lowQualScore                  :                                                                                                                                             111111111111111111111111111111111111111111111111111111111111111111111111111111111                                                                                                                                                                                                                                
lowQualScore                  :                                                                                                                                             555555555555555555555555555555555555555555555555555555555555555555555555555555555     1                                          22       1                                2222                      2     11                                                    2    3333                       11111           
lowQualScore                  :                                                                                                                               3             222222222222222222222222222222222222222222222222222222222222222222222222222222222     5               6   4     2         5      88 3     0                      9   6     1111                      0     66    7                                  88  6  3     1    4444     66666     44      66666           
lowQualScore                  :                                                                                                                               .             .................................................................................     .               .   .     .         .      .. .     .                      .   .     ....                      .     ..    .                                  ..  .  .     .    ....     .....     ..      .....           
lowQualScore                  :                                                                                                                               0             555555555555555555555555555555555555555555555555555555555555555555555555555555555     0               3   0     0         0      00 2     5                      0   0     2222                      0     00    8                                  55  2  1     2    0000     55555     66      66666           
consensus                     :                                                                                                                      GCCGGTGTANCGTTGTAAACTGA-----------------CCCCCT--------------ATAGAATAAT--GA----------------CCCC----------CCGGTCATAATATTATGACCGGGGG-GTCATAATATTATGA-CTCCCCCGCACGTAGAAAAATGACCCTCACATAGAATTGTGACCCCCT----ATAGAATAACGACCCCCTAACCCAAACCCTAACCCTAACCCATCTAAGGTACACTTACAACATAATTAT-CCC-CC-GCCGATAGGC-AT-GGAGG--GGGATATG--GTAATGG----CACCCGTCCGT
Reference ( gi|3 )            :                                                                                                                      GCCGGTGTAACGTTGTAAACTGA-----------------CCCCC---------------ATAGAATATT--GA----------------ACCC----------CCGGTGATAATATTATGACCGAGGG-GTCATAATATTATGA-CTCCCCACCACGTAGTAAAATGACCCTCACATAGAATTTTGATCCCCT----ATAGAATAACGACCCCCTAACCAAAACCATAACCTTAACCCATCTAAGGTACACTTACAACATAATTAT-CCC-CC-GCCGATAGGC-ATCGGAGG--AGAATATG--GTAATGA----CACCCGTCCGT
gi|1                          :                                                                                                                      GCCGGTGTACCGTTATAAACTGACCCCCATAGAATAATGACCCCCTGGTCATTATTTTATATATAATAGT--GA----------------CTCC----------CCGGTCATAATATTATGACCGGGGA-GTCATAATATTATGA-CTCCCCCACACGTAGAAAAATGACCCTCACATAGAATTGTGACCCCCT----ATAGAATAACGACCCCCTAACCCAAACCA------TAACCCATCTAAGGTACACTTACAACATAATTAT--CC-CC-ACCGATAGGA-ATCGGAGG--AAAATATG--GCAATGG----CACCCGTCCG
gi|2                          : ttatatttaaattcataaaattattaacatgattttgatcagtagaaaaattactagagttagaaactattgggtgactagacgatggtgaagttgtgtcattgtatgtatttggatGCCGGTGTAACGTTGTAAACTGA-----------------ACCCC---------------ATAGAATAAT--GATTTTATATAAAATAACGCCCCCCCCCCCCCCCGGTCATAATATTATGAC--------TC---------------CCTCA-CACGTAGAAAAATGACCCTCACATAGAATTTTGACCCCCTATAGATAGAATAACGACCTCCTAACCCAAACCCTAACCCTAACCCATCTACGGTACACTTACAACATAATTAT-CCC-CC-GCCGATAGGC-ATCAGAGG--AGAATATGCTATAATGG----CACC
gi|4                          :                                                                                                                                         tTGA-----------------CCCCCT--------------ATAGAATAAC--GA----------------ACCC----------C
gi|1                          :                                                                                                                             ggggtcattatattatgactcccccacacgtagaaaaatgaccctcacatagaattgAATATTATGA----------------CTCC----------CCGGTCATAATATTATGACCGGGGA-GTCAC--TATTATtaacccaaaccctaaccctaacccatctgaggttcacttacaacataattatcccccgccgataggcatcggaggagaatatggtaatggcacccgtcc
gi|7                          :        ttatatttaaattcataaaattattaacatgattttgatcagtagaaaaattactagagttagaaactattgggtgactagacgatggtgaagttgtgtcattgtatgtatttggatgccggtgtaccgttataaactgacccccatagaataatgaccccctggtcattattttatatT--GA----------------CCCC----------CCGGTCATAATATTATGACatgactcccccacacgtagaaaaatgaccctcacatagaattgtgaccccctatagaataacgaccccctaacccaaaccataacccatctaaggtacacttacaacataattatccccaccgataggaatcggaggaaaatatggcaatggcacccgtccg
gi|2                          :                                                                                                                                                                                     cataatataatgacatgtggtcataatcggagatcatattattaGTCATAATATTATGACCGGGGG-G
