lowQualScore                  :                                     1111                                                                        
lowQualScore                  :                            55   2   0000     2   2  2    2               0    33        2     7       2         
lowQualScore                  :                            ..   .   ....     .   .  .    .               .    ..        .     .       .         
lowQualScore                  :                            00   9   0000     9   9  9    7               4    44        5     1       7         
consensus                     :      CTCAGAAATTTTCCCCAATAAA-NTTT-TTT----CAGTC-GGT-GC-TTTT-TTCGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATTTTT-ATTTAGGCC
Reference ( gi|3 )            :      CTCAGAAATTTTCCCCAATAAA-TTTT-TTT----CAGTC-GGT-GC-TTTT-TTCGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATTTTT-ATTTAGGCC
gi|12                         :      CTTAGAAATTTTCCCCAATATA-ATTT-TTT----CAGTC-GTT-GC-TTTT-TTTGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATTTTT-ATTT
gi|13                         :   aacCTCAGAAATTTTTCACAATAAA-ACTT-TTT----CAGTC-GGT-GC-TTTT-TTCGTGGGTCAG-CGGGCAA--CAGGAAAC-AAACACTATTTTT-ATTTAGG
gi|14                         :      CTCAGAAATTTTC------AAA-TTTT-TTTTATTCAGTT-GGT-GC-TTTT-TTCGTGGGTTGGTCACGCAA--GGGGAAAC-AAACACTATTTTT-ATTT
gi|7                          :    aaCTCAGAAATTTCCCCCAATAAA-TTTTTTTT----CAGTT-GGT-GC-TTTT-TTCATTGGTCGGTCGCGCAA--GAGAAAAC-ACAGA-TATTTTT-AATTt
gi|8                          :     ccTCAGAAATTTTCCCCAATAAA-TTTT-TTT----CAGTT-GGT-GC-TTTT-TTCGTTGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATTTTT-ATTTAGGCgt
gi|5                          :      aTCAGAAATTTTTTACAATAAA-TTTT-TTT----CAGTC-GGT-GC-TTTT-TTGGTGGGTCGGTCTGGCAA--GGGGAAAC-AAACACTATTTTT-ATTTAGGC
gi|4                          :       aCAGAAATTTTTCCCAATAAA-ATTT-TTT----CAGTC-GGT-GC-TTTT-TTCGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACA-TATTTTTAATTTAGGCC
gi|15                         :        CAGAAATTTTCCCCACT-CA-TTTT-TTT----CAGTC-GGT-GCTTTTT-TTCGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATCTTT-ATTTAt
gi|10                         :        CAGAAATTTTTCCCAATAAA-ATTG-TTT----AAGTC-TGT-GC-TTTT-TTCGTGGGTTGGTTGCACAA--GGGGAAAC-AAACATTATTTTT-ATTTAAGCC
gi|16                         :         AGAAATTTTCCCGAATAAA-ATTT-TTT----CAGTC-GGT-GC-TTTT-TTCGTGGGTCGGTCACGCAA--GGGGAAAC-AAACAC
gi|11                         :    aatcaAAAAATTTTCTC-AATAAT-TTTT-TTT----CAGTC-AGT-GC-TTTT-TTCGTTGGTTGGTCGCGCAA--GGGGAAAC-AAACAATTTTTTA-ATTTAGGCC
gi|6                          :          gAAATTTTCCCCAATAAA-TTTT-TTTTT--CATTC-GTT-TT-TTTTTTTCGTGGGTCGGTCACGCAA--GGGGAAAC-AAACATT-TTTTT-ATTTAGGCCt
gi|2                          :             taTTTCAGCAATAAAATTTT-TTG----GGGTC-AG--GC-CGAT-TTTGAGGGTCGGTCGTGGGA--GGGGAAAC-AAAAAATATTTTA-ATTTAGG
gi|9                          : aaatatcatttcggTTTCGGCAATAAA-ATAT-TTT----TGGTCTGGCCGA-TTTT-TT--TGGGTCGG------AAGTGGGAAAACAAAAAAATATTTTA-ATTTAGGCt
gi|18                         :                                             atataattttggT-TTCGTCGGTCGGTCG-GCAA--CTGGAAAC-AAACA--ATTTTT-
gi|1                          :                                                                GGGTCGGTCGGGTAA--CCGGAAAC-AAACATCTTTTTT-TTTTAGGCcaatatggccca
2 sequences could not be aligned to this particular reference sequence:
Unaligned ( gi|17 ): ACAAAACTTAAGGGCCAGCAGGAAAAATTAGGGTCGTTCGGGTTACCTGAACCAGACATATTTTTTATTTAGCC
Unaligned ( gi|19 ): ATATCATTTCGGTTTCGGCAATAACTATTTTTGGGTTAGGCC






Alignments
lowQualScore                  :                                                                                  1111                                                                         
lowQualScore                  :                                                                           1      2222   2  2   2  2    2                    33        2     6       2         
lowQualScore                  :                                                                           .      ....   .  .   .  .    .                    ..        .     .       .         
