lowQualScore                  :                                           111111111111111111111     111111111111111111111             111111111111111             111111                                  
lowQualScore                  :                                           666666666666666666666     555555555555555555555 1      333  000000000000000 55555   333 888888   0            2                 
lowQualScore                  :                                           .....................     ..................... .      ...  ............... .....   ... ......   .            .                 
lowQualScore                  :                                           222222222222222222222     555555555555555555555 7      222  555555555555555 33333   777 000000   2            7                 
consensus                     :               CTTCCATTTTCCATTCCATGAAAAATAG---------------------AACGT---------------------T-CTATTT---TGG------A-------C-----CGA---CT--GG-AAATTTCTGAAGCTGC-AAAGACGAATGCTACAT
Reference ( gi|6 )            :               CTTCCATTTTCCATTCCATGAAAAATAG---------------------AACGT---------------------T-CTATTT---TGA------A-------C-----CGA---CT--TG-AAATTTCTGAAGCTGC-AAAGACGAATGCTACAT
gi|10                         :               CTTCCATTTCCCACTCCATAAAAAGTAG---------------------AACGT---------------------T-CTATTT---TGG------A-------C-----AAA---CT--GG-AAATTTCTGAAGCTGC-AAAAAC
gi|11                         :               CTTCCATTTTCCATTCCATGAAAAATAA---------------------AACAT---------------------T-CTTTTT---TGA------A-------C-----C-------------AATTTCTGAATTTGT-AAAGACAA
gi|13                         :              aCTTCTATTTTCCATTCTATGAAAAATAT---------------------AACGT---------------------T-CTATTT---TGA------A-------C-----CAA---C----------TTCTGAAGCTGggc
gi|8                          :               CTTCCATTTTCGTTTTCTTGTAAAATAG---------------------AACGT---------------------TCCTA-TT---TGA------A-------C-----TAA---CTTCTG-AAG---CTGAAGCTGC-AAAGACG-ATGCTACga
gi|12                         :               CTTTCATTTGTCATTGAATGAAAAATAG---------------------AACGT---------------------T-TTACTT---AGG------A-------C-----CGA---CT--GG-AAACTTCTGAAGCTGC-
gi|15                         :               CTTCCATTTTCCATTCCATGAAAAATAC---------------------AACGT---------------------T-CTATTT---TAT------A-------C-----CAA---C----------TTCTAAAGCTG
gi|14                         :               CTTCCATTTTCCATTCCATGAAAAATAC---------------------AACGT---------------------T-CTATTT---TAT------A-------C-----CAA---C----------TTCTAAAGCTGtc
gi|3                          :                TTCCATTTTCCGTTGCATGGAAAATAG---------------------AACGTACTTTTTTGCATGTTGAACGTT-CTTTTT---TGA--------------C-----CGA---CT--GG-AAATTTCTGAAGCTGC-AAAGACGATTGCTtc
gi|19                         :                TTCCATTTTCTATTCCATAGAAAATAG---------------------AATGT---------------------T-CTA
gi|9                          :               atTCCATTTTCCATTCCATGAAAAATAG---------------------AACGT---------------------T-CTATTT---TGG------A-------C-----CGA---CT--TG-AAATTTCTGAAGCTGC-AAAGACGAAT
gi|7                          :                 TTCATTTTCCATTCCATGAAAAATAG---------------------AACGT---------------------T-CTATTT---TGG------G-------C-----CGA---CT--GG-AAATTTCTGAAGCTGC-AAAAACGAATGCTTCA
gi|5                          :                gTCCATTTTCCATTCCATGAAAATTAG---------------------AACAT---------------------T-ATATTT---TGG------A-------C-----CGA---CT--GG-AAACTTCTGAAACTGCAAAAAACGAATGCTACAT
gi|2                          :                caCCACCTTTCATT------AAAATAG---------------------AACGT---------------------T-CTATTT---Tttttt
gi|1                          :  attgtttccattccatgaATTTTCAATTCCATGAAAAATAGAACTTTCTATTTTGTAGGGATAACGT---------------------T-CTATTT---TGG------A-------T-----CAA---C---TA-AAATTTTTT--GCAGC-AATGACGAATGCtgtgaagtctaatgaaaatttctgaagttccaaagacgaatgccacataatgtttaaatttaatc
gi|7                          :                      TTTCCAGTCGGCCCAAAATAG---------------------AACGT---------------------T-CTATTT---Taccaaaatgttttaatatgaaatcc
gi|10                         :  gttcattttccattccatgaTTTCCAGTTTGTCCAAAATAG---------------------AACGT---------------------T-CTACTT---Ttttctgaagctgcaaaaacgaatgcttca
gi|2                          : cttccatttcccactccataaTTTCCATTCCATGAAAAATAG---------------------AACGT---------------------T-CTATTTTAATGA------AAGGTGGTG-----TGAAGTCTAATGAAAATTTCTGAAGTTCC-AAAGACGAATGCCACATtttctgaagctgcaaaaac
