lowQualScore                  :                             11111                                                         
lowQualScore                  :                2     44     77777         4     33     33  66        66             4     
lowQualScore                  :                .     ..     .....         .     ..     ..  ..        ..             .     
lowQualScore                  :                7     33     11111         3     77     77  33        77             4     
consensus                     :   CAACATCAGATGG-CCAGAC-AAGAT-ACG-AAATGAAGACTTGTG--GGAGC--GA--GCGGGACAG-GAGCCAGTGGCTG-AGCAG
Reference ( gi|6 )            :   CAACATCAGATGG-CCAGAC-AAAAT-ACA-AAATGAAGACTTGTG--GGAGC--GA--GCGGGACAA-GAGCCAGTGGCTG-AGCAG
gi|8                          :   CAACATCAGATGG-CCAGAC-AACAT-ACG-AAATGAAGACTTGTG--GGAGC--GA--GCGGGACAG-GAGCCAGTGGCTG-AGCAG
gi|7                          :   CGACATCAGATGG-CCAGAC-AAAAT-ACG-AAATGAAGACTTGTG--GGAGC--GA--GCGGGACAG-GAGTCAGTGGTTG-AGCAG
gi|10                         :   CAATATCAGATGG-CCAGAC-AAAAT-ACG-AAATGAAGA-TTGTG--GGAGC--GA--GAGGGACAG-GAGCCAGTGGCTG-AGCAG
gi|4                          :   CAACATCAGATGA-CCAGAC-AAAAT-ACG-AAATGTAGACTTGTG--GGAGC--GAGCGCGGGACAG-GAGCCAGTTGCTG-AGCAG
gi|14                         :   CAA-ATCAGATAG-CTAGAC-AAA-T-ACG-AA-TGAAGACTAGTG--GGAGC--GA---CGGGACAG-GAATCAATGGCTG-AGCAGa
gi|13                         :   CAACATCAGATGA-CCAGAA-AGGAT--CAGAAATGAAGACTTATG--GGAAC--GA--GCGGGACAG-GAACCAGTa
gi|5                          :   CAACATCAGATGGACCGGAA-AAGATCAGA-AAACGAAGATCAGTT--GGAGC--GA--GC-GGACAGCGGACCAGTGGCCT-AGCAGtgtctagc
gi|16                         :   CAACATCAGATGG-CTGGAA-AGGAT-ATG-ATATAAAAATCTGTG--GAAAC--GA--GCGGAATAG-GAACCAGTGG
gi|9                          :    AACATCTGATGG-CCAGAC-AAAAT-ACG-AAATGAAGATTTGTT--GTAGA--GA--GTGGGACAG-GAGCCAGTGGCTG-AGCAGt
gi|2                          :    AACATTCGATGG-CCTGAA-AGGAT--CACAAATGAAGAACTATG--GAGGG--GA--GCAAAACAG-GAACCAATa
gi|3                          : cttAACATCCGATGG-CTTGAA-AGGAT--CACAAATGAAGAACTATG--AAGGA--GA--GCAAACCAA-GAAACAGTGGacacatgcaaatc
gi|18                         : cttAACATCCGATGG-CCTGAA-AGGAT--CACAAATGAAGAACTATA--GAGGA--GA--GCacatgcaaat
gi|1                          :   cttCATCCGATAG-CCTGAA-AGGAT--CATAAATGAAGAACTATGGAGGAGCTAGA--GCAAAGCAA-GAACCAATAGaaatc
gi|11                         :  cttacATCAGATGG-CCAGACTAAAAT-ACG-AAATGGAAATTTGTG--GGAGC--GAG-GCGGGACAG-GAGCCAGTGGCTGAAGCAGacatgcaaa
gi|17                         :              GG-CCAGTC-AAAAT-ATG-AAATGAAGACTTGTG--GGAGC--GA--GCGGGCCAG-TAGCCTGTGGCTG-AGCAG
3 sequences could not be aligned to this particular reference sequence:
Unaligned ( gi|12 ): TAACATACAATGGCCTGAAAGGATCACAAACGAGGAACTGTGGAGCAGGACAGGGGCAGATGGACTTACACACCA
Unaligned ( gi|15 ): CTTAACATCTGATGCTGAAAGGATAAAATGAAGAACTATGGAGGAGACAAATCAAGAACCAGTAAGACATGCA
Unaligned ( gi|19 ): GAACTATGGAGGTAGAGCAAAGAAGATCAATAGGTATGCAAATCAGG






Alignments
lowQualScore                  :                                 1                                                            
lowQualScore                  :            2       2  0  44  1  1  5         4     33     33  55         2             4     
lowQualScore                  :            .       .  .  ..  .  .  .         .     ..     ..  ..         .             .     
