lowQualScore : 888888888888888888888888888888
lowQualScore : 333 3333 1 5 1 2 1 1 666666666666666666666666666666 1 1 1 2 22 5 1 22 3333
lowQualScore : ... .... . . . . . . .............................. . . . . .. . . .. ....
lowQualScore : 555 9999 8 5 8 9 8 8 000000000000000000000000000000 7 7 7 3 44 5 8 55 9999
consensus : TCTCT---CGC----ACAGAG-TT-GT-CGNTCC-T-TTCAGT-CTCA--CT----G---T--GAGCACTGAA-A-GG-ANCGA--C-AA-CTCT--GT----GCGAGAG
Reference ( gi|3 ) : TCTCT---CAT----ACAGAG-TT-GT-CGATCC-T-TTCAGTGCTCA--CT----G---T--GAGCACTGAA-A-GG-ATCGA--C-AA-CTCT--GT----ATGAGAG
gi|7 : TCTCT---CAT----ACAGAG-TT-GT-CGATCC-T-TTCAG---------T----G---T--GAGCACTGAA-A-GG-ATCGA--CAAA-CTCT--GT----ATGAGAG
gi|7 : TCTCT---CAT----ACAGAG-TTTGT-CGATCC-T-TTCAGTGCTCA--C----------------ACTGAA-A-GG-ATCGA--C-AA-CTCT--GT----ATGAGAGa
gi|9 : tTCTCT---CAT----ACAGAG-TT-GT-CGATCC-T---------TCA--C------------GAG--CTGAG-A-GG-ATCGA--C-AA-CTCT--GT----ATGAAA
gi|1 : TTTCT---TGC----ACCGAG-TT-GT-CGGTCA-T-TTCGGGG-TCA--TT----TC--T--GAG-A--GAA-A-AG-ATCGA--C-AA-CTCT--GT----GCAAGAGt
gi|1 : attTCTCT---TGC----ACAGAG-TT-GT-CGATCT-T-TTC--T-CTCA--------GAAAT--GA-CCCCGAA-A-TG-ACCGA--C-AA-CTCG--GT----GCAAGAatgatcttctccgtta
gi|10 : atTCTCT---CAT----AGAGAG-TT-GT-CGATCC-T-TTCAGTGCaaatgatcttctccgtta
gi|17 : aagttactagagttcccaatctgtcgtTCTCC---CAT----ACCGAG-TT-GT-CGATCC-T-TTCAGTGCTCt
gi|11 : TCTCT---CAT----ACACGA-TT-GT-CGATCC-T-TACAGTGCTCA--AT------------AGCCATGGC-A-AG-GTCGA--
gi|15 : aaTCTCT---CAT----AC-GAG-TT-GT-CGATCC-TGTTCAGTGCTC
gi|12 : gaTCTCT---TAC----ACAAAG-TT-GT-CGGTCC-T-T---AT-----------------------------A-A-GG-ACCTA--C-AA-CTCT--GT----ATAAGAG
gi|12 : atTCTCT---TAT----ACAGAG-TT-GT-AGGTCC-T-T---AT-----------------------------A-A-GG-ACCGA--C-AA-CTTT--GT----GTAAGAGa
gi|16 : attTCTCT---TGC----ACAGAG-TT-GT-CGTTCC-T-TTC
gi|14 : tcatTCGCT---TGC----ACAGAG-TT-GT-CGTTCC-T-TTCtct
gi|2 : agaTCTCTTGCCAT----A--GAG-TT-GTCCGGTCC-T-TTC--T-CTCC--CTTGACG---T--AGGAGATAAA-A-GGTACCGAGCT-AA-CTCTGCGC----ATGAatgggg
gi|13 : aCTCT---TGC----ACAGAG-TT-GT-CGGTCC-T-TTatgt
gi|9 : TTT---CAT----ACAGAG-TT-GT-CGATCC-T-CTCAG--CTC---------G---T--GA---------A-GG-ATCGA--C-AA-CTCT--GT----ATGAGAGagataaaggaacgacagact