gi|4                          :                     attgCCATTCCAGGAAAAATAG---------------------AAC---------------------------ATTT---TGAGGAAAAA-------CGAAAGCAA---CT--TG-AAATTTTTGGAGCTAC-AAAGACGAATGCTAaatgtttaaatttaatc
gi|1                          :                             TCCCTACAAAATAG---------------------AAAGT---------------------T-CTATTT---TTC------A-------T-----GGA---AT--TG-AAAaaaaacatgttgaattaaa
gi|17                         :                           atTCTATGTAAAATAG---------------------AACGT---------------------T-CTTTTT---TGA------A-------C------------------AAACTTCTGAAGCTGC-taacgttctattttggatcaactaaaattttttgcagcaatgacgaatgcaccaaaatgttttaatatgaaatcc
gi|9                          :                                    AAAATAG---------------------AACGT---------------------T-CTATTT---Tca
gi|16                         :                                                 tccattttccattccatgaT---------------------T-CTATTT---TGG------G-------C-----TGA---CT--AG-AA-TCTCTAAAGCTTC-AAAGACGAATGCTACggaccgacttgaaatttctgaagctgcaaagacgaat
gi|18                         :                                                                                         ct-CTATTT---TGG------A-------C-----AGA---CT--GG-AAATTTCTGTAGCTGC-AGAGACAAATGCTA
gi|20                         :                                                                                                               -------C-----CGA---CT--GT-AAATTTCTGAAGCTGC-AAAGACGAGTACT





Alignments
lowQualScore                  :                                3333333333333333333333333333333333333333333                     111111111                                                  
lowQualScore                  :                                1111111111111111111111111111111111111111111    2       7777777  555555555  55555 1  7777                 2                 
lowQualScore                  :                                ...........................................    .       .......  .........  ..... .  ....                 .                 
lowQualScore                  :                                0000000000000000000000000000000000000000000    1       2222222  333333333  33333 2  7777                 5                 
consensus                     :   CTTCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGAATGCTACAT
Reference ( family-395 )      :   CTTCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGAATGCTACAT
gi|1                          :        ATTTTCAATTCCATGAAAAATAGA---------------------ACTTTCTATTTTGTAGGGATAACGTT-CTATTTT-------GG---------AT-----CAACT--AAAATTTTTTGCA---GC-AATGACGAATGC
gi|10                         :   CTTCCATTTCCCACTCCATAAAAAGTAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----AAACT--GGAAATTTCTGAAGCTGC-AAAAACaccaaaatgttttaatatgaaatcc
gi|11                         :   CTTCCATTTTCCATTCCATGAAAAATAAA---------------------A---------------------CATT-CTTTTTT-------GA---------AC-----C---------AATTTCTGAATTTGT-AAAGACAA
gi|12                         :  aCTTTCATTTGTCATTGAATGAAAAATAGA---------------------A---------------------CGTT-TTACTTA-------GG---------AC-----CGACT--GGAAACTTCTGAAGCTGC-ggc
gi|13                         :   CTTCTATTTTCCATTCTATGAAAAATATA---------------------A---------------------CGTT-CTATTTT-------GA---------AC-----CAAC---------TTCTGAAGCTG
gi|14                         :   CTTCCATTTTCCATTCCATGAAAAATACA---------------------A---------------------CGTT-CTATTTT-------AT---------AC-----CAAC---------TTCTAAAGCTGga
gi|15                         :   CTTCCATTTTCCATTCCATGAAAAATACA---------------------A---------------------CGTT-CTATTTT-------AT---------AC-----CAAC---------TTCTAAAGCTGtc
gi|16                         :                                                                             TT-CTATTTT-------GG---------GC-----TGACT--AGAA-TCTCTAAAGCTTC-AAAGACGAATGCTACtc
gi|17                         :               ctTCTATGTAAAATAGA---------------------A---------------------CGTT-CTTTTTT-------GA---------AC--------------AAACTTCTGAAGCTGC-
gi|18                         :                                                                               -CTATTTT-------GG---------AC-----AGACT--GGAAATTTCTGTAGCTGC-AGAGACAAATGCTAca
gi|19                         :    TTCCATTTTCTATTCCATAGAAAATAGA---------------------A---------------------TGTT-CTA
gi|2                          :        atTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTTAATGAAAGGTGGTGTGAAGT-----CTAAT--GAAAATTTCTGAAGTTCC-AAAGACGAATGCCACAT