lowQualScore                  :            5       4  4  11  0  8  1         1     22     22  66         5             0     
consensus                     :      CAACAT-CAGATGG-CCAGAC-AAGAT-ACGAAATGAAGACTTGTG--GGAGC--GA--GCGGGACAG-GAGCCAGTGGCTG-AGCAG
Reference ( family-4049 )     :      CAACAT-CAGATGG-CCAGAC-AAGAT-ACGAAATGAAGACTTGTG--GGAGC--GA--GCGGGACAG-GAGCCAGTGGCTG-AGCAG
gi|1                          :         CAT-CCGATAG-CCTGAA-AGGAT-CATAAATGAAGAACTATGGAGGAGCTAGA--GCAAAGCAA-GAACCAATAG
gi|10                         : cttacCAATAT-CAGATGG-CCAGAC-AAAAT-ACGAAATGAAGA-TTGTG--GGAGC--GA--GAGGGACAG-GAGCCAGTGGCTG-AGCAGacatgcaaa
gi|11                         :          AT-CAGATGG-CCAGACTAAAAT-ACGAAATGGAAATTTGTG--GGAGC--GAG-GCGGGACAG-GAGCCAGTGGCTGAAGCAG
gi|12                         :       AACATACA-ATGG-CCTGAA-AGGATCAC-AAACGAGGAACTGTG--G-------A--GCAGGACAG-GGGCAGATGG
gi|13                         :     tCAACAT-CAGATGA-CCAGAA-AGGAT-CAGAAATGAAGACTTATG--GGAAC--GA--GCGGGACAG-GAACCAGTacttacacacca
gi|14                         :      CAA-AT-CAGATAG-CTAGAC-AA-AT-ACGAA-TGAAGACTAGTG--GGAGC--GA---CGGGACAG-GAATCAATGGCTG-AGCAGtgtctagc
gi|16                         :      CAACAT-CAGATGG-CTGGAA-AGGAT-ATGATATAAAAATCTGTG--GAAAC--GA--GCGGAATAG-GAACCAGTGGa
gi|17                         :                  GG-CCAGTC-AAAAT-ATGAAATGAAGACTTGTG--GGAGC--GA--GCGGGCCAG-TAGCCTGTGGCTG-AGCAGt
gi|18                         :       AACAT-CCGATGG-CCTGAA-AGGATCAC-AAATGAAGAACTATA--GAGGA--GA--GCa
gi|2                          :    cttAACAT-TCGATGG-CCTGAA-AGGATCAC-AAATGAAGAACTATG--GAGGG--GA--GCAAAACAG-GAACCAATaaatc
gi|3                          :    cttAACAT-CCGATGG-CTTGAA-AGGATCAC-AAATGAAGAACTATG--AAGGA--GA--GCAAACCAA-GAAACAGTGGacacatgcaaatc
gi|4                          :   cttCAACAT-CAGATGA-CCAGAC-AAAAT-ACGAAATGTAGACTTGTG--GGAGC--GAGCGCGGGACAG-GAGCCAGTTGCTG-AGCAGacatgcaaat
gi|5                          :      CAACAT-CAGATGGACCGGAA-AAGATCAGAAAACGAAGATCAGTT--GGAGC--GA--GC-GGACAGCGGACCAGTGGCCT-AGCAGa
gi|6                          :      CAACAT-CAGATGG-CCAGAC-AAAAT-ACAAAATGAAGACTTGTG--GGAGC--GA--GCGGGACAA-GAGCCAGTGGCTG-AGCAG
gi|7                          :      CGACAT-CAGATGG-CCAGAC-AAAAT-ACGAAATGAAGACTTGTG--GGAGC--GA--GCGGGACAG-GAGTCAGTGGTTG-AGCAG
gi|8                          :      CAACAT-CAGATGG-CCAGAC-AACAT-ACGAAATGAAGACTTGTG--GGAGC--GA--GCGGGACAG-GAGCCAGTGGCTG-AGCAG
gi|9                          :       AACAT-CTGATGG-CCAGAC-AAAAT-ACGAAATGAAGATTTGTT--GTAGA--GA--GTGGGACAG-GAGCCAGTGGCTG-AGCAG
2 sequences could not be aligned to this reference sequence:
Unaligned ( gi|15 ): CTTAACATCTGATGCTGAAAGGATAAAATGAAGAACTATGGAGGAGACAAATCAAGAACCAGTAAGACATGCA
Unaligned ( gi|19 ): GAACTATGGAGGTAGAGCAAAGAAGATCAATAGGTATGCAAATCAGG






Alignments
lowQualScore                  :                                 1                                                            
lowQualScore                  :            2       2  0  44  1  1  5         4     33     33  55         2             4     
lowQualScore                  :            .       .  .  ..  .  .  .         .     ..     ..  ..         .             .     