gi|7                          :                                                                                                                                                              tgccggtgtaacgttgtaaactgaaccccatagaataatgattttatataaaataacgcccccccccGTCATAATATTATGACCGGGGG-GTCATAATAATATGATCTCCtccctcacacgtagaaaaatgaccctcacatagaattttgaccccctatagatagaataacgacctcctaacccaaaccctaaccctaacccatctacggtacacttacaacataattatcccccgccgataggcatcagaggagaatatgctataatggcacc
gi|7                          :                                                                                                                                                                                                        cataatataatgacatgtggtcataatcATATTATTATGACCCCCCG-GTCATAATATTATGA-C
gi|1                          :                                                                                                                                                                                                               cataatataatgacatgtggtcataatcggagatcGGGGA-GTCATAATATTATGA-CTCCCCGGT-CATAATATTATGACC
gi|4                          :                                               ttatatttaaattcataaaattattaacatgattttgatcagtagaaaaattactagagttagaaactattgggtgactagacgatggtgaagttgtgtcattgtatgtatttggatgccggtgtaccgttataaactgacccccatagaataatgaccccctggtcattattttatatataatagtgactccccGGGGA-GTCATAATATAATGA-CCCCcacacgtagaaaaatgaccctcacatagaattgtgaccccctatagaataacgaccccctaacccaaaccataacccatctaaggtacacttacaacataattatccccaccgataggaatcggaggaaaatatggcaatggcacccgtccg
gi|2                          :                                                                                                                                                                                                                                                  GAGGGAGTCATAATATTATGA-Ccacacgtagaaaaatgaccctcacatagaattgtgaccccctatagaataacgaacccctaacccaaaccctaaccctaacccatctgaggttcacttacaacataattatcccccgccgataggcatcggaggagaatatggtaatggcacccgtcc
gi|4                          :                                                                                                                                                                          tgccggtgtaacgttgtaaactgaaccccatagaataatgattttatataaaataacgcccccccccccccccgGGG-GTCATTATATTATGA-CTCCCCCACACGTAGAAAAATGACCCTCACATAGAATTGTGACCCCCT----ATAGAATAACGAACCCCTAACCCAAACCCTAACCCTAACCCATCTGAGGTTCACTTACAACATAATTAT-CCC-CC-GCCGATAGGC-ATCGGAGG--AGAATATG--GTAATGG----CACCCGTCCacacgtagaaaaatgaccctcacatagaattttgaccccctatagatagaataacgacctcctaacccaaaccctaaccctaacccatctacggtacacttacaacataattatcccccgccgataggcatcagaggagaatatgctataatggcacc
gi|5                          :                                                                                                                                                                                                                                                                                             GACCCTCACATAGAATTGTGACCCCCT----ATAGAATAATGACCCCCTAACCCAAATCCTAACCCTAACCCATCTAAGGTACACTTACAACATAATTAT--CC-CC-ACCGATCGGC-ATCGGAGG--AGAATATG--GTAATGG----CACCCGTCCG
gi|8                          :                                                                                                                                                                                                                                                                                                                                 ATAACGACCCCCTAACC-----CA-AACCCTAACCCATCTAAGGTAAACTTACAACATAATTAT--CC-CC-ACCGATA
gi|11                         :                                                                                                                                                                                                                                                                                                                                                                                         ATTATTAT-CAC-CT-GCCAA-AGGC----GAAGG--GGGATATG--GTAAAGG----TATCCGT
gi|12                         :                                                                                                                                                                                                                                                                                                                                                                                            ATTAT-CCC-CCCGCCGA-AGGC----GAAGC--GGGATATG--GTAATGtagtgcatgcg
gi|14                         :                                                                                                                                                                                                                                                                                                                                                                                          ttATTAT-ACTGCC-GCCGA-AGGCGAT--GAGG--G--ATATG--GTAATGg
gi|13                         :                                                                                                                                                                                                                                                                                                                                                                                           tATTAT-ACTGCC-GCCGA-AGGCGAT--GAGG--G--ATATG--GTAATGg