gi|6 : TCT---CGTTTGCACAGAGGTT-GT-CGTTCC-T-TTC--T-CTCA--CTTA--G---T--GAG-A--GAA-A-GG-AACGA--C-AA-CTCT--GT----at
gi|4 : gccTCT---TGC----ACAGAG-TT-AT-CGGTCC-T-TTCCGTACCC---TTAA--G---G--AAGAA--GAA-A-GG-ACCGA--CAAA-CTCT--GT----GCAAG
gi|4 : CT---TGC----ACAGAG-TTTGT-CGGTCC-T-TTC--TTCTTC--CT--------TAAGGGTACGGAA-A-GG-ACCGA--T-AA-CTCT--GT----GCAAGAt
gi|8 : CT---TGC----ACAGAG-TT-GT-CGTTCCTT-TTCA---CTCA--CT--------T--GA-----GAA-A-GG-AACGA--CAAA-CTCT--GT----t
gi|6 : ttc----ACAGAG-TT-GT-CGTTCC-T-TTC--T-CTCA--CTAA--G---T--GAG-A--GAA-A-GG-AACGA--C-AACCTCT--GTGCAAACGAGAgcaga
gi|8 : gcc----ACAGAG-TTTGT-CGTTCC-T-TTC-----TCA--A-----G---T--GAG---TGAA-AAGG-AACGA--C-AA-CTCT--GT----GCAAG
gi|10 : ttcAGTTCCCAATCT----G---TC-GTGCACTGAA-A-GG-ATCGA--C-AA-CTCT--CT----ATGAGAGgcaga
gi|11 : aagttactag---T--GAGCACTGTA-A-GG-ATCGA--C-AA-TCGT--GT----ATGAGAGat
gi|17 : aat--GAGCACTGAA-A-GG-ATCGA--C-AA-CTCG--GT----ATGGGAGatagccatggcaaggtcga
gi|15 : --GAGCACTGAACA-GG-ATCGA--C-AA-CTC---GT----ATGAGAGa
gi|16 : gatGAA-A-GG-AACGA--C-AA-CTCT--GT----GCAAGAG
gi|14 : tcattGAA-A-GG-AACGA--C-AA-CTCT--GT----GCAAGtct
gi|13 : agaAA-A-GG-ACCGA--C-AA-CTCT--GT----GCAAGAGcgaatgggg
1 sequences could not be aligned to this particular reference sequence:
Unaligned ( gi|5 ): TCTCTTGCACAGAGTTGTATGTCCAGGGAGAGATAGAACCACTCTGTGCAAGAAAATGGTTTATCTTGTC
Alignments
lowQualScore : 66666666666666666666666666666
lowQualScore : 55 1 3 3 3 3 3 1 3 66666666666666666666666666666 2 2 1 33 5
lowQualScore : .. . . . . . . . . ............................. . . . .. .
lowQualScore : 00 6 6 3 3 3 3 0 3 00000000000000000000000000000 9 9 0 99 7
consensus : TCTC--TCGC-ACAGAG-T-T-GT-CGNTCC-TTTC--T-CTCA--CT----G---T-GAGCACTGAA-AGG-ACCGA--C-AACTCTGTGCGAGAG
Reference ( family-9837 ) : TCTC--TCGC-ACAGAG-T-T-GT-CGNTCC-TTTCAGT-CTCA--CT----G---T-GAGCACTGAA-AGG-ANCGA--C-AACTCTGTGCGAGAG
gi|1 : TCTC--TTGC-ACAGAG-T-T-GT-CGATCT-TTTC--T-CTCA--------GAAAT-GA-CCCCGAA-ATG-ACCGA--C-AACTCGGTGCAAGA
gi|10 : atT-CCCAATCT----G---TCGTGCACTGAA-AGG-ATCGA--C-AACTCTCTATGAGAGaaatgatcttctccgtta
gi|11 : aagttactagagt---T-GAGCACTGTA-AGG-ATCGA--C-AATCGTGTATGAGAGat
gi|12 : aatTCTC--TTAT-ACAGAG-T-T-GT-AGGTCC-TT---AT----------------------------A-AGG-ACCGA--C-AACTTTGTGTAAGAGatagccatggcaaggtcga
