TTATGAA-GCTCTTGCCA-T-T--T-GTAG-AGCA-GGGTTC-A-AA-GAGAGTG----AAACCCTAAA--CTCGGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAT-GACTTG-AGATGGT---CATAT-ACA-GAATAACTGAAA-A------TACTATGTACAAAAAC-ATAACAA-TGT-AAAGGTGAC
gi|7                          :                                                                                                                                                                                                                                            AAACGAA-ATAA-TTTTTCAAA---CAA-AATT-A---C-AAATACT-GAGTCAAACAG-TTTATCC-----TAG----G-AACGT--AAAA---------T-GAGAAAAG----AAATT---GTAA----AGTAAAATGTTGTACTC----ACCTC---AGAA-GTCGT-----------TTGAAAT-TT-TA--AAGAA-TTATGAAAGCTCGTGCTA-G-T--T-GTAG-AGCA-CGGTTC-G-A-----AGAG----A-----------CTCAGG-T-G-AAGT-AAAATAC--AG---GT--ATCGAGGGG-TACCTTGAAAG-GGTGTAC-GACTCG-AGA-GGT---CCTAT-ACA-GGATAACTGAAACA------TACTATATACAAACAT-GTAACAC-TGT-CAATGTGACA
gi|8                          :                                                                                                                                                                                                                                     TA-TA-GAAACGAA-ATAAAGTTCTCAGAAGGCAAGAATT-AG--C-AAA-----GAGT-AA-CAGGTT-ATCCGTAGCTAG----G-ACCATTTAAAA---------TT---AAAA---------T---GTGTT-----TA---TCTCGTGATC----ACCTCGTTAGAATGTCG--GCTGGTACTTTTAAAAT-TGGTA--AAGAAGTTTTGAA-GC-CATGTTA-G-TGTT-GTC--AGCA-CGGTCC-GCA--AG-AGTG----AAACCCTAAA--ATCAGG-T-G-A--T-AA--TACTTAGTCAGT---TCGAGGGG-TACTTTACA-GCGGTGTACAGACTAG-AGA-GGT---CTT-T-ACA-GATTAACTCAACCA------CA
gi|9                          :                                                                                                                                                                                                                                                                  ---CAA-AATT-A---A-AAATACT-ATGTCAA-AAG-TT-ATCC-----TAG----G-ACCAC--AAGA---------TTGAAAACAT----AAATT---GTAAT----GTAAAATGTTTTACTC----CTCTG---AGAA-ATCGT-GTCTGAATTTTGAAAAT-GT-TA--ACGAA-TTATCAA-ACTCGTGACA-A-T--T-GTAG-AGCA-CGGT
gi|9                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    tcGG-TACCTTGAA-G-GCTGTAC-GACTAG-AAA-GGT---CCTAT-GCA-GGATAACTGAAACA------CGCTATATGCAAGCAT-GTTACAG-TGT-AAATGTAACaccttgaaggctgtacgactagaaaggtcctatgcaggataactgaaacacgctatatgcaagcatgttacagtgtaaatgtaac


blockSeqs                     :                        .                        .      .    A      T                     A         T              C  T    G  .     .     .                A    .     C                            T       .          . . AATT  ATG    T  .        .    AG        AGG   G    . GTA .       .       A   G  T    GTAGC   CTAG .     TT    .         TG       AAGA     AAA TAATGAAG          T     GATC     GTT    T    T      T C        C   G  AG     G       A          TA  GT C    .    .      GACAGAAGAGTGAAACTAAAA              . . C  G .   A   TT  TCA  .          T         A C       A      A   T   .       .   .              TACATG                .       .   C 
blockSeqs                     :                        .                        .      .    .      G                     .         T              .  .    G  .     .     .                .    .     .                            .       .          . . .     .      .  .        .    AG        AGG   G    . G   .       .       .   .  .    .       .    .     .     .         TG       .        .   TAAA              G     .        .      .    T      T C        C   .  .      .       .          G   .  .    .    .      AAAGAGAGTGAAACCCTAAA               . . .  . .   .   .   .    .          .         . .       .      .   T   .       .   .              .                     .       .   C 
blockSeqs                     :                        .                        .      .    .      .                     .         T              .  .    G  .     .     .                .    .     .                            .       .          . . .     .      .  .        .    T         .     .    . .   .       .       .   .  .    .       .    .     .     .         TA       .        .   TAAA              G     .        .      .    T      T C        C   .  .      .       .          G   .  .    .    .      AAAGAGAGTGAAACCCTAAA               . . .  . .   .   .   .    .          .         . .       .      .   .   .       .   .              .                     .       .   G 
