lowQualScore : 111
lowQualScore : 4 0 0 7 7777 3 4 4 4 3 22 5 666 5
lowQualScore : . . . . .... . . . . . .. . ... .
lowQualScore : 0 5 4 0 1111 6 0 4 0 0 66 0 666 0
consensus : TCAACAT-CAGGTGGCCTGAGAAGATCTCAAACGCAGAACTATGGA----AGAAAACCAGCCAAAT-TCCAGTCAGCGAG-GCCATCAAGAAGCGAAAGTGGGGCTGGATA-GGC-C-CACACTGAG
Reference ( gi|6 ) : TCAACAT-CAGGTGACCTGAGAAGATCTCAAATGCAGAGCTATGGA----AGCAAACCAGCCAAAT-TCCAGCCAGCGAG-GCCATCAAAAAGCGAAAGTGGAACTGGATA-GGC-C-CACACTGAGG
gi|9 : TCAACAT-CAGGTGGCCTGAGAAGATCTCAAATCCAGAACTATGGC----AGAAAACCAGCCAAAT-TCCAATCAGCGAA-GCCATTAAAAAGCGAAAGTGGGACTGG-TC-GTC-A-CACA-TGAG
gi|7 : TCAACAT-CAGGTGGTCGGAAAATATCTCAAACGCAAAACTATGGA----CGCAAACCAGCCAAAT-TCCAGTCAGCGAG-GCCATCAAGAGGCAAAAGTGGGGCTGGACA-GAC-CACACA
gi|12 : cTCAGCAT-CAGGTGACCTGAGAAGAACACAAACGCAGAACTATGGA----AGCAAACCAACCAAAT-TCCAGTCAGCGAG-GCCATCAAGAAGaa
gi|13 : ccTCAACAT-CAGGTGGCCTGAGA---TCTCAAACGCATAACTATGGA----ATAAAACCAGCCAAAT-TTCAATCAGCGAG-GCCATCAAGAAGC
gi|3 : cTCAACAT-CAGATGGCCAGAGGTGATCTCCAACCAAGACCTCTGGG----AGAGAACTAGACAAGTCCCCATCGAACAAGAG--ATTAAGAAATGGAAATGGGGATGGATT-GGCAC-CACAGTG
gi|14 : aaaccttcatcaacagatacccccgcaacatccTTAACAT-CCGATGGCCTGAAAGGATCACAAATGAAGAACTATGGAGGAGAGCAAATCAcgaaagcca
gi|16 : ccCAACTT-CAAGTGGCCTGAGAAGATATCAAACGCAGAACTATTGA----AGagaaccagtggacatgcata
gi|4 : ccaAACAC-CAGGTGACCTGA-AAGATCTCCAATGCCACCCTGTGGG----AAAGAACCAACAAAAT-TCCCTTCAGTCAA-AAAATCCAGAA-CGTAAATGGAGTTGGATAGGGC-A-TACACaa
gi|8 : caccagcagatatctacaccacatcataACATTCAGGTGACCTGAAGAGATCTCAAATGCAGAG-TATGAA----GCCAAGACAGCCAAAT-TCCAGTAAGCGAG-GCCATCAAAAAGCGAAAGTGGAACTGGATA-GGC-C-CACACatgaagacc
gi|2 : cctcACGT-CA--TAGCCTGAAAAGATCTCCGATGCCACCCTATGGG----AAAGAACCAACCAGAT-TCCCATCAGTCAA-GAAATCCAGAAACGTAAATGGAGTTGGATA-GG
gi|11 : ctaacaccaactctaacagactctggggacaggcattcactaacagatgcctACCTAAGAAGATCTCGAACACAGAATTATGGA----AGCAAACCAGCCAAAT-TTCAGTTAGCAAG-GCGATCAAGAAGCGAAAGTGGGGCTGGACA-GGC-C-gcatgcgaagac
gi|15 : A----AGAAAACCAGCCAAAT-TCCAGTTTGCGAG-GCCGTCAAGAAGCGAAAATGGGGCTGGATA-GGT-TACACACTGAatac
