lowQualScore : 7777 444 222 888888888888888888
lowQualScore : 2222 1 000 111 8 8 666666666666666666 3 555 4 2
lowQualScore : .... . ... ... . . .................. . ... . .
lowQualScore : 6666 1 666 000 8 4 111111111111111111 6 444 0 8
consensus : CATATCAAAGCACGTTG---TCGAACGATTTG--ATATTTTTT-ATTTGATCGTC--T-GCTA------A---AAG-GG---GCTAGTCTCACCCCTATTACGGCGATTAAATGAGAC
Reference ( gi|1 ) : CATATCAAAGCACGTTAAATTCAAACAATTTT-TATATTTTTTTAGTTGATCTTC--C-TCTA--A---A---AAG-GG---GCTAGTCTCACCCTTATTACGGCAATTAAATGAGAC
gi|5 : CATATCAAAGCACGTTGA---CAAACAATTTA-AAAAAAAATTTATTTGATCGTC--T-GCT-------G---AAG-GG---GCTAATCTCACCCCTATCACAGCAATTAAATGAGAC
gi|4 : gCATATCAAAGCATGTTG---TCAATTGATTTG--ATATTTTTT-ATTTGATCATC--TGTTTA--A---T---AAT-GG---GCTAGTCTCATCCCTATTATGGTGATTAAATGAGA
gi|2 : gCACATCAAAGCATGTTG---TCAAACGATTAT--GTATTTT---AGTTGATCGTC--T-GCTACGATGTA---AAG-GG---GCTTGTCTCACCATTATAACGGCGAATAAATGAGA
gi|3 : CATATCAAAGCATATTG---TCAAGCGATTTG--ATTTTTTTATATTTGAT-TTC--T-GCTA--CGT-A---AAT-GG---GCTAGTCTCGCCCCTATAACGTCGATTAAATGAGACt
gi|9 : CATATCAAAGCACGTTG---TTGAACAA-TTT-GATACTTTTTAAGTTGAT
gi|8 : ATATCAATGTGCATTG---TCAAACAATTTAATAAATTTA---ATTTGATCGTC--T------------------------GCAAGTCTCACCCCTATTATAGCGATTAAATGAGACtgtttgttacg
gi|7 : ATTTCAAGGCATGTTG---TCGGACTATTCG--ATATTTTTA-ATTTGGTCGTC------------------GGGCGG---GCTAGTCTCGTCCCTATTACGGCGAATAAATG
gi|6 : TTATTTGATTTTTGAT-TCTA--T---ATTCAAT-GGTCCGCTAGTTTCACCCGTATTACGACGATTTTATGAGAC
gi|13 : ttaaggcacgttgtcgaaG-GG---GCTAGTCTCACCCCTATTACGGCGATTAAATGAGAC
gi|14 : G-GG---GCTAGTCTCACCCCTATTATGGCGATTAAATGAGACt
gi|12 : G-GG---GTTAGTCTCACCCCTATTACGGCGATTAAATGAGACt
gi|11 : G-GG---GTTAGTCTCATACCTATTACGGTAATTAAATGAGACt
gi|17 : G---GCTTATCTCACTCCTATTACAGCAATTAAATGAGACt
gi|15 : ---GCTAGTCTCACACCTATCACGGCGATTAAATGAGAC
gi|10 : gaaCTAGTCCCACCCTTATTACGGCGATTAAATGAGACt
gi|19 : cgtcctTAGTCTCACCCCTATTACAGTAATTAAATGAGACt
gi|16 : AATCTCACCCTTATTACGGCGATTAAATGAGAt
gi|20 : ccgcGTCTCACCCCTATTACGGCGATTAAATGAGACt
gi|18 : tGTCTCACCCCTATTACGGCGATTAAATGAGACt
gi|21 : ttTATTACGGCGATTAAATGAGACta
Alignments
lowQualScore : 11111 111 33333333333333333
lowQualScore : 777 0 2 4 11111 1 88888 000 0 99999999999999999
lowQualScore : ... . . . ..... . ..... ... . .................