blockSeqs                     :                        .                        .      .    .      .                     .         T              .  .    G  .     .     .                .    .     .                            .       .          . . .     .      .  .        .    T         .     .    . .   .       .       .   .  .    .       .    .     .     .         TG       .        .   TAAA              A     .        .      .    T      T T        C   .  .      .       .          G   .  .    .    .      GAAGAGGGAAAAAAACAAA                . . .  . .   .   .   .    .          .         . .       .      .   .   .       .   .              .                     .       .   A 
blockSeqs                     :                        .                        .      .    .      .                     .         T              .  .    G  .     .     .                .    .     .                            .       .          . . .     .      .  .        .    T         .     .    . .   .       .       .   .  .    .       .    .     .     .         TG       .        .   TAAA              T     .        .      .    T      T C        C   .  .      .       .          G   .  .    .    .      GCAAGAGTGAAACCCTAAA                . . .  . .   .   .   .    .          .         . .       .      .   .   .       .   .              .                     .       .   A 
blockSeqs                     :                                                 .      .    .      .                     .         .              .  .    A  .     .     .                .    .     .                            .       .          . . .     .      .  .        .    G         .     .    . .   .       .       .   .  .    .       .    .     .     .         T        .        .   TGTT              T     .        .      .    T      T T        T   .  .      .       .          T   .  .    .    .      AGAAGTGA                           . . .  . .   .   .   .    .          .         . .       .      .   .   .       .   .              .                     .       .   C 
blockSeqs                     :                                                                                                    .              .  .    A  .     .     .                .    .     .                            .       .          . . .     .      .  .        .    T         .     .    . .   .       .       .   .  .    .       .    .     .     .         G        .        .   TAAT              G     .        .      .    T      A .        T   .  .      .       .          T   .  .    .    .      GAAGAGA                            . . .  . .   .   .   .    .          .         . .       .      .   .   .       .   .              .                     .       .   A 
blockSeqs                     :                                                                                                    .              .  .    .  .                                                                                       . . .     .      .  .        .    .         .     .    . .   .       .       .   .  .    .       .    .     .     .         G        .        .   .                 G     .        .      .    .      . .        T   .  .      .       .          G   .  .    .    .      GAAGAGA                            . . .  . .   .   .   .    .          .         . .       .      .   .   .       .   .              .                                   
blockSeqs                     :                                                                                                                                                                                                                                       .  .        .    .         .     .    . .   .       .       .   .  .    .       .    .     .     .         T        .        .   .                 T     .        .      .    .      . .        .   .  .      .       .          G   .  .    .    .                                                                              .         . .                                                                                     