7 sequences could not be aligned to this particular reference sequence:
Unaligned ( gi|1 ): GCAAACCTTCCATTTCGAAAAGATTGGCTCTCCGACAACTCCGCAAAATCCTCATTGCTCTGCAGAAAGTAATGCAGAGATGTCCCAGAGGTGATCTCCAATAACCAAGAACTCTGGGAGAGACCTAGACAAGTCCCCATCAAACAAGAAGATCAAAAGAAAAGGAAATGGGGATGGATCGGCCATACGTTGCAAAGCCAAA
Unaligned ( gi|5 ): TCCTTTGCATCAAGTGGCAAGACATGGTACCAAACAAAAAAAACTTTGGAGAAAGACCAGACAGGAGCCCATAGAATCAACACAGAAAGTGGGGATGGCTCGGTCACACTATTCGCAAAC
Unaligned ( gi|10 ): CCGCAACATCAGATGGTCAGAGGTGATCTCCGATCAATCCCCATCGAGCAAGATATCAAGAAAAAGAAATGGGGATGGATCGGCCACATGCTGCGAAAGCCAACG
Unaligned ( gi|17 ): CTGATTTCAACTCTAACAGACTCCAGGCATTTCACTAACAGATGCGTA
Unaligned ( gi|18 ): CCTTAGCGTCCGATGGCCTGAAAGGATCACAAATGAAGA
Unaligned ( gi|19 ): GGAGAGCAAATCAAGAACCAGTGGACACGCAAATC
Unaligned ( gi|20 ): AGACTTTCGTCAACAAGTGCTTGAGACGCAT
Alignments
lowQualScore : 1111
lowQualScore : 2 0 1 0 33 33 6 3 1 999999 3 1111
lowQualScore : . . . . .. .. . . . ...... . ....
lowQualScore : 9 3 5 1 99 77 2 1 5 666666 6 8888
consensus : TCAACAT-CAGGTGGCCTGAGAAGATCTCAAACGCAGAA--CTATGGAAG--AAAACCAGCCAAATTCCAGTC-AGCGAG-GCCATCAAGAAGC------GAAAGTGGGGCTGGATA-GGC-C-CACACTGAG
Reference ( family-3123 ) : TCAACAT-CAGGTGGCCTGAGAAGATCTCAAACGCAGAA--CTATGGAAG--AAAACCAGCCAAATTCCAGTC-AGCGAG-GCCATCAAGAAGC------GAAAGTGGGGCTGGATA-GGC-C-CACACTGAG
gi|10 : CAACAT-CAGATGGTCAGAGGTGATCTC---CG---------------------ATCA-----ATCCCCATCGAGCAAG-A-TATCAAGAAAA------AGAAATGGGGATGGATC-GGC-CACATGCTG
gi|11 : ccgCCTAAGAAGATCTCGAACACAGAA--TTATGGAAG--CAAACCAGCCAAATTTCAGTT-AGCAAG-GCGATCAAGAAGC------GAAAGTGGGGCTGGACA-GGC-C-cgaaagccaacg
gi|12 : aTCAGCAT-CAGGTGACCTGAGAAGAACACAAACGCAGAA--CTATGGAAG--CAAACCAACCAAATTCCAGTC-AGCGAG-GCCATCAAGAAGatac
gi|13 : ccTCAACAT-CAGGTGGCCTGAGA---TCTCAAACGCATAA--CTATGGAAT--AAAACCAGCCAAATTTCAATC-AGCGAG-GCCATCAAGAAGC------
gi|14 : cTTAACAT-CCGATGGCCTGAAAGGATCACAAATGAAGAA--CTATGGAGG--AGAGCAAATCAAGAACCAGT
gi|15 : ccAAG--AAAACCAGCCAAATTCCAGTT-TGCGAG-GCCGTCAAGAAGC------GAAAATGGGGCTGGATA-GGT-TACACACTGAggacatgcata