lowQualScore                  :            5       4  4  11  0  8  1         1     22     22  66         5             0     
consensus                     :      CAACAT-CAGATGG-CCAGAC-AAGAT-ACGAAATGAAGACTTGTG--GGAGC--GA--GCGGGACAG-GAGCCAGTGGCTG-AGCAG
Reference ( family-4049 )     :      CAACAT-CAGATGG-CCAGAC-AAGAT-ACGAAATGAAGACTTGTG--GGAGC--GA--GCGGGACAG-GAGCCAGTGGCTG-AGCAG
gi|1                          :         CAT-CCGATAG-CCTGAA-AGGAT-CATAAATGAAGAACTATGGAGGAGCTAGA--GCAAAGCAA-GAACCAATAG
gi|10                         : cttacCAATAT-CAGATGG-CCAGAC-AAAAT-ACGAAATGAAGA-TTGTG--GGAGC--GA--GAGGGACAG-GAGCCAGTGGCTG-AGCAGacatgcaaa
gi|11                         :          AT-CAGATGG-CCAGACTAAAAT-ACGAAATGGAAATTTGTG--GGAGC--GAG-GCGGGACAG-GAGCCAGTGGCTGAAGCAG
gi|12                         :       AACATACA-ATGG-CCTGAA-AGGATCAC-AAACGAGGAACTGTG--G-------A--GCAGGACAG-GGGCAGATGG
gi|13                         :     tCAACAT-CAGATGA-CCAGAA-AGGAT-CAGAAATGAAGACTTATG--GGAAC--GA--GCGGGACAG-GAACCAGTacttacacacca
gi|14                         :      CAA-AT-CAGATAG-CTAGAC-AA-AT-ACGAA-TGAAGACTAGTG--GGAGC--GA---CGGGACAG-GAATCAATGGCTG-AGCAGtgtctagc
gi|16                         :      CAACAT-CAGATGG-CTGGAA-AGGAT-ATGATATAAAAATCTGTG--GAAAC--GA--GCGGAATAG-GAACCAGTGGa
gi|17                         :                  GG-CCAGTC-AAAAT-ATGAAATGAAGACTTGTG--GGAGC--GA--GCGGGCCAG-TAGCCTGTGGCTG-AGCAGt
gi|18                         :       AACAT-CCGATGG-CCTGAA-AGGATCAC-AAATGAAGAACTATA--GAGGA--GA--GCa
gi|2                          :    cttAACAT-TCGATGG-CCTGAA-AGGATCAC-AAATGAAGAACTATG--GAGGG--GA--GCAAAACAG-GAACCAATaaatc
gi|3                          :    cttAACAT-CCGATGG-CTTGAA-AGGATCAC-AAATGAAGAACTATG--AAGGA--GA--GCAAACCAA-GAAACAGTGGacacatgcaaatc
gi|4                          :   cttCAACAT-CAGATGA-CCAGAC-AAAAT-ACGAAATGTAGACTTGTG--GGAGC--GAGCGCGGGACAG-GAGCCAGTTGCTG-AGCAGacatgcaaat
gi|5                          :      CAACAT-CAGATGGACCGGAA-AAGATCAGAAAACGAAGATCAGTT--GGAGC--GA--GC-GGACAGCGGACCAGTGGCCT-AGCAGa
gi|6                          :      CAACAT-CAGATGG-CCAGAC-AAAAT-ACAAAATGAAGACTTGTG--GGAGC--GA--GCGGGACAA-GAGCCAGTGGCTG-AGCAG
gi|7                          :      CGACAT-CAGATGG-CCAGAC-AAAAT-ACGAAATGAAGACTTGTG--GGAGC--GA--GCGGGACAG-GAGTCAGTGGTTG-AGCAG
gi|8                          :      CAACAT-CAGATGG-CCAGAC-AACAT-ACGAAATGAAGACTTGTG--GGAGC--GA--GCGGGACAG-GAGCCAGTGGCTG-AGCAG
gi|9                          :       AACAT-CTGATGG-CCAGAC-AAAAT-ACGAAATGAAGATTTGTT--GTAGA--GA--GTGGGACAG-GAGCCAGTGGCTG-AGCAG


blockSeqs                     :            A       A     CT  A  C  G         T     .      .   GC         C             A
blockSeqs                     :            .       .     C   A  C  G         A     .      .   G          .             .