blockSeqs                     :                                                                                                                                                                                                                                       .  .        .    .         .     .    . .   .       .       .   .  .    .       .    .                                                                                                                                .          A   .  .    .    .                                                                                                                                                                                
blockSeqs                     :                                                                                                                                                                                                                                                                  .     .    . .   .       .                                                                                                                                                                                                                                                                                                                                                                              


blockSeqCons                  :                        **                                                                                                          **                                                                     **                                                                                                                           *********                       TAAA****                                     T*                C*                               G**                     GAAGAGAGTGAAACCTAAA**********                           ***  **                                            ***                                                          N*
originalCons                  :            NGTATTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAC-TGCA-TTGACA-TAACTTACACACTTCACTGTT-AGAATCATTTATGAATTATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-CTCTG-CTCATATTTCCTCAATCAATACACTATA-CACAAAC--GAAACAAGT-T-C----AC---TATA-TA-CAAACGAA-ATAA-TTTCTCAAA---CAA-AATT-A---C-AAATACT-GAGTCAA-CAG-TT-ATCC-----TAG----G-ACCGT--AAAA---------TTGAGAAAAG----AAATT---GTAAT-AAAGTAAAATGTTGTACTC----ACCTC---AGAA-GTCGT-GTCTGTACTTTTAAAAC-TT-TA--AAGAA-TTATGAA-GCTCGTGCTA-G-T--T-GTAG-AGCA-CGGTTC-G-A--GA-AGNG----AAACC---AA--CTCAGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAC-GACTAG-AGA-GGT---CCTAT-ACA-GGATAACTGAAACA------TACTATATACAAACAC-GTAACAC-TGT-NAATGTGACA
finalCons                     :            NGTATTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAC-TGCA-TTGACA-TAACTTACACACTTCACTGTT-AGAATCATTTATGAATTATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-CTCTG-CTCATATTTCCTCAATCAATACACTATA-CACAAAC--GAAACAAGT-T-C----AC---TATA-TA-CAAACGAA-ATAA-TTTCTCAAA---CAA-AATT-A---C-AAATACT-GAGTCAA-CAG-TT-ATCC-----TAG----G-ACCGT--AAAA---------TTGAGAAAAG----AAATT---GTAAA----GTAAAATGTTGTACTC----ACCTC---AGAA-GTCGT-GTCTGTACTTTTAAAAC-TT-TA--AAGAA-TTATGAA-GCTCGTGCTAG--T--T-GTAG-AGCA-CGGTTCGAAGAGAGTGAAACCTAAA----------CTCAGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAC-GACTAG-AGA-GGT---CCTAT-ACA-GGATAACTGAAACA------TACTATATACAAACAC-GTAACAC-TGTN-AATGTGACA
2 sequences could not be aligned to this reference sequence:
Unaligned ( gi|16 ): AAGTGTAAGACTTTATGCTCTACAATAAGGCTATTGTGATGGTATGTTCAAGGGA
Unaligned ( gi|17 ): ATAACTTTCTGAAAATGTTTCCAGATTTTAAATACTGGGT






Alignments
lowQualScore                  :                                                                    1                                                                                                                                                      11111111                               111                                                                   111111111                  1111111111                                                                                                                                44444444444444                            111                                                                           111111                                       