gi|16 : CAACTT-CAAGTGGCCTGAGAAGATATCAAACGCAGAA--CTATTGAAG--AA
gi|18 : ccaTTAGCGT-CCGATGGCCTGAAAGGATCACAAATGAAGA
gi|2 : ccACGT-CA--TAGCCTGAAAAGATCTCCGATGCCACC--CTATGGGAA--AGAACCAACCAGATTCCCATC-AGTCAA-GAAATCCAGAAAC------GTAAATGGAGTTGGATA-GG
gi|3 : ctaacaccaactctaacagactctggggacaggcattcactaacagatgcctTCAACAT-CAGATGGCCAGAGGTGATCTCCAACCAAGAC--CTCTGGGAG--AGAACTAGACAAGTCCCCATCGAACAAGAG--ATTAAGAAAT------GGAAATGGGGATGGATT-GGCAC-CACAGTGgcatgcgaagac
gi|4 : aaaccttcatcaacagatacccccgcaacatccAACAC-CAGGTGACCTGA-AAGATCTCCAATGCCACC--CTGTGGGAA--AGAACCAACAAAATTCCCTTC-AGTCAA-AAAATCCAGAA-C------GTAAATGGAGTTGGATAGGGC-A-TACACTcgaaagcca
gi|5 : caccagcagatatctacaccacatcataCAT-CAAGTGGCAAGACATGGTACCAAACAAAAAAAACTTTGGAGA--AAGACCAGACAG-------------GAG-CCCAT--AGAATCAACACAGAAAGTGGGGATGGCTC-GG--T-CACACTatgaagacc
gi|6 : tcctttgTCAACAT-CAGGTGACCTGAGAAGATCTCAAATGCAGAG--CTATGGAAG--CAAACCAGCCAAATTCCAGCC-AGCGAG-GCCATCAAAAAGC------GAAAGTGGAACTGGATA-GGC-C-CACACTGAGattcgcaaac
gi|7 : TCAACAT-CAGGTGGTCGGAAAATATCTCAAACGCAAAA--CTATGGACG--CAAACCAGCCAAATTCCAGTC-AGCGAG-GCCATCAAGAGGC------AAAAGTGGGGCTGGACA-GA--C-CACACg
gi|8 : cACATTCAGGTGACCTGAAGAGATCTCAAATGCAGAG---TATG-AAGCCAAGAC-AGCCAAATTCCAGTA-AGCGAG-GCCATCAAAAAGC------GAAAGTGGAACTGGATA-GGC-C-CACACTaaa
gi|9 : cctcTCAACAT-CAGGTGGCCTGAGAAGATCTCAAATCCAGAA--CTATGGCAG--AAAACCAGCCAAATTCCAATC-AGCGAA-GCCATTAAAAAGC------GAAAGTGGGACTGG-TC-GTC-A-CACA-TGAG
4 sequences could not be aligned to this reference sequence:
Unaligned ( gi|1 ): GCAAACCTTCCATTTCGAAAAGATTGGCTCTCCGACAACTCCGCAAAATCCTCATTGCTCTGCAGAAAGTAATGCAGAGATGTCCCAGAGGTGATCTCCAATAACCAAGAACTCTGGGAGAGACCTAGACAAGTCCCCATCAAACAAGAAGATCAAAAGAAAAGGAAATGGGGATGGATCGGCCATACGTTGCAAAGCCAAA
Unaligned ( gi|17 ): CTGATTTCAACTCTAACAGACTCCAGGCATTTCACTAACAGATGCGTA
Unaligned ( gi|19 ): GGAGAGCAAATCAAGAACCAGTGGACACGCAAATC
Unaligned ( gi|20 ): AGACTTTCGTCAACAAGTGCTTGAGACGCAT
Alignments
lowQualScore : 1111
lowQualScore : 2 0 1 0 33 33 6 3 1 999999 3 1111
lowQualScore : . . . . .. .. . . . ...... . ....