gi|13 : attAG-TCT-GT-CGTTCC-TTT--AT-CT------------------------AA-AGG-ACCGA--C-AACTCTGTGCAAGAG
gi|14 : TCGC--TTGC-ACAGAG-T-T-GT-CGTTCC-TTTC
gi|15 : aga-GAGCACTGAACAGG-ATCGA--C-AACTC-GTATGAGAGatgggg
gi|16 : gatTCTC--TTGC-ACAGAG-T-T-GT-CGTTCC-TTTC
gi|17 : tcat-GAGCACTGAA-AGG-ATCGA--C-AACTCGGTATGGGAGtct
gi|2 : TCTC--TTGCCATAGAG-T-T-GTCCGGTCC-TTTC--T-CTCC--CTTGACG---T-AGGAGATAAA-AGGTACCGAGCT-AACTCTGCGCa
gi|3 : atcatTCTC--TCAT-ACAGAG-T-T-GT-CGATCC-TTTCAGTGCTCA--CT----G---T-GAGCACTGAA-AGG-ATCGA--C-AACTCTGTATGAGAGatgt
gi|4 : C--TTGC-ACAGAG-T-TTGT-CGGTCC-TTTCTTC-TTCC--TT----A---A-GGGTACGGAA-AGG-ACCGA--T-AACTCTGTGCAAGA
gi|6 : TCTCGTTTGC-ACAGAGGT-T-GT-CGTTCC-TTTC--T-CTCA--CTTA--G---T-GAG-A--GAA-AGG-AACGA--C-AACTCTGTGt
gi|7 : gcTCTC--TCAT-ACAGAG-T-T-GT-CGATCC-TTTCAG---------T----G---T-GAGCACTGAA-AGG-ATCGA--CAAACTCTGTATGAGAG
gi|8 : C--TTGC-ACAGAG-T-T-GT-CGTTCCTTTTCA---CTCA--CT--------T-GA-----GAA-AGG-AACGA--CAAACTCTGTGC-AGAa
gi|9 : ttcTCTC--TCAT-ACAGAG-T-T-GT-CGATCC-TT--------CA--C-----------GAGC--TGAG-AGG-ATCGA--C-AACTCTGTATGAAA
1 sequences could not be aligned to this reference sequence:
Unaligned ( gi|5 ): TCTCTTGCACAGAGTTGTATGTCCAGGGAGAGATAGAACCACTCTGTGCAAGAAAATGGTTTATCTTGTC
Alignments
lowQualScore : 4444444444444444444444444444444
lowQualScore : 44 2 3 3 3 3 3 1 3 0000000000000000000000000000000 2 2 0 33 5
lowQualScore : .. . . . . . . . . ............................... . . . .. .
lowQualScore : 66 0 3 1 1 1 1 0 1 7777777777777777777777777777777 7 7 8 77 3
consensus : TCTC--TCGC-ACAGAG-T-T-GTC-GNTCC-TTTC--T-C--TCA--CT----G---T-GAGCACTGAA-AGG-ACCGA--C-AACTCTGTGCGAGAG
Reference ( family-9837 ) : TCTC--TCGC-ACAGAG-T-T-GTC-GNTCC-TTTC--T-C--TCA--CT----G---T-GAGCACTGAA-AGG-ACCGA--C-AACTCTGTGCGAGAG
gi|1 : TCTC--TTGC-ACAGAG-T-T-GTC-GATCT-TTTC--T-C--TCA--------GAAAT-GA-CCCCGAA-ATG-ACCGA--C-AACTCGGTGCAAGA
gi|10 : at--T-C--CCAATCT----G---TCGTGCACTGAA-AGG-ATCGA--C-AACTCTCTATGAGAGaaatgatcttctccgtta
gi|11 : aagttactagagt---T-GAGCACTGTA-AGG-ATCGA--C-AATCGTGTATGAGAGat
gi|12 : aatTCTC--TTAT-ACAGAG-T-T-GTA-GGTCC-TT------------------------------AT---A-AGG-ACCGA--C-AACTTTGTGTAAGAGatagccatggcaaggtcga
gi|13 : attAG-TCT-GTC-GTTCC-TTTA--T-C--T------------------------AA-AGG-ACCGA--C-AACTCTGTGCAAGAG