lowQualScore : 888 7 7 4 11111 0 33333 111 1 11111111111111111
consensus : CATATCAAAGCACGTTG---TCGAACGATTTG-AT-----ATTT-----TT-T-ATTTGATCGTCTG-CTA------A-AA-G-GGGCTAGTCTCACCCCTATTACGGCGATTAAATGAGAC
Reference ( family-997 ) : CATATCAAAGCACGTTG---TCGAACGATTTG-AT-----ATTT-----TT-T-ATTTGATCGTCTG-CTA------A-AA-G-GGGCTAGTCTCACCCCTATTACGGCGATTAAATGAGAC
gi|1 : CATATCAAAGCACGTTAAATTCAAACAATTTTTAT-----ATTT-----TT-TTAGTTGATCTTCCT-CTA------A-AAAG-GGGCTAGTCTCACCCTTATTACGGCAATTAAATGAGAC
gi|10 : CTAGTCCCACCCTTATTACGGCGATTAAATGAGAC
gi|11 : cgtcct-G-GGGTTAGTCTCATACCTATTACGGTAATTAAATGAGACt
gi|12 : -G-GGGTTAGTCTCACCCCTATTACGGCGATTAAATGAGACt
gi|13 : -G-GGGCTAGTCTCACCCCTATTACGGCGATTAAATGAGACt
gi|14 : -G-GGGCTAGTCTCACCCCTATTATGGCGATTAAATGAGACt
gi|15 : GCTAGTCTCACACCTATCACGGCGATTAAATGAGACt
gi|16 : gaaAATCTCACCCTTATTACGGCGATTAAATGAGAt
gi|17 : ccgcGGCTTATCTCACTCCTATTACAGCAATTAAATGAGACt
gi|18 : GTCTCACCCCTATTACGGCGATTAAATGAGAC
gi|19 : ttTAGTCTCACCCCTATTACAGTAATTAAATGAGACta
gi|2 : CACATCAAAGCATGTTG---TCAAACGATT---AT-----GTAT-----TT-T-AGTTGATCGTCTG-CTACGATGTA-AA-G-GGGCTTGTCTCACCATTATAACGGCGAATAAATGAGAt
gi|20 : GTCTCACCCCTATTACGGCGATTAAATGAGACt
gi|21 : tCTATTACGGCGATTAAATGAGACt
gi|3 : CATATCAAAGCATATTG---TCAAGCGATTTG-AT-----TTTT-----TTAT-ATTTGATT-TCTG-CTACGT---A-AA-T-GGGCTAGTCTCGCCCCTATAACGTCGATTAAATGAGACtac
gi|4 : CATATCAAAGCATGTTG---TCAATTGATTTG-AT-----ATTT-----TT-T-ATTTGATCATCTGTTTA------ATAA-T-GGGCTAGTCTCATCCCTATTATGGTGATTAAATGAGA
gi|5 : gCATATCAAAGCACGTTG---ACAAACAATTTA-AA-----A---AAAAATT-T-ATTTGATCGTCTG-CT-------G-AA-G-GGGCTAATCTCACCCCTATCACAGCAATTAAATGAGAC
gi|6 : gTTAAGGCACGTTG---TCGAATTATTTG-ATTTTTGATTC-----TA-T-ATTCAATGGTCCG-CTA-------------------GTTTCACCCGTATTACGACGATTTTATGAGAC
gi|7 : ATTTCAAGGCATGTTG---TCGGACTATTCG-AT-----ATTT-----TT-A-ATTTGGTCGTCGG---------------GCGGGCTAGTCTCGTCCCTATTACGGCGAATAAATG
gi|8 : ATATCAATGTGCATTG---TCAAACAATTTA-AT-----AAAT-----TT-A-ATTTGATCGTCTG-C-----------A--------AGTCTCACCCCTATTATAGCGATTAAATGAGAC
gi|9 : CATATCAAAGCACGTTG---TTGAACAATTTG-AT-----ACTT-----TT-TAAGTTGATTGTTTG-TTA------
Alignments
lowQualScore : 11111 111 33333333333333333
lowQualScore : 777 0 2 4 11111 1 88888 000 0 99999999999999999
lowQualScore : ... . . . ..... . ..... ... . .................