gi|10                         :                                                                                                                                                                                                                                                                                                                                                                                           ttTTATTCCC-CC-ACCGA-AGGC----GAAGG--GGGATATG--GTAATGG----TTTCCATCCATg
gi|16                         :                                                                                                                                                                                                                                                                                                                                                                                           ttTTAT-CCC-CC-GCTGA-AGGT-A---AAGG--GGAATATG--GTAAgcatgcat
gi|9                          :                                                                                                                                                                                                                                                                                                                                                                                             TTAT-CCC-CC-ACTGA-AGGT----GAAGGTGGGGATATG--GTAATGG----TCTCCGTCTGT
gi|6                          :                                                                                                                                                                                                                                                                                                                                                                                             TTAT-CCC-TC-GCCAA-ACGC----GAAGT--GGGATATG--GTAATGGTCTCCATCTGTCCGTctgtgagtgcgtgcgt
1 sequences could not be aligned to this particular reference sequence:
Unaligned ( gi|15 ): GTAATCCCCCCGCAGAAGGCGAAGGGGGATATGATAA






Alignments
lowQualScore                  :                         222222222222222222222222222222222222222222222222222222                                                                                                                                                                                                                                               
lowQualScore                  :                         111111111111111111111111111111111111111111111111111111                                                                                                             1111                        1                                                     2    333                                        
lowQualScore                  :           1             111111111111111111111111111111111111111111111111111111   4    1    0   2      0  8888888    1  2              6       4                                            7777                        0  3                                     66  5  2     0    888   5  33        33       7777           
lowQualScore                  :           .             ......................................................   .    .    .   .      .  .......    .  .              .       .                                            ....                        .  .                                     ..  .  .     .    ...   .  ..        ..       ....           
lowQualScore                  :           0             111111111111111111111111111111111111111111111111111111   2    2    2   5      8  6666666    0  5              7       6                                            0000                        8  2                                     00  3  7     4    000   7  99        99       1111           
consensus                     :  GCCGGTGTAACGTTGTAAACTGA-----------------CCCCC-----------------T--------------ATAAAATAATGACCCCCCGGTCATAATATTATGACCGGGGGGTCATAATATTATGA-CTCCCCCACACGTAGAAAAATGACCCTCACATAGAATTGTGACCCCCTATAG----AATAACGACCCCCTAACCCAAACCCTAACCCTAACCCATCTAAGGTACACTTACAACATAATTAT-CCC-CC-GCCGATAGGCAT-GGA-GG--GGGATATG--GTAATGG----CACCCGTCCGT
Reference ( family-6277 )     :  GCCGGTGTANCGTTGTAAACTGA-----------------CCCCC-----------------T--------------ATAGAATAATGACCCCCCGGTCATAATATTATGACCGGGGGGTCATAATATTATGA-CTCCCCCGCACGTAGAAAAATGACCCTCACATAGAATTGTGACCCCCTATAG----AATAACGACCCCCTAACCCAAACCCTAACCCTAACCCATCTAAGGTACACTTACAACATAATTAT-CCC-CC-GCCGATAGGCAT-GGA-GG--GGGATATG--GTAATGG----CACCCGTCCGT
gi|1                          :  GCCGGTGTACCGTTATAAACTGACCCCCATAGAATAATGACCCCC-----------------TGGTCATTATTTTATATATAATAGTGACTCCCCGGTCATAATATTATGACCGGGGAGTCATAATATTATGA-CTCCCCCACACGTAGAAAAATGACCCTCACATAGAATTGTGACCCCCTATAG----AATAACGACCCCCTAACCCAAACC--A----TAACCCATCTAAGGTACACTTACAACATAATTAT--CC-CC-ACCGATAGGAATCGGA-GG--AAAATATG--GCAATGG----CACCCGTCCG
gi|10                         :                                                                                                                                        ttatatttaaattcataaaattattaacatgattttgatcagtagaaaaattactagagttagaaactattgggtgactagacgatggtgaagttgtgtcattgtatgtatttggatTTATTCCC-CC-ACCGA-AGGC---GAA-GG--GGGATATG--GTAATGG----TTTCCATCCAT
gi|11                         :                                                                                                                                                                                                                                                       ttATTATTAT-CAC-CT-GCCAA-AGGC---GAA-GG--GGGATATG--GTAAAGG----TATCCGTgcatgcat
gi|12                         :                                                                                                                                                                                                                                                            ATTAT-CCC-CCCGCCGA-AGGC---GAA-GC--GGGATATG--GTAATGG----tagtgcatgcg