lowQualScore                  :                        99                       5      5    5      1  0           0      5         7              4  4    1  4     66    5                5    5     5     33                   0 5       66         4 4  00000000    3  3        3    99        111   6    3 999 3   0 444       3   3  3    99999   7777 3     55    666666666 22       8888    4444444444 4444 0        1     8888     777    4    44     3 3   0    55  4  55     4       3          444 55 3    3    3    666   44   4 66666666666666       4 4 4  4 4   4   66  222  66         4         4 8       4      4   8   777     4   4              222222                5  0    5   66         
lowQualScore                  :                        ..                       .      .    .      .  .           .      .         .              .  .    .  .     ..    .                .    .     .     ..                   . .       ..         . .  ........    .  .        .    ..        ...   .    . ... .   . ...       .   .  .    .....   .... .     ..    ......... ..       ....    .......... .... .        .     ....     ...    .    ..     . .   .    ..  .  ..     .       .          ... .. .    .    .    ...   ..   . ..............       . . .  . .   .   ..  ...  ..         .         . .       .      .   .   ...     .   .              ......                .  .    .   ..         
lowQualScore                  :                        22                       7      7    7      4  1           7      7         3              4  4    9  4     99    0                0    0     0     55                   9 0       99         4 4  00000000    6  6        6    22        777   7    3 222 3   4 888       6   6  6    11111   7777 6     55    000000000 44       5555    9999999999 4444 7        6     5555     000    0    88     3 2   7    44  0  55     0       6          777 00 6    6    6    444   77   4 99999999999999       4 4 4  4 4   4   11  222  11         0         0 0       4      4   9   888     4   4              888888                0  4    0   00         
consensus                     :            NGTATTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAC-TGCA-TTGACA-TAACTTACACACTTCACTGTT-AGAATCATTTATGAATTATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-CTCTG-CTCATATTTCCTCAATCAATACACTATA-CACAAAC--GAAACAAGT-T-CA----C---TATA-TA-CAAACGAA-ATAA-TTTCTCAAA---CAA-AATT-A---C-AAATACT-GAGTCAA-CAG-TT-ATCC-----TAG----G-ACCGT--AAAA---------TTGAGAAAAG----AAAT--------T-GTAAAGTAAAATGTTGTACTC----ACCTC---AGAA-GTCGT-GTCTGTACTTTTAAAAC-TT-TA--AAGAA-TTATGAA-GCTCGTGCTA-G-T--T-GTAG-AGCA-CGGT---TCGA-AGA-GAGTGAAA-CC--AAACTCAGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAC-GACTAG-AGA-GGT---CCTAT-ACA-GGATAACTGAAACA------TACTATATACAAACAC-GTAACAC-TGT-NAATGTGACA
Reference ( family-3450 )     :            NGTATTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAC-TGCA-TTGACA-TAACTTACACACTTCACTGTT-AGAATCATTTATGAATTATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-CTCTG-CTCATATTTCCTCAATCAATACACTATA-CACAAAC--GAAACAAGT-T-CA----C---TATA-TA-CAAACGAA-ATAA-TTTCTCAAA---CAA-AATT-A---C-AAATACT-GAGTCAA-CAG-TT-ATCC-----TAG----G-ACCGT--AAAA---------TTGAGAAAAG----AAAT--------T-GTAAAGTAAAATGTTGTACTC----ACCTC---AGAA-GTCGT-GTCTGTACTTTTAAAAC-TT-TA--AAGAA-TTATGAA-GCTCGTGCTA-G-T--T-GTAG-AGCA-CGGT---TCGA-AGA-GAGTGAAA-CC-TAAACTCAGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAC-GACTAG-AGA-GGT---CCTAT-ACA-GGATAACTGAAACA------TACTATATACAAACAC-GTAACAC-TGT-NAATGTGACA
gi|1                          :              TATTTTTATTTAACACCATTTTAGTTTACTCGAGAACTTAACCTGCA-TTGACA-TAACTTTCACACTT-ACTGT---AAATCATTTATGA-TCATATTCA-CA-TTATTATTACTGATAAAATGACAAGAGCCAA-CGA--TACATCTCTG-CTCATATTTCCTCAATCAATACACTA-A-CACGAACCGAAAACAAGTATGCA----C---TATA-TACCAAACGAACATAA-TTCGTCAAA---CAA-GTTTCA---CAAAATACTAGAGTCAA-CAG-TT-ATCC-----TAG----ATAACG---AAAAGGTTCTTTTCTGCGGAAAG----AAAT--------TGGTAAAG-AAAAGATTGTA-TC----A-CTC----GAA-GTCGTAGTCTG-ACTTTTAAAATATT-TA--AAAGA-ATATGAA-GCTCGTGGTA-GAT--T-GAAGAAACACCGGT---TCG--AGA-G--------------GCTCAGGATGG-AA-TGGAA-TAC--AGA--GTCGATCGA--GG-TACCTTGAA-GAGGTGTAC-GACTAG-AGA-AGTTTCCTTATAACAGGGATAACTGAAATA------TACTATATACAAACACTGT-ACACATGTCAAATGT