lowQualScore : 9 3 5 1 99 77 2 1 5 666666 6 8888
consensus : TCAACAT-CAGGTGGCCTGAGAAGATCTCAAACGCAGAA--CTATGGAAG--AAAACCAGCCAAATTCCAGTC-AGCGAG-GCCATCAAGAAGC------GAAAGTGGGGCTGGATA-GGC-C-CACACTGAG
Reference ( family-3123 ) : TCAACAT-CAGGTGGCCTGAGAAGATCTCAAACGCAGAA--CTATGGAAG--AAAACCAGCCAAATTCCAGTC-AGCGAG-GCCATCAAGAAGC------GAAAGTGGGGCTGGATA-GGC-C-CACACTGAG
gi|10 : CAACAT-CAGATGGTCAGAGGTGATCTC---CG---------------------ATCA-----ATCCCCATCGAGCAAG-A-TATCAAGAAAA------AGAAATGGGGATGGATC-GGC-CACATGCTG
gi|11 : ccgCCTAAGAAGATCTCGAACACAGAA--TTATGGAAG--CAAACCAGCCAAATTTCAGTT-AGCAAG-GCGATCAAGAAGC------GAAAGTGGGGCTGGACA-GGC-C-cgaaagccaacg
gi|12 : aTCAGCAT-CAGGTGACCTGAGAAGAACACAAACGCAGAA--CTATGGAAG--CAAACCAACCAAATTCCAGTC-AGCGAG-GCCATCAAGAAGatac
gi|13 : ccTCAACAT-CAGGTGGCCTGAGA---TCTCAAACGCATAA--CTATGGAAT--AAAACCAGCCAAATTTCAATC-AGCGAG-GCCATCAAGAAGC------
gi|14 : cTTAACAT-CCGATGGCCTGAAAGGATCACAAATGAAGAA--CTATGGAGG--AGAGCAAATCAAGAACCAGT
gi|15 : ccAAG--AAAACCAGCCAAATTCCAGTT-TGCGAG-GCCGTCAAGAAGC------GAAAATGGGGCTGGATA-GGT-TACACACTGAggacatgcata
gi|16 : CAACTT-CAAGTGGCCTGAGAAGATATCAAACGCAGAA--CTATTGAAG--AA
gi|18 : ccaTTAGCGT-CCGATGGCCTGAAAGGATCACAAATGAAGA
gi|2 : ccACGT-CA--TAGCCTGAAAAGATCTCCGATGCCACC--CTATGGGAA--AGAACCAACCAGATTCCCATC-AGTCAA-GAAATCCAGAAAC------GTAAATGGAGTTGGATA-GG
gi|3 : ctaacaccaactctaacagactctggggacaggcattcactaacagatgcctTCAACAT-CAGATGGCCAGAGGTGATCTCCAACCAAGAC--CTCTGGGAG--AGAACTAGACAAGTCCCCATCGAACAAGAG--ATTAAGAAAT------GGAAATGGGGATGGATT-GGCAC-CACAGTGgcatgcgaagac
gi|4 : aaaccttcatcaacagatacccccgcaacatccAACAC-CAGGTGACCTGA-AAGATCTCCAATGCCACC--CTGTGGGAA--AGAACCAACAAAATTCCCTTC-AGTCAA-AAAATCCAGAA-C------GTAAATGGAGTTGGATAGGGC-A-TACACTcgaaagcca
gi|5 : caccagcagatatctacaccacatcataCAT-CAAGTGGCAAGACATGGTACCAAACAAAAAAAACTTTGGAGA--AAGACCAGACAG-------------GAG-CCCAT--AGAATCAACACAGAAAGTGGGGATGGCTC-GG--T-CACACTatgaagacc
gi|6 : tcctttgTCAACAT-CAGGTGACCTGAGAAGATCTCAAATGCAGAG--CTATGGAAG--CAAACCAGCCAAATTCCAGCC-AGCGAG-GCCATCAAAAAGC------GAAAGTGGAACTGGATA-GGC-C-CACACTGAGattcgcaaac
gi|7 : TCAACAT-CAGGTGGTCGGAAAATATCTCAAACGCAAAA--CTATGGACG--CAAACCAGCCAAATTCCAGTC-AGCGAG-GCCATCAAGAGGC------AAAAGTGGGGCTGGACA-GA--C-CACACg
gi|8 : cACATTCAGGTGACCTGAAGAGATCTCAAATGCAGAG---TATG-AAGCCAAGAC-AGCCAAATTCCAGTA-AGCGAG-GCCATCAAAAAGC------GAAAGTGGAACTGGATA-GGC-C-CACACTaaa
gi|9 : cctcTCAACAT-CAGGTGGCCTGAGAAGATCTCAAATCCAGAA--CTATGGCAG--AAAACCAGCCAAATTCCAATC-AGCGAA-GCCATTAAAAAGC------GAAAGTGGGACTGG-TC-GTC-A-CACA-TGAG
blockSeqs : T A AA CC G A C AACACA G TTA
blockSeqs : . A . . . . C . . CAC
blockSeqs : . G . . . . C . . CC
blockSeqs : . A . . . . C . . CA
blockSeqs : . G . . . . A . . CC
blockSeqs : . A . . . . A . . CC
blockSeqs : . T . . . . C . . CA
blockSeqs : . A . . . . C . . T
blockSeqs : . T . . . . C . . C
blockSeqs : . A . . . . C . .