gi|13                         :                                                                                                                                                                                                                                                          ttATTAT-ACTGCC-GCCGA-AGGC----GATGA--GGGATATG--GTAATGG----
gi|14                         :                                                                                                                                                                                                                                                          ttATTAT-ACTGCC-GCCGA-AGGC----GATGA--GGGATATG--GTAATGG----
gi|15                         :                                                                                                                                                                                                                                                                t-CCC-CC-GCAGA-AGGC---GAA-GG--GGGATATG--ATAA
gi|16                         :                                                                                                                                                                                                                                                       gtaatcTTAT-CCC-CC-GCTGA-AGGTA---AA-GG--GGAATATG--GTAA
gi|2                          :  GCCGGTGTAACGTTGTAAACTGA-----------------ACCCCATAGAATAATGATTTTAT--------------ATAAAATAACGCCCCCCCCCCCCC----------CCGG----TCATAATATTATGA-CTCCCTCACACGTAGAAAAATGACCCTCACATAGAATTTTGACCCCCTATAGATAGAATAACGACCTCCTAACCCAAACCCTAACCCTAACCCATCTACGGTACACTTACAACATAATTAT-CCC-CC-GCCGATAGGCATCAGA-GG--AGAATATGCTATAATGG----CACC
gi|3                          : tGCCGGTGTAACGTTGTAAACTGA-----------------CCCCC--------------------------------ATAGAATATTGAACCCCCGGTGATAATATTATGACCGAGGGGTCATAATATTATGA-CTCCCCACCACGTAGTAAAATGACCCTCACATAGAATTTTGATCCCCTATAG----AATAACGACCCCCTAACCAAAACCATAACCTTAACCCATCTAAGGTACACTTACAACATAATTAT-CCC-CC-GCCGATAGGCATCGGA-GG--AGAATATG--GTAATGA----CACCCGTCCGT
gi|4                          :                                                                                                                     GGGGTCATTATATTATGA-CTCCCCCACACGTAGAAAAATGACCCTCACATAGAATTGTGACCCCCTATAG----AATAACGAACCCCTAACCCAAACCCTAACCCTAACCCATCTGAGGTTCACTTACAACATAATTAT-CCC-CC-GCCGATAGGCATCGGA-GG--AGAATATG--GTAATGG----CACCCGTCC
gi|5                          :                                                                                                                                                             GACCCTCACATAGAATTGTGACCCCCTATAG----AATAATGACCCCCTAACCCAAATCCTAACCCTAACCCATCTAAGGTACACTTACAACATAATTAT--CC-CC-ACCGATCGGCATCGGA-GG--AGAATATG--GTAATGG----CACCCGTCCG
gi|6                          :                                                                                                                                                                                                                                                             TTAT-CCC-TC-GCCAA-ACGC---GAA-GT--GGGATATG--GTAATGGTCTCCATCTGTCCGT
gi|7                          :                                                               tt--------------ATAATATAATGACATGT-GGTCATAAT--------CGGAGA-TCATATTATTATGA-C-CCCCCGgtgtgtgtgtgtgtgtg
gi|7                          :                                                                                                 cGTCATAATATTATGACCGGGGGGTCATAATAATATGATCTCCgtcataatattatgac
gi|8                          :                                                                                                                                                                     cataatataatgacatgtggtcataatcATAACGACCCCCTAACCCAAACC------CTAACCCATCTAAGGTAAACTTACAACATAATTAT--CC-CC-ACCGATA
gi|9                          :                                                                                                                                                                                                                                                             TTAT-CCC-CC-ACTGA-AGG--T-GAA-GGTGGGGATATG--GTAATGG----TCTCCGTCTGT





Alignments
lowQualScore                  :                         222222222222222222222222222222222222222222222222222222                                                                                                                                                                                                                                               
lowQualScore                  :                         111111111111111111111111111111111111111111111111111111                                                                                                             1111                        1                                                     2    333                                        
lowQualScore                  :                         111111111111111111111111111111111111111111111111111111   1    1    0   2      0  8888888    1  2              6                                                    7777                        0  3                                     66  5  2     0    888   5  33        33       7777           
lowQualScore                  :                         ......................................................   .    .    .   .      .  .......    .  .              .                                                    ....                        .  .                                     ..  .  .     .    ...   .  ..        ..       ....           