lowQualScore                  :                                                                           0      0000   7  7   7  7    5                    22        4     1       5         
consensus                     :                                                     CTCAGAAATTTTCCCCAATAAANTTTTTT----CAG-TC-GGT-GC-TTTT-TTCGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATTTTT-ATTTAGGCC
Reference ( family-624 )      :                                                     CTCAGAAATTTTCCCCAATAAANTTTTTT----CAG-TC-GGT-GC-TTTT-TTCGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATTTTT-ATTTAGGCC
gi|1                          :                                                                                                              GGGTCGGTCGGGTAA--CCGGAAAC-AAACATCTTTTTT-TTTTAGGC
gi|10                         : atccgatgccgattttttggacataaaaacttttgagtcggcagttaaaatataCAGAAATTTTTCCCAATAAAATTGTTT----AAG-TC-TGT-GC-TTTT-TTCGTGGGTTGGTTGCACAA--GGGGAAAC-AAACATTATTTTT-ATTTAAGCC
gi|11                         :                                                        AAAAATTTTCTC-AATAATTTTTTTT----CAG-TC-AGT-GC-TTTT-TTCGTTGGTTGGTCGCGCAA--GGGGAAAC-AAACAATTTTTTA-ATTTAGGCC
gi|12                         :                                                    gCTTAGAAATTTTCCCCAATATAATTTTTT----CAG-TC-GTT-GC-TTTT-TTTGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATTTTT-ATTTt
gi|13                         :                                                  aacCTCAGAAATTTTTCACAATAAAACTTTTT----CAG-TC-GGT-GC-TTTT-TTCGTGGGTCAG-CGGGCAA--CAGGAAAC-AAACACTATTTTT-ATTTAGG
gi|14                         :                                                     CTCAGAAATTTTC------AAATTTTTTTTATTCAG-TT-GGT-GC-TTTT-TTCGTGGGTTGGTCACGCAA--GGGGAAAC-AAACACTATTTTT-ATTT
gi|15                         :                                                     aaCAGAAATTTTCCCCACT-CATTTTTTT----CAG-TC-GGT-GCTTTTT-TTCGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATCTTT-ATTTAt
gi|16                         :                                                        AGAAATTTTCCCGAATAAAATTTTTT----CAG-TC-GGT-GC-TTTT-TTCGTGGGTCGGTCACGCAA--GGGGAAAC-AAACAC
gi|18                         :                                                                                                  aatcaT-TTCGTCGGTCGGTCG-GCAA--CTGGAAAC-AAACA--ATTTTT-
gi|2                          :                                                              TTTCAGCAATAAAATTTTTT----GGGGTC-AG--GC-CGAT-TTTGAGGGTCGGTCGTGGGA--GGGGAAAC-AAAAAATATTTTA-ATTTAGGcaatatggccca
gi|3                          :                                       aaatatcatttcggCTCAGAAATTTTCCCCAATAAATTTTTTT----CAG-TC-GGT-GC-TTTT-TTCGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATTTTT-ATTTAGGCCt
gi|4                          :                                                       CAGAAATTTTTCCCAATAAAATTTTTT----CAG-TC-GGT-GC-TTTT-TTCGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACA-TATTTTTAATTTAGGCC
gi|5                          :                                                      TCAGAAATTTTTTACAATAAATTTTTTT----CAG-TC-GGT-GC-TTTT-TTGGTGGGTCGGTCTGGCAA--GGGGAAAC-AAACACTATTTTT-ATTTAGGCt
gi|6                          :                                                         aAAATTTTCCCCAATAAATTTTTTTTT--CAT-TC-GTT-TT-TTTTTTTCGTGGGTCGGTCACGCAA--GGGGAAAC-AAACATT-TTTTT-ATTTAGGCC
gi|7                          :                                                   taCTCAGAAATTTCCCCCAATAAATTTTTTTT---CAG-TT-GGT-GC-TTTT-TTCATTGGTCGGTCGCGCAA--GAGAAAAC-ACAGA-TATTTTT-AATT
gi|8                          :                                                    ccTCAGAAATTTTCCCCAATAAATTTTTTT----CAG-TT-GGT-GC-TTTT-TTCGTTGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATTTTT-ATTTAGGCgt
gi|9                          :                                                             aTTTCGGCAATAAAATATTTT----TGG-TCTGGCCGA-TTTT-TT--TGGGTCGG------AAGTGGGAAAACAAAAAAATATTTTA-ATTTAGGC
2 sequences could not be aligned to this reference sequence:
Unaligned ( gi|17 ): ACAAAACTTAAGGGCCAGCAGGAAAAATTAGGGTCGTTCGGGTTACCTGAACCAGACATATTTTTTATTTAGCC
Unaligned ( gi|19 ): ATATCATTTCGGTTTCGGCAATAACTATTTTTGGGTTAGGCC






Alignments
lowQualScore                  :                                                                                  1111                                                                         
lowQualScore                  :                                                                           1      2222   2  2   2  2    2                    33        2     6       2         
lowQualScore                  :                                                                           .      ....   .  .   .  .    .                    ..        .     .       .         