blockSeqs : . A . . . . C .
blockSeqs : . A . . . . .
blockSeqs : . A . .
blockSeqs : . .
blockSeqCons : CC**
originalCons : TCAACAT-CAGGTGGCCTGAGAAGATCTCAAACGCAGAA--CTATGGAAG--AAAACCAGCCAAATTCCAGTC-AGCGAG-GCCATCAAGAAGC------GAAAGTGGGGCTGGATA-GGC-C-CACACTGAG
finalCons : TCAACAT-CAGGTGGCCTGAGAAGATCTCAAACGCAGAA--CTATGGAAG--AAAACCAGCCAAATTCCAGTC-AGCGAG-GCCATCAAGAAGC------GAAAGTGGGGCTGGATA-GGCC--CACACTGAG
4 sequences could not be aligned to this reference sequence:
Unaligned ( gi|1 ): GCAAACCTTCCATTTCGAAAAGATTGGCTCTCCGACAACTCCGCAAAATCCTCATTGCTCTGCAGAAAGTAATGCAGAGATGTCCCAGAGGTGATCTCCAATAACCAAGAACTCTGGGAGAGACCTAGACAAGTCCCCATCAAACAAGAAGATCAAAAGAAAAGGAAATGGGGATGGATCGGCCATACGTTGCAAAGCCAAA
Unaligned ( gi|17 ): CTGATTTCAACTCTAACAGACTCCAGGCATTTCACTAACAGATGCGTA
Unaligned ( gi|19 ): GGAGAGCAAATCAAGAACCAGTGGACACGCAAATC
Unaligned ( gi|20 ): AGACTTTCGTCAACAAGTGCTTGAGACGCAT
Alignments
lowQualScore : 1111
lowQualScore : 2 0 1 0 33 33 6 3 1 999999 3 1111
lowQualScore : . . . . .. .. . . . ...... . ....
lowQualScore : 9 3 5 1 99 77 2 1 5 666666 6 8888
consensus : TCAACAT-CAGGTGGCCTGAGAAGATCTCAAACGCAGAA--CTATGGAAG--AAAACCAGCCAAATTCCAGTC-AGCGAG-GCCATCAAGAAGC------GAAAGTGGGGCTGGATA-GGC-C-CACACTGAG
Reference ( family-3123 ) : TCAACAT-CAGGTGGCCTGAGAAGATCTCAAACGCAGAA--CTATGGAAG--AAAACCAGCCAAATTCCAGTC-AGCGAG-GCCATCAAGAAGC------GAAAGTGGGGCTGGATA-GGC-C-CACACTGAG
gi|10 : CAACAT-CAGATGGTCAGAGGTGATCTC---CG---------------------ATCA-----ATCCCCATCGAGCAAG-A-TATCAAGAAAA------AGAAATGGGGATGGATC-GGC-CACATGCTG
gi|11 : ccgCCTAAGAAGATCTCGAACACAGAA--TTATGGAAG--CAAACCAGCCAAATTTCAGTT-AGCAAG-GCGATCAAGAAGC------GAAAGTGGGGCTGGACA-GGC-C-cgaaagccaacg
gi|12 : aTCAGCAT-CAGGTGACCTGAGAAGAACACAAACGCAGAA--CTATGGAAG--CAAACCAACCAAATTCCAGTC-AGCGAG-GCCATCAAGAAGatac
gi|13 : ccTCAACAT-CAGGTGGCCTGAGA---TCTCAAACGCATAA--CTATGGAAT--AAAACCAGCCAAATTTCAATC-AGCGAG-GCCATCAAGAAGC------
gi|14 : cTTAACAT-CCGATGGCCTGAAAGGATCACAAATGAAGAA--CTATGGAGG--AGAGCAAATCAAGAACCAGT