lowQualScore                  :                         111111111111111111111111111111111111111111111111111111   2    2    2   5      8  6666666    0  5              7                                                    0000                        8  2                                     00  3  7     4    000   7  99        99       1111           
consensus                     :  GCCGGTGTAACGTTGTAAACTGA-----------------CCCCC-----------------T--------------ATAAAATAATGACCCCCCGGTCATAATATTATGACCGGGGGGTCATAATATTATGA-CTCCCCCACACGTAGAAAAATGACCCTCACATAGAATTGTGACCCCCTATAG----AATAACGACCCCCTAACCCAAACCCTAACCCTAACCCATCTAAGGTACACTTACAACATAATTAT-CCC-CC-GCCGATAGGCAT-GGA-GG--GGGATATG--GTAATGG----CACCCGTCCGT
Reference ( family-6277 )     :  GCCGGTGTAACGTTGTAAACTGA-----------------CCCCC-----------------T--------------ATAAAATAATGACCCCCCGGTCATAATATTATGACCGGGGGGTCATAATATTATGA-CTCCCCCACACGTAGAAAAATGACCCTCACATAGAATTGTGACCCCCTATAG----AATAACGACCCCCTAACCCAAACCCTAACCCTAACCCATCTAAGGTACACTTACAACATAATTAT-CCC-CC-GCCGATAGGCAT-GGA-GG--GGGATATG--GTAATGG----CACCCGTCCGT
gi|1                          :  GCCGGTGTACCGTTATAAACTGACCCCCATAGAATAATGACCCCC-----------------TGGTCATTATTTTATATATAATAGTGACTCCCCGGTCATAATATTATGACCGGGGAGTCATAATATTATGA-CTCCCCCACACGTAGAAAAATGACCCTCACATAGAATTGTGACCCCCTATAG----AATAACGACCCCCTAACCCAAACC--A----TAACCCATCTAAGGTACACTTACAACATAATTAT--CC-CC-ACCGATAGGAATCGGA-GG--AAAATATG--GCAATGG----CACCCGTCCG
gi|10                         :                                                                                                                                        ttatatttaaattcataaaattattaacatgattttgatcagtagaaaaattactagagttagaaactattgggtgactagacgatggtgaagttgtgtcattgtatgtatttggatTTATTCCC-CC-ACCGA-AGGC---GAA-GG--GGGATATG--GTAATGG----TTTCCATCCAT
gi|11                         :                                                                                                                                                                                                                                                       ttATTATTAT-CAC-CT-GCCAA-AGGC---GAA-GG--GGGATATG--GTAAAGG----TATCCGTgcatgcat
gi|12                         :                                                                                                                                                                                                                                                            ATTAT-CCC-CCCGCCGA-AGGC---GAA-GC--GGGATATG--GTAATGG----tagtgcatgcg
gi|13                         :                                                                                                                                                                                                                                                          ttATTAT-ACTGCC-GCCGA-AGGC----GATGA--GGGATATG--GTAATGG----
gi|14                         :                                                                                                                                                                                                                                                          ttATTAT-ACTGCC-GCCGA-AGGC----GATGA--GGGATATG--GTAATGG----
gi|15                         :                                                                                                                                                                                                                                                                t-CCC-CC-GCAGA-AGGC---GAA-GG--GGGATATG--ATAA
gi|16                         :                                                                                                                                                                                                                                                       gtaatcTTAT-CCC-CC-GCTGA-AGGTA---AA-GG--GGAATATG--GTAA
gi|2                          :  GCCGGTGTAACGTTGTAAACTGA-----------------ACCCCATAGAATAATGATTTTAT--------------ATAAAATAACGCCCCCCCCCCCCC----------CCGG----TCATAATATTATGA-CTCCCTCACACGTAGAAAAATGACCCTCACATAGAATTTTGACCCCCTATAGATAGAATAACGACCTCCTAACCCAAACCCTAACCCTAACCCATCTACGGTACACTTACAACATAATTAT-CCC-CC-GCCGATAGGCATCAGA-GG--AGAATATGCTATAATGG----CACC
gi|3                          : tGCCGGTGTAACGTTGTAAACTGA-----------------CCCCC--------------------------------ATAGAATATTGAACCCCCGGTGATAATATTATGACCGAGGGGTCATAATATTATGA-CTCCCCACCACGTAGTAAAATGACCCTCACATAGAATTTTGATCCCCTATAG----AATAACGACCCCCTAACCAAAACCATAACCTTAACCCATCTAAGGTACACTTACAACATAATTAT-CCC-CC-GCCGATAGGCATCGGA-GG--AGAATATG--GTAATGA----CACCCGTCCGT
gi|4                          :                                                                                                                     GGGGTCATTATATTATGA-CTCCCCCACACGTAGAAAAATGACCCTCACATAGAATTGTGACCCCCTATAG----AATAACGAACCCCTAACCCAAACCCTAACCCTAACCCATCTGAGGTTCACTTACAACATAATTAT-CCC-CC-GCCGATAGGCATCGGA-GG--AGAATATG--GTAATGG----CACCCGTCC
gi|5                          :                                                                                                                                                             GACCCTCACATAGAATTGTGACCCCCTATAG----AATAATGACCCCCTAACCCAAATCCTAACCCTAACCCATCTAAGGTACACTTACAACATAATTAT--CC-CC-ACCGATCGGCATCGGA-GG--AGAATATG--GTAATGG----CACCCGTCCG
gi|6                          :                                                                                                                                                                                                                                                             TTAT-CCC-TC-GCCAA-ACGC---GAA-GT--GGGATATG--GTAATGGTCTCCATCTGTCCGT
gi|7                          :                                                               tt--------------ATAATATAATGACATGT-GGTCATAAT--------CGGAGA-TCATATTATTATGA-CCCCCCgtgtgtgtgtgtgtgtg