blockSeqs                     :            .       .     A   G  C  G         C     .      .   .          .             .
blockSeqs                     :            .       .     A   G  C  G         C     .      .   .          .             .
blockSeqs                     :            .       .     C   G  C  G         T     .      .   .          .             .
blockSeqs                     :            .       .     A   A  .  G         C     .      .   .          .             .
blockSeqs                     :            .       .     C   G  .  G         A     .      .   .          .             .
blockSeqs                     :            .       .     A   G  .  A         A     .      .   .          .             .
blockSeqs                     :            .       .     A   G  .  A         A     .      .   .          .             .
blockSeqs                     :            .       .     A   A  .  G         C     .      .   .          .              
blockSeqs                     :            .       .     C   G  .  G         T     .      .   .          .              
blockSeqs                     :            .       .     A   A  .  G         C     .      .   .          .              
blockSeqs                     :            .       .     C   A  .  .         C     .      .   .          .              
blockSeqs                     :            .       .     C   C  .  .         C     .      .   .          .              
blockSeqs                     :            .       .     C   A  .  .         T     .      .   .          .              
blockSeqs                     :                    .     C   .  .  .         .     .      .   .                         


blockSeqCons                  :                                                    **     **
originalCons                  :      CAACAT-CAGATGG-CCAGAC-AAGAT-ACGAAATGAAGACTTGTG--GGAGC--GA--GCGGGACAG-GAGCCAGTGGCTG-AGCAG
finalCons                     :      CAACAT-CAGATGG-CCAGAC-AAGAT-ACGAAATGAAGACTTGTG--GGAGC--GA--GCGGGACAG-GAGCCAGTGGCTG-AGCAG
2 sequences could not be aligned to this reference sequence:
Unaligned ( gi|15 ): CTTAACATCTGATGCTGAAAGGATAAAATGAAGAACTATGGAGGAGACAAATCAAGAACCAGTAAGACATGCA
Unaligned ( gi|19 ): GAACTATGGAGGTAGAGCAAAGAAGATCAATAGGTATGCAAATCAGG






Alignments
lowQualScore                  :                                 1                                                            
lowQualScore                  :            2       2  0  44  1  1  5         4     33     33  55         2             4     
lowQualScore                  :            .       .  .  ..  .  .  .         .     ..     ..  ..         .             .     