gi|15 : ccAAG--AAAACCAGCCAAATTCCAGTT-TGCGAG-GCCGTCAAGAAGC------GAAAATGGGGCTGGATA-GGT-TACACACTGAggacatgcata
gi|16 : CAACTT-CAAGTGGCCTGAGAAGATATCAAACGCAGAA--CTATTGAAG--AA
gi|18 : ccaTTAGCGT-CCGATGGCCTGAAAGGATCACAAATGAAGA
gi|2 : ccACGT-CA--TAGCCTGAAAAGATCTCCGATGCCACC--CTATGGGAA--AGAACCAACCAGATTCCCATC-AGTCAA-GAAATCCAGAAAC------GTAAATGGAGTTGGATA-GG
gi|3 : ctaacaccaactctaacagactctggggacaggcattcactaacagatgcctTCAACAT-CAGATGGCCAGAGGTGATCTCCAACCAAGAC--CTCTGGGAG--AGAACTAGACAAGTCCCCATCGAACAAGAG--ATTAAGAAAT------GGAAATGGGGATGGATT-GGCAC-CACAGTGgcatgcgaagac
gi|4 : aaaccttcatcaacagatacccccgcaacatccAACAC-CAGGTGACCTGA-AAGATCTCCAATGCCACC--CTGTGGGAA--AGAACCAACAAAATTCCCTTC-AGTCAA-AAAATCCAGAA-C------GTAAATGGAGTTGGATAGGGC-A-TACACTcgaaagcca
gi|5 : caccagcagatatctacaccacatcataCAT-CAAGTGGCAAGACATGGTACCAAACAAAAAAAACTTTGGAGA--AAGACCAGACAG-------------GAG-CCCAT--AGAATCAACACAGAAAGTGGGGATGGCTC-GG--T-CACACTatgaagacc
gi|6 : tcctttgTCAACAT-CAGGTGACCTGAGAAGATCTCAAATGCAGAG--CTATGGAAG--CAAACCAGCCAAATTCCAGCC-AGCGAG-GCCATCAAAAAGC------GAAAGTGGAACTGGATA-GGC-C-CACACTGAGattcgcaaac
gi|7 : TCAACAT-CAGGTGGTCGGAAAATATCTCAAACGCAAAA--CTATGGACG--CAAACCAGCCAAATTCCAGTC-AGCGAG-GCCATCAAGAGGC------AAAAGTGGGGCTGGACA-GA--C-CACACg
gi|8 : cACATTCAGGTGACCTGAAGAGATCTCAAATGCAGAG---TATG-AAGCCAAGAC-AGCCAAATTCCAGTA-AGCGAG-GCCATCAAAAAGC------GAAAGTGGAACTGGATA-GGC-C-CACACTaaa
gi|9 : cctcTCAACAT-CAGGTGGCCTGAGAAGATCTCAAATCCAGAA--CTATGGCAG--AAAACCAGCCAAATTCCAATC-AGCGAA-GCCATTAAAAAGC------GAAAGTGGGACTGG-TC-GTC-A-CACA-TGAG
4 sequences could not be aligned to this reference sequence:
Unaligned ( gi|1 ): GCAAACCTTCCATTTCGAAAAGATTGGCTCTCCGACAACTCCGCAAAATCCTCATTGCTCTGCAGAAAGTAATGCAGAGATGTCCCAGAGGTGATCTCCAATAACCAAGAACTCTGGGAGAGACCTAGACAAGTCCCCATCAAACAAGAAGATCAAAAGAAAAGGAAATGGGGATGGATCGGCCATACGTTGCAAAGCCAAA
Unaligned ( gi|17 ): CTGATTTCAACTCTAACAGACTCCAGGCATTTCACTAACAGATGCGTA
Unaligned ( gi|19 ): GGAGAGCAAATCAAGAACCAGTGGACACGCAAATC
Unaligned ( gi|20 ): AGACTTTCGTCAACAAGTGCTTGAGACGCAT