gi|7                          :                                                                                                 cGTCATAATATTATGACCGGGGGGTCATAATAATATGATCTCCggtcataatattatgac
gi|8                          :                                                                                                                                                                     cataatataatgacatgtggtcataatcATAACGACCCCCTAACCCAAACC------CTAACCCATCTAAGGTAAACTTACAACATAATTAT--CC-CC-ACCGATA
gi|9                          :                                                                                                                                                                                                                                                             TTAT-CCC-CC-ACTGA-AGG--T-GAA-GGTGGGGATATG--GTAATGG----TCTCCGTCTGT


blockSeqs                     :                         ACCCCATAGAATAATGATTTTAT                                  A    A        C         ATTATGA    G  G              T                                                    ATAG                        C  A                                     TC  G  C     T    ATC   T  TG        CT       TCTC
blockSeqs                     :                         CCCCC                                                    G    T        C         ATTATGA    G  G              .                                                    .                           A  A                                     C   G  .     T    ATC   T  .         .        .   
blockSeqs                     :                                                                                  A    A        .         .          A  G              .                                                    .                           C  A                                     C   .  .     T    ATC   .  .         .        .   
blockSeqs                     :                                                                                                          .          G  .              .                                                    .                           C  A                                     A   .  .     T    ATC   .  .         .        .   
blockSeqs                     :                                                                                                                     .  .              .                                                                                .  .                                     A   .  .     T    A     .  .         .        .   
blockSeqs                     :                                                                                                                                                                                                                                                                 C   .  .     .    T     .  .         .        .   
blockSeqs                     :                                                                                                                                                                                                                                                                 C   .  .     .    .     .  .         .        .   
blockSeqs                     :                                                                                                                                                                                                                                                                 C   .  .     .    .     .  .         .        .   
blockSeqs                     :                                                                                                                                                                                                                                                                 C   .  .     .    .     .  .         .        .   
blockSeqs                     :                                                                                                                                                                                                                                                                 C   .  .     .    .     .  .         .        .   
blockSeqs                     :                                                                                                                                                                                                                                                                 C   .  .     .    .     .  .         .        .   
blockSeqs                     :                                                                                                                                                                                                                                                                 C   .  .     .    .     .  .         .            
blockSeqs                     :                                                                                                                                                                                                                                                                 .   .  .     .    .     .  .         .            
blockSeqs                     :                                                                                                                                                                                                                                                                 .   .  .     .                                    