lowQualScore                  :            5       4  4  11  0  8  1         1     22     22  66         5             0     
consensus                     :      CAACAT-CAGATGG-CCAGAC-AAGAT-ACGAAATGAAGACTTGTG--GGAGC--GA--GCGGGACAG-GAGCCAGTGGCTG-AGCAG
Reference ( family-4049 )     :      CAACAT-CAGATGG-CCAGAC-AAGAT-ACGAAATGAAGACTTGTG--GGAGC--GA--GCGGGACAG-GAGCCAGTGGCTG-AGCAG
gi|1                          :         CAT-CCGATAG-CCTGAA-AGGAT-CATAAATGAAGAACTATGGAGGAGCTAGA--GCAAAGCAA-GAACCAATAG
gi|10                         : cttacCAATAT-CAGATGG-CCAGAC-AAAAT-ACGAAATGAAGA-TTGTG--GGAGC--GA--GAGGGACAG-GAGCCAGTGGCTG-AGCAGacatgcaaa
gi|11                         :          AT-CAGATGG-CCAGACTAAAAT-ACGAAATGGAAATTTGTG--GGAGC--GAG-GCGGGACAG-GAGCCAGTGGCTGAAGCAG
gi|12                         :       AACATACA-ATGG-CCTGAA-AGGATCAC-AAACGAGGAACTGTG--G-------A--GCAGGACAG-GGGCAGATGG
gi|13                         :     tCAACAT-CAGATGA-CCAGAA-AGGAT-CAGAAATGAAGACTTATG--GGAAC--GA--GCGGGACAG-GAACCAGTacttacacacca
gi|14                         :      CAA-AT-CAGATAG-CTAGAC-AA-AT-ACGAA-TGAAGACTAGTG--GGAGC--GA---CGGGACAG-GAATCAATGGCTG-AGCAGtgtctagc
gi|16                         :      CAACAT-CAGATGG-CTGGAA-AGGAT-ATGATATAAAAATCTGTG--GAAAC--GA--GCGGAATAG-GAACCAGTGGa
gi|17                         :                  GG-CCAGTC-AAAAT-ATGAAATGAAGACTTGTG--GGAGC--GA--GCGGGCCAG-TAGCCTGTGGCTG-AGCAGt
gi|18                         :       AACAT-CCGATGG-CCTGAA-AGGATCAC-AAATGAAGAACTATA--GAGGA--GA--GCa
gi|2                          :    cttAACAT-TCGATGG-CCTGAA-AGGATCAC-AAATGAAGAACTATG--GAGGG--GA--GCAAAACAG-GAACCAATaaatc
gi|3                          :    cttAACAT-CCGATGG-CTTGAA-AGGATCAC-AAATGAAGAACTATG--AAGGA--GA--GCAAACCAA-GAAACAGTGGacacatgcaaatc
gi|4                          :   cttCAACAT-CAGATGA-CCAGAC-AAAAT-ACGAAATGTAGACTTGTG--GGAGC--GAGCGCGGGACAG-GAGCCAGTTGCTG-AGCAGacatgcaaat
gi|5                          :      CAACAT-CAGATGGACCGGAA-AAGATCAGAAAACGAAGATCAGTT--GGAGC--GA--GC-GGACAGCGGACCAGTGGCCT-AGCAGa
gi|6                          :      CAACAT-CAGATGG-CCAGAC-AAAAT-ACAAAATGAAGACTTGTG--GGAGC--GA--GCGGGACAA-GAGCCAGTGGCTG-AGCAG
gi|7                          :      CGACAT-CAGATGG-CCAGAC-AAAAT-ACGAAATGAAGACTTGTG--GGAGC--GA--GCGGGACAG-GAGTCAGTGGTTG-AGCAG
gi|8                          :      CAACAT-CAGATGG-CCAGAC-AACAT-ACGAAATGAAGACTTGTG--GGAGC--GA--GCGGGACAG-GAGCCAGTGGCTG-AGCAG
gi|9                          :       AACAT-CTGATGG-CCAGAC-AAAAT-ACGAAATGAAGATTTGTT--GTAGA--GA--GTGGGACAG-GAGCCAGTGGCTG-AGCAG
2 sequences could not be aligned to this reference sequence:
Unaligned ( gi|15 ): CTTAACATCTGATGCTGAAAGGATAAAATGAAGAACTATGGAGGAGACAAATCAAGAACCAGTAAGACATGCA
Unaligned ( gi|19 ): GAACTATGGAGGTAGAGCAAAGAAGATCAATAGGTATGCAAATCAGG