gi|10                         :           acaataTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAC-TGCA-TTGACA-TAACTTACACACTTCACTGTT-AGAATCATTTATGAATCATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-ATCTA-CTCATAAGTCCCCAATTAATACATTATA-CACAAAC--GAAATAAGT-T-CA----C---TATA-T--------AA-ATCA-TTTATCAAA---CAA-ATTT-A---C-AAATACT-
gi|11                         :              TATTTTTATT--ACACCATTTTAATTTACTCGAGA-CTTAAC-TGCA-TTGACATTAGCTTACACACTTCACTGTTAAGAATCATTTATGAATGATATTCA-CATTTATGAT-ACTAA--GTA--ACAAGAGCCAAACGAA-TACA-CTCTGCCTCATATTTCCT-AATCAATACACTATATCACAAAC--AAAACAA-T-T-CA----C---TATATTA-CA
gi|12                         :                                                                                                                                                                                                                               taatatTA-TA-GAAACGAA-ATAAAGTTCTCAGAAGGCAAGAATT-AGTAC-AAA-----GAGTAAG-CAG-TT-ATCC-----TAGCTAGG-ACCAT--AAAA---------TT---------------------------------AAAATGTTTTACTCGATCACCTC---AGAA-GTCGT-GATTGTACTTTTAAAAC-TT-TA--AAGAA-TTTTGAA-GCTCATGTTA-G-T--T-GTAC-AGCA-CGGT---
gi|13                         :                TTTTTATT--GCAC-ATTTTAGTTTATT-GAGA-CTTAAC--GCA-TTGCTT-TA---TA-ACACTTCACTGTT-ATAATCATTTATCAATTATATTCACCG-TTAT-AT-ACTc
gi|14                         :                                                                                                                                                                                                                                                                                                                                                                                                                                                    attggTATGAA---CCGTGCTATA-T--TCGAAG-AACA-CGGT---TCGACAGAAGAGTGAAA-CT-AAAACTCAGG-T-GCAA-T-AAA-TAC--AG---GT--ATCGAGGGGTTACCTTGAA-G-GG
gi|15                         :                                                                                                                                                                                                                ACAAGT-T-CA----C---TATA-TA-CA---GAA-ATTA-TTTCTCAAA---CAA-AA-----------ATACT-GAGTCAA-CAG-TT-ATCC-----TAG----G-A
gi|2                          :             GTATTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAC-TGCAATTGACA-TAACTTGCACACTTCACTGTT-AGAATCATTTATGAATTATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-CTCTG-CTCATATTTTCTCAATCAATACACTATA-CAGAAAC--GAAACAAGT-T-CAATTACATGTATA-TA-CAAACGAA-ATAA-TT-CTCAAA---CAA-AATT-A---C-AAATACT-GACTCAA-CAG-TT-ATCC-----TAA----G-ACCGT--AAAA---------TTGAGAAAAG----AAAT--------T-GTAAAGTAAAATGTTGTACTC----ACCTC---AGAG-GTCGT-GTCTGTACTTTTAAAAC-TT-TA--AAGAA-TTATGAA-GCTCGTGCTA-G-T--T-GTAG-AGCA-CGGT---TCGA-AGA-G--------------ACTCAGG-T-G-AA-T-AAA-TAC--AG---GT--ATC-AAGGG-TACCTTGAA-G-GGTGTTC-GACTAGAAGA-GGT---CCTAT-ACA-GGATACCTGAAACATACATGTACTATATACAAACAT-GTAACAC-TGT-CAATGTGA
gi|3                          : tatatacatatgGTATTTTTATT--ACACCATTTTAGTTTACTCGAGA-CTTAAT-TGCA-TTGACA-AAACTTACACACGTCACTGTT-AGAATCATTTATGAATCATATTCA-CA-TTATGAT-ACTAA--AAAT-ACAAGAGCCAAACGAA-TACA-CTCTG-CTCATATTTCCTCAATCAATACACTGTA-CAGAAAC--GAAAGCAGT-T-CA----C---TATA-TA-CAAACGAA-ATAA-TTTCTCAAA---CAA-AATT-A---C-AAATACT-GACTCAA-CAG-TT-ATCC-----TAG----G-ACCGT--AAAA---------TTGAGAAAAGAAGAAAATGAAAGTAAT-G-AAGGTAAAATGTTGCACTC----ACCTC---AGAG-ATCGT-GTCTGTACTTTTAAAAC-TT-AA--AAGAA-TTATGAA-GCTCGTGCTA-G-T--T-GTAG-AGCA-CGGT---T----AGA--AGTG----------ACTCAGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAC-GACTAG-AGA-TGT---CCTAT-ACA-GGATAGCTGAAACA------TACTATATACAAACAT-GTAACAC-TGT-CAATGTGACA