gi|14 : TCGC--TTGC-ACAGAG-T-T-GTC-GTTCC-TTTC--T-C--T
gi|15 : -GAGCACTGAACAGG-ATCGA--C-AACTC-GTATGAGAGatgggg
gi|16 : gatTCTC--TTGC-ACAGAG-T-T-GTC-GTTCC-TTTC--T-C--T
gi|17 : tcat-GAGCACTGAA-AGG-ATCGA--C-AACTCGGTATGGGAG
gi|2 : TCTC--TTGCCATAGAG-T-T-GTCCGGTCC-TTTC--T-C--TCC--CTTGACG---T-AGGAGATAAA-AGGTACCGAGCT-AACTCTGCGCa
gi|3 : atcatTCTC--TCAT-ACAGAG-T-T-GTC-GATCC-TTTCAGTGC--TCA--CT----G---T-GAGCACTGAA-AGG-ATCGA--C-AACTCTGTATGAGAGatgt
gi|4 : C--TTGC-ACAGAG-T-TTGTC-GGTCC-TTTC--T-TCTTCC--TT----A---A-GGGTACGGAA-AGG-ACCGA--T-AACTCTGTGCAAGA
gi|5 : TTTC--TTGC-ACAGAG-T-------GGTTC-TATC--T-C--TCC--CT----G------------------G-ACATA--C-AACTCTGTGCAAGAGt
gi|6 : tTCTCGTTTGC-ACAGAGGT-T-GTC-GTTCC-TTTC--T-C--TCA--CTTA--G---T-GAG-A--GAA-AGG-AACGA--C-AACTCTGTGatggtttatcttgtc
gi|7 : gcTCTC--TCAT-ACAGAG-T-T-GTC-GATCC-TTTC---------A--GT----G---T-GAGCACTGAA-AGG-ATCGA--CAAACTCTGTATGAGAG
gi|8 : C--TTGC-ACAGAG-T-T-GTC-GTTCCTTTTC--A-C--TCA--CT--------T-GA-----GAA-AGG-AACGA--CAAACTCTGTGC-AGAa
gi|9 : ttcTCTC--TCAT-ACAGAG-T-T-GTC-GATCC-T----------TCA--C-----------GAG--CTGAG-AGG-ATCGA--C-AACTCTGTATGAAA
Alignments
lowQualScore : 4444444444444444444444444444444
lowQualScore : 44 2 3 3 3 3 3 1 3 0000000000000000000000000000000 2 2 0 33 5
lowQualScore : .. . . . . . . . . ............................... . . . .. .
lowQualScore : 66 0 3 1 1 1 1 0 1 7777777777777777777777777777777 7 7 8 77 3
consensus : TCTC--TCGC-ACAGAG-T-T-GTC-GNTCC-TTTC--T-C--TCA--CT----G---T-GAGCACTGAA-AGG-ACCGA--C-AACTCTGTGCGAGAG
Reference ( family-9837 ) : TCTC--TCGC-ACAGAG-T-T-GTC-GNTCC-TTTC--T-C--TCA--CT----G---T-GAGCACTGAA-AGG-ACCGA--C-AACTCTGTGCGAGAG
gi|1 : TCTC--TTGC-ACAGAG-T-T-GTC-GATCT-TTTC--T-C--TCA--------GAAAT-GA-CCCCGAA-ATG-ACCGA--C-AACTCGGTGCAAGA
gi|10 : at--T-C--CCAATCT----G---TCGTGCACTGAA-AGG-ATCGA--C-AACTCTCTATGAGAGaaatgatcttctccgtta
gi|11 : aagttactagagt---T-GAGCACTGTA-AGG-ATCGA--C-AATCGTGTATGAGAGat
gi|12 : aatTCTC--TTAT-ACAGAG-T-T-GTA-GGTCC-TT------------------------------AT---A-AGG-ACCGA--C-AACTTTGTGTAAGAGatagccatggcaaggtcga
gi|13 : attAG-TCT-GTC-GTTCC-TTTA--T-C--T------------------------AA-AGG-ACCGA--C-AACTCTGTGCAAGAG
gi|14 : TCGC--TTGC-ACAGAG-T-T-GTC-GTTCC-TTTC--T-C--T