lowQualScore                  :                                                                           0      0000   7  7   7  7    5                    22        4     1       5         
consensus                     :                                                     CTCAGAAATTTTCCCCAATAAANTTTTTT----CAG-TC-GGT-GC-TTTT-TTCGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATTTTT-ATTTAGGCC
Reference ( family-624 )      :                                                     CTCAGAAATTTTCCCCAATAAANTTTTTT----CAG-TC-GGT-GC-TTTT-TTCGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATTTTT-ATTTAGGCC
gi|1                          :                                                                                                              GGGTCGGTCGGGTAA--CCGGAAAC-AAACATCTTTTTT-TTTTAGGC
gi|10                         : atccgatgccgattttttggacataaaaacttttgagtcggcagttaaaatataCAGAAATTTTTCCCAATAAAATTGTTT----AAG-TC-TGT-GC-TTTT-TTCGTGGGTTGGTTGCACAA--GGGGAAAC-AAACATTATTTTT-ATTTAAGCC
gi|11                         :                                                        AAAAATTTTCTC-AATAATTTTTTTT----CAG-TC-AGT-GC-TTTT-TTCGTTGGTTGGTCGCGCAA--GGGGAAAC-AAACAATTTTTTA-ATTTAGGCC
gi|12                         :                                                    gCTTAGAAATTTTCCCCAATATAATTTTTT----CAG-TC-GTT-GC-TTTT-TTTGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATTTTT-ATTTt
gi|13                         :                                                  aacCTCAGAAATTTTTCACAATAAAACTTTTT----CAG-TC-GGT-GC-TTTT-TTCGTGGGTCAG-CGGGCAA--CAGGAAAC-AAACACTATTTTT-ATTTAGG
gi|14                         :                                                     CTCAGAAATTTTC------AAATTTTTTTTATTCAG-TT-GGT-GC-TTTT-TTCGTGGGTTGGTCACGCAA--GGGGAAAC-AAACACTATTTTT-ATTT
gi|15                         :                                                     aaCAGAAATTTTCCCCACT-CATTTTTTT----CAG-TC-GGT-GCTTTTT-TTCGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATCTTT-ATTTAt
gi|16                         :                                                        AGAAATTTTCCCGAATAAAATTTTTT----CAG-TC-GGT-GC-TTTT-TTCGTGGGTCGGTCACGCAA--GGGGAAAC-AAACAC
gi|18                         :                                                                                                  aatcaT-TTCGTCGGTCGGTCG-GCAA--CTGGAAAC-AAACA--ATTTTT-
gi|2                          :                                                              TTTCAGCAATAAAATTTTTT----GGGGTC-AG--GC-CGAT-TTTGAGGGTCGGTCGTGGGA--GGGGAAAC-AAAAAATATTTTA-ATTTAGGcaatatggccca
gi|3                          :                                       aaatatcatttcggCTCAGAAATTTTCCCCAATAAATTTTTTT----CAG-TC-GGT-GC-TTTT-TTCGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATTTTT-ATTTAGGCCt
gi|4                          :                                                       CAGAAATTTTTCCCAATAAAATTTTTT----CAG-TC-GGT-GC-TTTT-TTCGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACA-TATTTTTAATTTAGGCC
gi|5                          :                                                      TCAGAAATTTTTTACAATAAATTTTTTT----CAG-TC-GGT-GC-TTTT-TTGGTGGGTCGGTCTGGCAA--GGGGAAAC-AAACACTATTTTT-ATTTAGGCt
gi|6                          :                                                         aAAATTTTCCCCAATAAATTTTTTTTT--CAT-TC-GTT-TT-TTTTTTTCGTGGGTCGGTCACGCAA--GGGGAAAC-AAACATT-TTTTT-ATTTAGGCC
gi|7                          :                                                   taCTCAGAAATTTCCCCCAATAAATTTTTTTT---CAG-TT-GGT-GC-TTTT-TTCATTGGTCGGTCGCGCAA--GAGAAAAC-ACAGA-TATTTTT-AATT
gi|8                          :                                                    ccTCAGAAATTTTCCCCAATAAATTTTTTT----CAG-TT-GGT-GC-TTTT-TTCGTTGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATTTTT-ATTTAGGCgt
gi|9                          :                                                             aTTTCGGCAATAAAATATTTT----TGG-TCTGGCCGA-TTTT-TT--TGGGTCGG------AAGTGGGAAAACAAAAAAATATTTTA-ATTTAGGC


blockSeqs                     :                                                                           T      TATT   G  T   C  T    T                    GT        A     T       A