blockSeqCons                  :                                                                                                                                                                                                                                                                 C*                ***
originalCons                  :  GCCGGTGTAACGTTGTAAACTGA-----------------CCCCC-----------------T--------------ATAAAATAATGACCCCCCGGTCATAATATTATGACCGGGGGGTCATAATATTATGA-CTCCCCCACACGTAGAAAAATGACCCTCACATAGAATTGTGACCCCCTATAG----AATAACGACCCCCTAACCCAAACCCTAACCCTAACCCATCTAAGGTACACTTACAACATAATTAT-CCC-CC-GCCGATAGGCAT-GGA-GG--GGGATATG--GTAATGG----CACCCGTCCGT
finalCons                     :  GCCGGTGTAACGTTGTAAACTGA-----------------CCCCC-----------------T--------------ATAAAATAATGACCCCCCGGTCATAATATTATGACCGGGGGGTCATAATATTATGA-CTCCCCCACACGTAGAAAAATGACCCTCACATAGAATTGTGACCCCCTATAG----AATAACGACCCCCTAACCCAAACCCTAACCCTAACCCATCTAAGGTACACTTACAACATAATTATC-CC-CC-GCCGATAGGC---GGA-GG--GGGATATG--GTAATGG----CACCCGTCCGT





Alignments
lowQualScore                  :                         222222222222222222222222222222222222222222222222222222                                                                                                                                                                                                                                              
lowQualScore                  :                         111111111111111111111111111111111111111111111111111111                                                                                                             1111                        1                                                     2   222                                        
lowQualScore                  :                         111111111111111111111111111111111111111111111111111111   1    1    0   2      0  8888888    1  2              6                                                    7777                        0  3                                     66  5  2     0   555  0   33        33       7777           
lowQualScore                  :                         ......................................................   .    .    .   .      .  .......    .  .              .                                                    ....                        .  .                                     ..  .  .     .   ...  .   ..        ..       ....           
lowQualScore                  :                         111111111111111111111111111111111111111111111111111111   2    2    2   5      8  6666666    0  5              7                                                    0000                        8  2                                     00  3  7     4   000  3   99        99       1111           
consensus                     :  GCCGGTGTAACGTTGTAAACTGA-----------------CCCCC-----------------T--------------ATAAAATAATGACCCCCCGGTCATAATATTATGACCGGGGGGTCATAATATTATGA-CTCCCCCACACGTAGAAAAATGACCCTCACATAGAATTGTGACCCCCTATAG----AATAACGACCCCCTAACCCAAACCCTAACCCTAACCCATCTAAGGTACACTTACAACATAATTAT-CCC-CC-GCCGATAGG---CGAAGG--GGGATATG--GTAATGG----CACCCGTCCGT
Reference ( family-6277 )     :  GCCGGTGTAACGTTGTAAACTGA-----------------CCCCC-----------------T--------------ATAAAATAATGACCCCCCGGTCATAATATTATGACCGGGGGGTCATAATATTATGA-CTCCCCCACACGTAGAAAAATGACCCTCACATAGAATTGTGACCCCCTATAG----AATAACGACCCCCTAACCCAAACCCTAACCCTAACCCATCTAAGGTACACTTACAACATAATTAT-CCC-CC-GCCGATAGG---CGGAGG--GGGATATG--GTAATGG----CACCCGTCCGT
gi|1                          :  GCCGGTGTACCGTTATAAACTGACCCCCATAGAATAATGACCCCC-----------------TGGTCATTATTTTATATATAATAGTGACTCCCCGGTCATAATATTATGACCGGGGAGTCATAATATTATGA-CTCCCCCACACGTAGAAAAATGACCCTCACATAGAATTGTGACCCCCTATAG----AATAACGACCCCCTAACCCAAACC--A----TAACCCATCTAAGGTACACTTACAACATAATTAT--CC-CC-ACCGATAGGAATCGGAGG--AAAATATG--GCAATGG----CACCCGTCCG
gi|10                         :                                                                                                                                        ttatatttaaattcataaaattattaacatgattttgatcagtagaaaaattactagagttagaaactattgggtgactagacgatggtgaagttgtgtcattgtatgtatttggatTTATTCCC-CC-ACCGA-AGG---CGAAGG--GGGATATG--GTAATGG----TTTCCATCCAT
gi|11                         :                                                                                                                                                                                                                                                       ttATTATTAT-CAC-CT-GCCAA-AGG---CGAAGG--GGGATATG--GTAAAGG----TATCCGTgcatgcat