gi|15 : -GAGCACTGAACAGG-ATCGA--C-AACTC-GTATGAGAGatgggg
gi|16 : gatTCTC--TTGC-ACAGAG-T-T-GTC-GTTCC-TTTC--T-C--T
gi|17 : tcat-GAGCACTGAA-AGG-ATCGA--C-AACTCGGTATGGGAG
gi|2 : TCTC--TTGCCATAGAG-T-T-GTCCGGTCC-TTTC--T-C--TCC--CTTGACG---T-AGGAGATAAA-AGGTACCGAGCT-AACTCTGCGCa
gi|3 : atcatTCTC--TCAT-ACAGAG-T-T-GTC-GATCC-TTTCAGTGC--TCA--CT----G---T-GAGCACTGAA-AGG-ATCGA--C-AACTCTGTATGAGAGatgt
gi|4 : C--TTGC-ACAGAG-T-TTGTC-GGTCC-TTTC--T-TCTTCC--TT----A---A-GGGTACGGAA-AGG-ACCGA--T-AACTCTGTGCAAGA
gi|5 : TTTC--TTGC-ACAGAG-T-------GGTTC-TATC--T-C--TCC--CT----G------------------G-ACATA--C-AACTCTGTGCAAGAGt
gi|6 : tTCTCGTTTGC-ACAGAGGT-T-GTC-GTTCC-TTTC--T-C--TCA--CTTA--G---T-GAG-A--GAA-AGG-AACGA--C-AACTCTGTGatggtttatcttgtc
gi|7 : gcTCTC--TCAT-ACAGAG-T-T-GTC-GATCC-TTTC---------A--GT----G---T-GAGCACTGAA-AGG-ATCGA--CAAACTCTGTATGAGAG
gi|8 : C--TTGC-ACAGAG-T-T-GTC-GTTCCTTTTC--A-C--TCA--CT--------T-GA-----GAA-AGG-AACGA--CAAACTCTGTGC-AGAa
gi|9 : ttcTCTC--TCAT-ACAGAG-T-T-GTC-GATCC-T----------TCA--C-----------GAG--CTGAG-AGG-ATCGA--C-AACTCTGTATGAAA
blockSeqs : GT T C G C T C G T TCTCCCTTGACGTAGGAGAT C T GC A
blockSeqs : . T . . . . . T . TCCCAATCTGTCGTGCACT . . . A
blockSeqs : . T . . . . . T . AGTGCTCACTGTGAGCACT . . . .
blockSeqs : . T . . . . . T . TTCTTCCTTAAGGGTACG . . . .
blockSeqs : . C . . . . . G . TCTCACTTAGTGAGA . . . .
blockSeqs : . T . . . . . A . AGTGTGAGCACT . . . .
blockSeqs : . T . . . . . G . ACTCACTTGA . . . .
blockSeqs : . T . . . . . G . TCACGAGCT . . . .
blockSeqs : . C . . . . . T . TCTCCCTG . . . .
blockSeqs : . T . . . . . A . TCT . . . .
blockSeqs : . C . . . . . T . AT . . . .
blockSeqs : . . . . A . . . . .
blockSeqs : . . . .
blockSeqs : . . . .
blockSeqCons : TCTCACTTGTGAGA*****************
originalCons : TCTC--TCGC-ACAGAG-T-T-GTC-GNTCC-TTTC--T-C--TCA--CT----G---T-GAGCACTGAA-AGG-ACCGA--C-AACTCTGTGCGAGAG
finalCons : TCTC--TCGC-ACAGAG-T-T-GTC-GNTCC-TTTCTCTCACTTGTGAGA-----------------GAA-AGG-ACCGA--C-AACTCTGTGCGAGAG
Alignments
lowQualScore : 66666666666666666666666666666666666
lowQualScore : 33 0 2 2 2 5 2 1 2 88888888888888888888888888888888888 3 0 55 3 4
lowQualScore : .. . . . . . . . . ................................... . . .. . .