gi|20                         :                                                                                                      attgC-----CGACT--GTAAATTTCTGAAGCTGC-AAAGACGAGTACTaatgtttaaatttaatc
gi|3                          :    TTCCATTTTCCGTTGCATGGAAAATAGAACGTACTTTTTTGCATGTTGAA---------------------CGTT-CT-TTTT-------TG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGATTGCT
gi|4                          :             CCATTCCAGGAAAAATAGA---------------------A---------------------C------ATTTT-------GAGGAAAA---ACGAAAGCAACT--TGAAATTTTTGGAGCTAC-AAAGACGAATGCTA
gi|5                          :     TCCATTTTCCATTCCATGAAAATTAGA---------------------A---------------------CATT-ATATTTT-------GG---------AC-----CGACT--GGAAACTTCTGAAACTGCAAAAAACGAATGCTACATaaaaacatgttgaattaaa
gi|6                          : caCTTCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GA---------AC-----CGACT--TGAAATTTCTGAAGCTGC-AAAGACGAATGCTACATttttt
gi|7                          :     TTCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------GC-----CGACT--GGAAATTTCTGAAGCTGC-AAAAACGAATGCTTCA
gi|8                          :  gCTTCCATTTTCGTTTTCTTGTAAAATAGA---------------------A---------------------CGTTCCTA-TTT-------GA---------AC-----TAACTTCTGAAG---CTGAAGCTGC-AAAGACG-ATGCTAC
gi|9                          :     TCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----CGACT--TGAAATTTCTGAAGCTGC-AAAGACGAAT





Alignments
lowQualScore                  :                                3333333333333333333333333333333333333333333                     111111111                                                  
lowQualScore                  :                                1111111111111111111111111111111111111111111    2       7777777  555555555  55555 1  7777                 2                 
lowQualScore                  :                                ...........................................    .       .......  .........  ..... .  ....                 .                 
lowQualScore                  :                                0000000000000000000000000000000000000000000    1       2222222  333333333  33333 2  7777                 5                 
consensus                     :   CTTCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGAATGCTACAT
Reference ( family-395 )      :   CTTCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGAATGCTACAT
gi|1                          :        ATTTTCAATTCCATGAAAAATAGA---------------------ACTTTCTATTTTGTAGGGATAACGTT-CTATTTT-------GG---------AT-----CAACT--AAAATTTTTTGCA---GC-AATGACGAATGC
gi|10                         :   CTTCCATTTCCCACTCCATAAAAAGTAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----AAACT--GGAAATTTCTGAAGCTGC-AAAAACaccaaaatgttttaatatgaaatcc
gi|11                         :   CTTCCATTTTCCATTCCATGAAAAATAAA---------------------A---------------------CATT-CTTTTTT-------GA---------AC-----C---------AATTTCTGAATTTGT-AAAGACAA
gi|12                         :  aCTTTCATTTGTCATTGAATGAAAAATAGA---------------------A---------------------CGTT-TTACTTA-------GG---------AC-----CGACT--GGAAACTTCTGAAGCTGC-ggc
gi|13                         :   CTTCTATTTTCCATTCTATGAAAAATATA---------------------A---------------------CGTT-CTATTTT-------GA---------AC-----CAAC---------TTCTGAAGCTG
gi|14                         :   CTTCCATTTTCCATTCCATGAAAAATACA---------------------A---------------------CGTT-CTATTTT-------AT---------AC-----CAAC---------TTCTAAAGCTGga
gi|15                         :   CTTCCATTTTCCATTCCATGAAAAATACA---------------------A---------------------CGTT-CTATTTT-------AT---------AC-----CAAC---------TTCTAAAGCTGtc
gi|16                         :                                                                             TT-CTATTTT-------GG---------GC-----TGACT--AGAA-TCTCTAAAGCTTC-AAAGACGAATGCTACtc
gi|17                         :               ctTCTATGTAAAATAGA---------------------A---------------------CGTT-CTTTTTT-------GA---------AC--------------AAACTTCTGAAGCTGC-
gi|18                         :                                                                               -CTATTTT-------GG---------AC-----AGACT--GGAAATTTCTGTAGCTGC-AGAGACAAATGCTAca
gi|19                         :    TTCCATTTTCTATTCCATAGAAAATAGA---------------------A---------------------TGTT-CTA
gi|2                          :        atTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTTAATGAAAGGTGGTGTGAAGT-----CTAAT--GAAAATTTCTGAAGTTCC-AAAGACGAATGCCACAT