gi|12                         :                                                                                                                                                                                                                                                            ATTAT-CCC-CCCGCCGA-AGG---CGAAGC--GGGATATG--GTAATGG----tagtgcatgcg
gi|13                         :                                                                                                                                                                                                                                                          ttATTAT-ACTGCC-GCCGA-AGG---CGATGA--GGGATATG--GTAATGG----
gi|14                         :                                                                                                                                                                                                                                                          ttATTAT-ACTGCC-GCCGA-AGG---CGATGA--GGGATATG--GTAATGG----
gi|15                         :                                                                                                                                                                                                                                                                t-CCC-CC-GCAGA-AGG---CGAAGG--GGGATATG--ATAA
gi|16                         :                                                                                                                                                                                                                                                       gtaatcTTAT-CCC-CC-GCTGA-AGG---TAAAGG--GGAATATG--GTAA
gi|2                          :  GCCGGTGTAACGTTGTAAACTGA-----------------ACCCCATAGAATAATGATTTTAT--------------ATAAAATAACGCCCCCCCCCCCCC----------CCGG----TCATAATATTATGA-CTCCCTCACACGTAGAAAAATGACCCTCACATAGAATTTTGACCCCCTATAGATAGAATAACGACCTCCTAACCCAAACCCTAACCCTAACCCATCTACGGTACACTTACAACATAATTAT-CCC-CC-GCCGATAGGCATCAGAGG--AGAATATGCTATAATGG----CACC
gi|3                          : tGCCGGTGTAACGTTGTAAACTGA-----------------CCCCC--------------------------------ATAGAATATTGAACCCCCGGTGATAATATTATGACCGAGGGGTCATAATATTATGA-CTCCCCACCACGTAGTAAAATGACCCTCACATAGAATTTTGATCCCCTATAG----AATAACGACCCCCTAACCAAAACCATAACCTTAACCCATCTAAGGTACACTTACAACATAATTAT-CCC-CC-GCCGATAGGCATCGGAGG--AGAATATG--GTAATGA----CACCCGTCCGT
gi|4                          :                                                                                                                     GGGGTCATTATATTATGA-CTCCCCCACACGTAGAAAAATGACCCTCACATAGAATTGTGACCCCCTATAG----AATAACGAACCCCTAACCCAAACCCTAACCCTAACCCATCTGAGGTTCACTTACAACATAATTAT-CCC-CC-GCCGATAGGCATCGGAGG--AGAATATG--GTAATGG----CACCCGTCC
gi|5                          :                                                                                                                                                             GACCCTCACATAGAATTGTGACCCCCTATAG----AATAATGACCCCCTAACCCAAATCCTAACCCTAACCCATCTAAGGTACACTTACAACATAATTAT--CC-CC-ACCGATCGGCATCGGAGG--AGAATATG--GTAATGG----CACCCGTCCG
gi|6                          :                                                                                                                                                                                                                                                             TTAT-CCC-TC-GCCAA-ACG---CGAAGT--GGGATATG--GTAATGGTCTCCATCTGTCCGT
gi|7                          :                                                               tt--------------ATAATATAATGACATGT-GGTCATAAT--------CGGAGA-TCATATTATTATGA-CCCCCCgtgtgtgtgtgtgtgtg
gi|7                          :                                                                                                 cGTCATAATATTATGACCGGGGGGTCATAATAATATGATCTCCggtcataatattatgac
gi|8                          :                                                                                                                                                                     cataatataatgacatgtggtcataatcATAACGACCCCCTAACCCAAACC------CTAACCCATCTAAGGTAAACTTACAACATAATTAT--CC-CC-ACCGATA
gi|9                          :                                                                                                                                                                                                                                                             TTAT-CCC-CC-ACTGA-AGG---TGAAGGTGGGGATATG--GTAATGG----TCTCCGTCTGT