gi|4                          :                                          aTCGAGA-TCTTAT-TGCA-TTGTCAGTAATTTATAC-------CGTT-AGAATCGTT-ATGAAATATATTCA-CA-TTGTGAT-ACTAT--AAAT-ACAACAGCCAAACGAAATACA-CTCTA-TTCATATTTCCTCAATTGATACACTATA-CCCAAAC--GAAAAAAGT-T-CA----A---TGTA-TA-CAAACGAA-ATGA-GTTATCAAG---CAA-AATT-A---C-AAACACT-GAGTT---CAG-TT-ATCC-----TAG----G-ACCGT--AAAA---------TTAAGAAAAG----AAAT--------T-G------AAAA----ATACTC----AC--------AA-ATAG--------------AAAA-----TAAGAAAAA-TTATGAG-ACCCGTGCTG-G-T--T-GTTA-AACA-CGGT---TCGA-AGA-GGGAAAAA-AA-CAAACTCAGG-T-G-AA-T-AAG-CAC--AG---GT--ATCGGGTAG-TACCTTGAA-G-GATGTTA-GACTAA-AAA-GGT---CCTTT-ATA-AGATAATTCAAACA------TACTATATACAAACAT-GTAAAAC-TGT-GAATGTGGCA
gi|5                          :                                                                                            GAATCATG-ATGAATTATATCCA-CA-TTATAAT-ACTAA--AAAT-ACGAGAGCCAAACAAA-TACA-CTCTA-CTCAT--TCCCTCAATTAAAACACTACA-CACATGC--GAAACAAGT-T-CG----C---TATA-TA-CAAACGAA-ATA----TCTCTAA---CAA-ACTT-A---C-AAATA-----GTCAA-CAG-TT-ATCC-----TAG----G-ACTGT--AAAA---------TTGAGAAAAG----AAAT--------C-GTAAAGTAGAATGTTTTACTC----ACCTA---AGAA-GTCGT-GTCTGTA-TTTTAAAAC-TT-TA--ACGAA-TTATGAA-GCTCTTGCCA-T-T--T-GTAG-AGCA-CGGT---TCAA-AGA-GAGTGAAACCC-TAAACTCGGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAT-GACTTG-AGATGGT---CATAT-ACA-GAATAACTGAAACA------TACTATGTACAAAAAC-ATAACAA-TGT-AAAGGTGACg
gi|6                          :                                                                                            GAATCATG-ATGAATTATATCCA-CA-TTATAAT-ACTAA--AAAT-ACGAGAGC-AAACAAA-TACA-CTCTA-CTCAT--TCCCTCAATTAAAACACTACA-CACATGC--GAAACAAGT-T-CG----C---TATA-TA-CAAACGAA-ATA----TCTCTAA---CAA-ACTT-A---C-AAATA-----GTCAA-CAG-TT-ATCC-----TAG----G-ACTGT--AAAA---------T-GAGAAAAG----AAAT--------C-GTAAAGTAGAATGTTTTACTC----ACCTA---AGAA-GTCGT-GTCTGTATTTT--AAAC-TT-TA--ACGAA-TTATGAA-GCTCTTGCCA-T-T--T-GTAG-AGCA-GGGT---TCAA-AGA-GAGTGAAA-CCCTAAACTCGGG-T-G-AA-T-AAA-TAC--AG---GT--ATCGAGGGG-TACCTTGAA-G-GGTGTAT-GACTTG-AGATGGT---CATAT-ACA-GAATAACTGAAA-A------TACTATGTACAAAAAC-ATAACAA-TGT-AAAGGTGAC
gi|7                          :                                                                                                                                                                                                                                            AAACGAA-ATAA-TTTTTCAAA---CAA-AATT-A---C-AAATACT-GAGTCAAACAG-TTTATCC-----TAG----G-AACGT--AAAA---------T-GAGAAAAG----AAAT--------T-GTAAAGTAAAATGTTGTACTC----ACCTC---AGAA-GTCGT-----------TTGAAAT-TT-TA--AAGAA-TTATGAAAGCTCGTGCTA-G-T--T-GTAG-AGCA-CGGT---TCGA-AGA-GA--------------CTCAGG-T-G-AAGT-AAAATAC--AG---GT--ATCGAGGGG-TACCTTGAAAG-GGTGTAC-GACTCG-AGA-GGT---CCTAT-ACA-GGATAACTGAAACA------TACTATATACAAACAT-GTAACAC-TGT-CAATGTGACA
gi|8                          :                                                                                                                                                                                                                                     TA-TA-GAAACGAA-ATAAAGTTCTCAGAAGGCAAGAATT-AG--C-AAA-----GAGT-AA-CAGGTT-ATCCGTAGCTAG----G-ACCATTTAAAA---------TT---AAAA-----------------T-GT---GTTTA-TCTCGTGATC----ACCTCGTTAGAATGTCG--GCTGGTACTTTTAAAAT-TGGTA--AAGAAGTTTTGAA-GC-CATGTTA-G-TGTT-GTC--AGCA-CGGT---CCGC-A-A-GAGTGAAACCC-TAAAATCAGG-T-G--A-T--AA-TACTTAGTCAGT---TCGAGGGG-TACTTTACA-GCGGTGTACAGACTAG-AGA-GGT---CTT-T-ACA-GATTAACTCAACCA------CA
gi|9                          :                                                                                                                                                                                                                                                                  ---CAA-AATT-A---A-AAATACT-ATGTCAA-AAG-TT-ATCC-----TAG----G-ACCAC--AAGA---------TTGAAAACAT----AAAT--------T-GTAATGTAAAATGTTTTACTC----CTCTG---AGAA-ATCGT-GTCTGAATTTTGAAAAT-GT-TA--ACGAA-TTATCAA-ACTCGTGACA-A-T--T-GTAG-AGCA-CGGTACCTTGA-AG
gi|9                          :                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   tcGG-TACCTTGAA-G-GCTGTAC-GACTAG-AAA-GGT---CCTAT-GCA-GGATAACTGAAACA------CGCTATATGCAAGCAT-GTTACAG-TGT-AAATGTAACgctgtacgactagaaaggtcctatgcaggataactgaaacacgctatatgcaagcatgttacagtgtaaatgtaac
2 sequences could not be aligned to this reference sequence:
Unaligned ( gi|16 ): AAGTGTAAGACTTTATGCTCTACAATAAGGCTATTGTGATGGTATGTTCAAGGGA
Unaligned ( gi|17 ): ATAACTTTCTGAAAATGTTTCCAGATTTTAAATACTGGGT