gi|20                         :                                                                                                      attgC-----CGACT--GTAAATTTCTGAAGCTGC-AAAGACGAGTACTaatgtttaaatttaatc
gi|3                          :    TTCCATTTTCCGTTGCATGGAAAATAGAACGTACTTTTTTGCATGTTGAA---------------------CGTT-CT-TTTT-------TG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGATTGCT
gi|4                          :             CCATTCCAGGAAAAATAGA---------------------A---------------------C------ATTTT-------GAGGAAAA---ACGAAAGCAACT--TGAAATTTTTGGAGCTAC-AAAGACGAATGCTA
gi|5                          :     TCCATTTTCCATTCCATGAAAATTAGA---------------------A---------------------CATT-ATATTTT-------GG---------AC-----CGACT--GGAAACTTCTGAAACTGCAAAAAACGAATGCTACATaaaaacatgttgaattaaa
gi|6                          : caCTTCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GA---------AC-----CGACT--TGAAATTTCTGAAGCTGC-AAAGACGAATGCTACATttttt
gi|7                          :     TTCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------GC-----CGACT--GGAAATTTCTGAAGCTGC-AAAAACGAATGCTTCA
gi|8                          :  gCTTCCATTTTCGTTTTCTTGTAAAATAGA---------------------A---------------------CGTTCCTA-TTT-------GA---------AC-----TAACTTCTGAAG---CTGAAGCTGC-AAAGACG-ATGCTAC
gi|9                          :     TCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----CGACT--TGAAATTTCTGAAGCTGC-AAAGACGAAT


blockSeqs                     :                                ACGTACTTTTTTGCATGTTGAA                         C       AATGAAA  TGGTGTGAA  GAAAG A  TTCT                 A
blockSeqs                     :                                A                                              .       .        GGAAAA     .     G  TG                   .
blockSeqs                     :                                A                                              .       .        .          .     A  TG                   .
blockSeqs                     :                                A                                              .       .        .          .     A  TA                   .
blockSeqs                     :                                A                                              .       .        .          .     A  TG                   .
blockSeqs                     :                                A                                              .       .        .          .     G  TG                   .
blockSeqs                     :                                A                                              .       .        .          .     G  TG                   .
blockSeqs                     :                                A                                              .       .        .          .     T  TG                   .
blockSeqs                     :                                A                                              .       .        .          .     G  TT                   .
blockSeqs                     :                                A                                              .       .        .          .     G  TG                   .
blockSeqs                     :                                A                                              .       .        .          .     A  TT                   .
blockSeqs                     :                                A                                              .       .        .          .     G  TG                   .
blockSeqs                     :                                A                                              .       .        .          .     G  TT                   .
blockSeqs                     :                                A                                              .       .        .          .     G  .                    .
blockSeqs                     :                                A                                              .       .        .          .     A  .                    .
blockSeqs                     :                                A                                              .       .        .          .     G  .                     
blockSeqs                     :                                                                               .       .        .          .     .  .                     
blockSeqs                     :                                                                               .                           .     .  .                     