blockSeqs                     :                                                                           A      TT     .  .   .  .    .                    .         .     A       .
blockSeqs                     :                                                                           A      T      .  .   .  .    .                    .         .     C       .
blockSeqs                     :                                                                           T      .      .  .   .  .    .                    .         .     C       .
blockSeqs                     :                                                                           T      .      .  .   .  .    .                    .         .     C       .
blockSeqs                     :                                                                           A      .      .  .   .  .    .                    .         .     C       .
blockSeqs                     :                                                                           A      .      .  .   .  .    .                    .         .     C       .
blockSeqs                     :                                                                           T      .      .  .   .  .    .                    .         .     A       .
blockSeqs                     :                                                                           A      .      .  .   .  .    .                    .         .     C       .
blockSeqs                     :                                                                           T      .      .  .   .  .    .                    .         .     C       .
blockSeqs                     :                                                                           T      .      .  .   .  .    .                    .         .     T       .
blockSeqs                     :                                                                           T      .      .  .   .  .    .                    .         .     C       .
blockSeqs                     :                                                                           T      .      .  .   .  .    .                    .         .     A       .
blockSeqs                     :                                                                           A      .      .  .   .  .    .                    .         .     .       .
blockSeqs                     :                                                                                                        .                    .         .     .       .
blockSeqs                     :                                                                                                                             .         .     .        


blockSeqCons                  :                                                     
originalCons                  :                                                     CTCAGAAATTTTCCCCAATAAANTTTTTT----CAG-TC-GGT-GC-TTTT-TTCGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATTTTT-ATTTAGGCC
finalCons                     :                                                     CTCAGAAATTTTCCCCAATAAANTTTTTT----CAG-TC-GGT-GC-TTTT-TTCGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATTTTT-ATTTAGGCC
2 sequences could not be aligned to this reference sequence:
Unaligned ( gi|17 ): ACAAAACTTAAGGGCCAGCAGGAAAAATTAGGGTCGTTCGGGTTACCTGAACCAGACATATTTTTTATTTAGCC
Unaligned ( gi|19 ): ATATCATTTCGGTTTCGGCAATAACTATTTTTGGGTTAGGCC






Alignments
lowQualScore                  :                                                                                  1111                                                                         
lowQualScore                  :                                                                           1      2222   2  2   2  2    2                    33        2     6       2         
lowQualScore                  :                                                                           .      ....   .  .   .  .    .                    ..        .     .       .         