lowQualScore : 99 3 9 7 7 3 7 0 7 99999999999999999999999999999999999 6 4 00 6 4
consensus : TCTC--TCGC-ACAGAG-T-T-GTC-GNTCC-TTTC-----T-C--TCA-CTT---GTGAG---A--G---AAAGG-ACCGA--C-AACTCTGTGCGAGAG
Reference ( family-9837 ) : TCTC--TCGC-ACAGAG-T-T-GTC-GNTCC-TTTC-----T-C--TCA-CTT---GTGAG---A--G---AAAGG-ACCGA--C-AACTCTGTGCGAGAG
gi|1 : TTTC--TTGC-ACCGAG-T-T-GTC-GGTCA-TTTC-----G-GGGTCA-TTT---CTGAG---A--G---AAAAG-ATCGA--C-AACTCTGTGCAAGAG
gi|10 : attTCTC--TCAT-AGAGAG-T-T-GTC-GATCC-TTTC-----atgatcttctccgtta
gi|12 : aagttactagagttcccaatctgtcgtgcactTCTC--TTAT-ACAGAG-T-T-GTA-GGTCC-TT----------------------AT--------------AAGG-ACCGA--C-AACTTTGTGTAAGAGt
gi|13 : attAG-TCT-GTC-GTTCC-TTTA-----T-C--T------------------------AAAGG-ACCGA--C-AACTCTGTGCAAGAG
gi|14 : TCGC--TTGC-ACAGAG-T-T-GTC-GTTCC-TTTC-----T-C--T
gi|16 : TCTC--TTGC-ACAGAG-T-T-GTC-GTTCC-TTTC-----T-C--Tatgggg
gi|17 : tcatTCTC--CCAT-ACCGAG-T-T-GTC-GATCC-TTTC-----
gi|2 : gagcactTCTC--TTGCCATAGAG-T-T-GTCCGGTCC-TTTC-----T-C--TCC-CTTGACGTAGG---A--GATAAAAGGTACCGAGCT-AACTCTGCGC
gi|3 : atcatTCTC--TCAT-ACAGAG-T-T-GTC-GATCC-TTTCAG---TGC--TCA-C-T---GTGAGC--ACTG---AAAGG-ATCGA--C-AACTCTGTATGAGAGatgt
gi|4 : C--TTGC-ACAGAG-T-TTGTC-GGTCC-TTTC-----TTC--TTC-CTT---AAGGGTACG--G---AAAGG-ACCGA--T-AACTCTGTGCAAGA
gi|5 : TTTC--TTGC-ACAGAG-T-------GGTTC-TATC-----T-C--TCC-CT----------------------GG-ACATA--C-AACTCTGTGCAAGAGt
gi|6 : tTCTCGTTTGC-ACAGAGGT-T-GTC-GTTCC-TTTC-----T-C--TCA-CTTA--GTGAG---A--G---AAAGG-AACGA--C-AACTCTGTGatggtttatcttgtc
gi|7 : gcTCTC--TCAT-ACAGAG-T-TTGTC-GATCC-TTTCAGTGCT-C--ACA-CT---------------G---AAAGG-ATCGA--C-AACTCTGTATGAGAG
gi|8 : tC--TTGC-ACAGAG-T-T-GTC-GTTCCTTTTC-----A-C--TCA-CTT-------G---A--G---AAAGG-AACGA--CAAACTCTGTGC-AGA
gi|9 : ttcTT--TCAT-ACAGAG-T-T-GTC-GATCC-T----------C--TCAGCTC---GTGA-------------AGG-ATCGA--C-AACTCTGTATGAGAG
2 sequences could not be aligned to this reference sequence:
Unaligned ( gi|11 ): AATCTCTCATACACGATTGTCGATCCTTACAGTGCTCAATAGCCATGGCAAGGTCGA
Unaligned ( gi|15 ): GATCTCTCATACGAGTTGTCGATCCTGTTCAGTGCTC