blockSeqCons                  :                                A******************************************
originalCons                  :   CTTCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGAATGCTACAT
finalCons                     :   CTTCCATTTTCCATTCCATGAAAAATAGAA------------------------------------------CGTT-CTATTTT-------GG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGAATGCTACAT





Alignments
lowQualScore                  :                                3333333333333333333333333333333333333333333                     111111111                                                  
lowQualScore                  :                                1111111111111111111111111111111111111111111    2       7777777  555555555  55555 1  7777                 2                 
lowQualScore                  :                                ...........................................    .       .......  .........  ..... .  ....                 .                 
lowQualScore                  :                                0000000000000000000000000000000000000000000    1       2222222  333333333  33333 2  7777                 5                 
consensus                     :   CTTCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGAATGCTACAT
Reference ( family-395 )      :   CTTCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGAATGCTACAT
gi|1                          :        ATTTTCAATTCCATGAAAAATAGA---------------------ACTTTCTATTTTGTAGGGATAACGTT-CTATTTT-------GG---------AT-----CAACT--AAAATTTTTTGCA---GC-AATGACGAATGC
gi|10                         :   CTTCCATTTCCCACTCCATAAAAAGTAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----AAACT--GGAAATTTCTGAAGCTGC-AAAAACaccaaaatgttttaatatgaaatcc
gi|11                         :   CTTCCATTTTCCATTCCATGAAAAATAAA---------------------A---------------------CATT-CTTTTTT-------GA---------AC-----C---------AATTTCTGAATTTGT-AAAGACAA
gi|12                         :  aCTTTCATTTGTCATTGAATGAAAAATAGA---------------------A---------------------CGTT-TTACTTA-------GG---------AC-----CGACT--GGAAACTTCTGAAGCTGC-ggc
gi|13                         :   CTTCTATTTTCCATTCTATGAAAAATATA---------------------A---------------------CGTT-CTATTTT-------GA---------AC-----CAAC---------TTCTGAAGCTG
gi|14                         :   CTTCCATTTTCCATTCCATGAAAAATACA---------------------A---------------------CGTT-CTATTTT-------AT---------AC-----CAAC---------TTCTAAAGCTGga
gi|15                         :   CTTCCATTTTCCATTCCATGAAAAATACA---------------------A---------------------CGTT-CTATTTT-------AT---------AC-----CAAC---------TTCTAAAGCTGtc
gi|16                         :                                                                             TT-CTATTTT-------GG---------GC-----TGACT--AGAA-TCTCTAAAGCTTC-AAAGACGAATGCTACtc
gi|17                         :               ctTCTATGTAAAATAGA---------------------A---------------------CGTT-CTTTTTT-------GA---------AC--------------AAACTTCTGAAGCTGC-
gi|18                         :                                                                               -CTATTTT-------GG---------AC-----AGACT--GGAAATTTCTGTAGCTGC-AGAGACAAATGCTAca
gi|19                         :    TTCCATTTTCTATTCCATAGAAAATAGA---------------------A---------------------TGTT-CTA
gi|2                          :        atTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTTAATGAAAGGTGGTGTGAAGT-----CTAAT--GAAAATTTCTGAAGTTCC-AAAGACGAATGCCACAT
gi|20                         :                                                                                                      attgC-----CGACT--GTAAATTTCTGAAGCTGC-AAAGACGAGTACTaatgtttaaatttaatc
gi|3                          :    TTCCATTTTCCGTTGCATGGAAAATAGAACGTACTTTTTTGCATGTTGAA---------------------CGTT-CT-TTTT-------TG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGATTGCT
gi|4                          :             CCATTCCAGGAAAAATAGA---------------------A---------------------C------ATTTT-------GAGGAAAA---ACGAAAGCAACT--TGAAATTTTTGGAGCTAC-AAAGACGAATGCTA
gi|5                          :     TCCATTTTCCATTCCATGAAAATTAGA---------------------A---------------------CATT-ATATTTT-------GG---------AC-----CGACT--GGAAACTTCTGAAACTGCAAAAAACGAATGCTACATaaaaacatgttgaattaaa
gi|6                          : caCTTCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GA---------AC-----CGACT--TGAAATTTCTGAAGCTGC-AAAGACGAATGCTACATttttt
gi|7                          :     TTCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------GC-----CGACT--GGAAATTTCTGAAGCTGC-AAAAACGAATGCTTCA
gi|8                          :  gCTTCCATTTTCGTTTTCTTGTAAAATAGA---------------------A---------------------CGTTCCTA-TTT-------GA---------AC-----TAACTTCTGAAG---CTGAAGCTGC-AAAGACG-ATGCTAC
gi|9                          :     TCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----CGACT--TGAAATTTCTGAAGCTGC-AAAGACGAAT