lowQualScore                  :                                                                           0      0000   7  7   7  7    5                    22        4     1       5         
consensus                     :                                                     CTCAGAAATTTTCCCCAATAAANTTTTTT----CAG-TC-GGT-GC-TTTT-TTCGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATTTTT-ATTTAGGCC
Reference ( family-624 )      :                                                     CTCAGAAATTTTCCCCAATAAANTTTTTT----CAG-TC-GGT-GC-TTTT-TTCGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATTTTT-ATTTAGGCC
gi|1                          :                                                                                                              GGGTCGGTCGGGTAA--CCGGAAAC-AAACATCTTTTTT-TTTTAGGC
gi|10                         : atccgatgccgattttttggacataaaaacttttgagtcggcagttaaaatataCAGAAATTTTTCCCAATAAAATTGTTT----AAG-TC-TGT-GC-TTTT-TTCGTGGGTTGGTTGCACAA--GGGGAAAC-AAACATTATTTTT-ATTTAAGCC
gi|11                         :                                                        AAAAATTTTCTC-AATAATTTTTTTT----CAG-TC-AGT-GC-TTTT-TTCGTTGGTTGGTCGCGCAA--GGGGAAAC-AAACAATTTTTTA-ATTTAGGCC
gi|12                         :                                                    gCTTAGAAATTTTCCCCAATATAATTTTTT----CAG-TC-GTT-GC-TTTT-TTTGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATTTTT-ATTTt
gi|13                         :                                                  aacCTCAGAAATTTTTCACAATAAAACTTTTT----CAG-TC-GGT-GC-TTTT-TTCGTGGGTCAG-CGGGCAA--CAGGAAAC-AAACACTATTTTT-ATTTAGG
gi|14                         :                                                     CTCAGAAATTTTC------AAATTTTTTTTATTCAG-TT-GGT-GC-TTTT-TTCGTGGGTTGGTCACGCAA--GGGGAAAC-AAACACTATTTTT-ATTT
gi|15                         :                                                     aaCAGAAATTTTCCCCACT-CATTTTTTT----CAG-TC-GGT-GCTTTTT-TTCGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATCTTT-ATTTAt
gi|16                         :                                                        AGAAATTTTCCCGAATAAAATTTTTT----CAG-TC-GGT-GC-TTTT-TTCGTGGGTCGGTCACGCAA--GGGGAAAC-AAACAC
gi|18                         :                                                                                                  aatcaT-TTCGTCGGTCGGTCG-GCAA--CTGGAAAC-AAACA--ATTTTT-
gi|2                          :                                                              TTTCAGCAATAAAATTTTTT----GGGGTC-AG--GC-CGAT-TTTGAGGGTCGGTCGTGGGA--GGGGAAAC-AAAAAATATTTTA-ATTTAGGcaatatggccca
gi|3                          :                                       aaatatcatttcggCTCAGAAATTTTCCCCAATAAATTTTTTT----CAG-TC-GGT-GC-TTTT-TTCGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATTTTT-ATTTAGGCCt
gi|4                          :                                                       CAGAAATTTTTCCCAATAAAATTTTTT----CAG-TC-GGT-GC-TTTT-TTCGTGGGTCGGTCGCGCAA--GGGGAAAC-AAACA-TATTTTTAATTTAGGCC
gi|5                          :                                                      TCAGAAATTTTTTACAATAAATTTTTTT----CAG-TC-GGT-GC-TTTT-TTGGTGGGTCGGTCTGGCAA--GGGGAAAC-AAACACTATTTTT-ATTTAGGCt
gi|6                          :                                                         aAAATTTTCCCCAATAAATTTTTTTTT--CAT-TC-GTT-TT-TTTTTTTCGTGGGTCGGTCACGCAA--GGGGAAAC-AAACATT-TTTTT-ATTTAGGCC
gi|7                          :                                                   taCTCAGAAATTTCCCCCAATAAATTTTTTTT---CAG-TT-GGT-GC-TTTT-TTCATTGGTCGGTCGCGCAA--GAGAAAAC-ACAGA-TATTTTT-AATT
gi|8                          :                                                    ccTCAGAAATTTTCCCCAATAAATTTTTTT----CAG-TT-GGT-GC-TTTT-TTCGTTGGTCGGTCGCGCAA--GGGGAAAC-AAACACTATTTTT-ATTTAGGCgt
gi|9                          :                                                             aTTTCGGCAATAAAATATTTT----TGG-TCTGGCCGA-TTTT-TT--TGGGTCGG------AAGTGGGAAAACAAAAAAATATTTTA-ATTTAGGC
2 sequences could not be aligned to this reference sequence:
Unaligned ( gi|17 ): ACAAAACTTAAGGGCCAGCAGGAAAAATTAGGGTCGTTCGGGTTACCTGAACCAGACATATTTTTTATTTAGCC
Unaligned ( gi|19 ): ATATCATTTCGGTTTCGGCAATAACTATTTTTGGGTTAGGCC