lowQualScore : 888 7 7 4 11111 0 33333 111 1 11111111111111111
consensus : CATATCAAAGCACGTTG---TCGAACGATTTG-AT-----ATTT-----TT-T-ATTTGATCGTCTG-CTA------A-AA-G-GGGCTAGTCTCACCCCTATTACGGCGATTAAATGAGAC
Reference ( family-997 ) : CATATCAAAGCACGTTG---TCGAACGATTTG-AT-----ATTT-----TT-T-ATTTGATCGTCTG-CTA------A-AA-G-GGGCTAGTCTCACCCCTATTACGGCGATTAAATGAGAC
gi|1 : CATATCAAAGCACGTTAAATTCAAACAATTTTTAT-----ATTT-----TT-TTAGTTGATCTTCCT-CTA------A-AAAG-GGGCTAGTCTCACCCTTATTACGGCAATTAAATGAGAC
gi|10 : CTAGTCCCACCCTTATTACGGCGATTAAATGAGAC
gi|11 : cgtcct-G-GGGTTAGTCTCATACCTATTACGGTAATTAAATGAGACt
gi|12 : -G-GGGTTAGTCTCACCCCTATTACGGCGATTAAATGAGACt
gi|13 : -G-GGGCTAGTCTCACCCCTATTACGGCGATTAAATGAGACt
gi|14 : -G-GGGCTAGTCTCACCCCTATTATGGCGATTAAATGAGACt
gi|15 : GCTAGTCTCACACCTATCACGGCGATTAAATGAGACt
gi|16 : gaaAATCTCACCCTTATTACGGCGATTAAATGAGAt
gi|17 : ccgcGGCTTATCTCACTCCTATTACAGCAATTAAATGAGACt
gi|18 : GTCTCACCCCTATTACGGCGATTAAATGAGAC
gi|19 : ttTAGTCTCACCCCTATTACAGTAATTAAATGAGACta
gi|2 : CACATCAAAGCATGTTG---TCAAACGATT---AT-----GTAT-----TT-T-AGTTGATCGTCTG-CTACGATGTA-AA-G-GGGCTTGTCTCACCATTATAACGGCGAATAAATGAGAt
gi|20 : GTCTCACCCCTATTACGGCGATTAAATGAGACt
gi|21 : tCTATTACGGCGATTAAATGAGACt
gi|3 : CATATCAAAGCATATTG---TCAAGCGATTTG-AT-----TTTT-----TTAT-ATTTGATT-TCTG-CTACGT---A-AA-T-GGGCTAGTCTCGCCCCTATAACGTCGATTAAATGAGACtac
gi|4 : CATATCAAAGCATGTTG---TCAATTGATTTG-AT-----ATTT-----TT-T-ATTTGATCATCTGTTTA------ATAA-T-GGGCTAGTCTCATCCCTATTATGGTGATTAAATGAGA
gi|5 : gCATATCAAAGCACGTTG---ACAAACAATTTA-AA-----A---AAAAATT-T-ATTTGATCGTCTG-CT-------G-AA-G-GGGCTAATCTCACCCCTATCACAGCAATTAAATGAGAC
gi|6 : gTTAAGGCACGTTG---TCGAATTATTTG-ATTTTTGATTC-----TA-T-ATTCAATGGTCCG-CTA-------------------GTTTCACCCGTATTACGACGATTTTATGAGAC
gi|7 : ATTTCAAGGCATGTTG---TCGGACTATTCG-AT-----ATTT-----TT-A-ATTTGGTCGTCGG---------------GCGGGCTAGTCTCGTCCCTATTACGGCGAATAAATG
gi|8 : ATATCAATGTGCATTG---TCAAACAATTTA-AT-----AAAT-----TT-A-ATTTGATCGTCTG-C-----------A--------AGTCTCACCCCTATTATAGCGATTAAATGAGAC
gi|9 : CATATCAAAGCACGTTG---TTGAACAATTTG-AT-----ACTT-----TT-TAAGTTGATTGTTTG-TTA------
blockSeqs : . G . TTTTG T AAAAA AT CTACGATGTAAAG
blockSeqs : . G . . T . TA CTACGTAAAT
blockSeqs : . G . . T . T TTTAATAAT
blockSeqs : . A . . T . T CTGAAG
blockSeqs : . T . . T . T CTA
blockSeqs : . T . . A . T GC
blockSeqs : . A . . C . A CA
blockSeqs : . A . . . . A
blockSeqCons : *** T** CTAAA************
originalCons : CATATCAAAGCACGTTG---TCGAACGATTTG-AT-----ATTT-----TT-T-ATTTGATCGTCTG-CTA------A-AA-G-GGGCTAGTCTCACCCCTATTACGGCGATTAAATGAGAC
finalCons : CATATCAAAGCACGTTG---TCGAACGATTTG-AT-----ATTT-----TTT--ATTTGATCGTCTGCTAAA------------GGGCTAGTCTCACCCCTATTACGGCGATTAAATGAGAC
Alignments
lowQualScore : 11111 111 55555555555555555555
lowQualScore : 777 0 2 4 11111 1 88888 000 0 4 44444444444444444444
lowQualScore : ... . . . ..... . ..... ... . . ....................
lowQualScore : 888 7 7 4 11111 0 33333 111 1 4 00000000000000000000
consensus : CATATCAAAGCACGTTG---TCGAACGATTTG-AT-----ATTT-----TT-T-ATTTGATCGTC-TGC----T-A--------AA---GGGCTAGTCTCACCCCTATTACGGCGATTAAATGAGAC
Reference ( family-997 ) : CATATCAAAGCACGTTG---TCGAACGATTTG-AT-----ATTT-----TT-T-ATTTGATCGTC-TGC----T-A--------AA---GGGCTAGTCTCACCCCTATTACGGCGATTAAATGAGAC
gi|1 : CATATCAAAGCACGTTAAATTCAAACAATTTTTAT-----ATTT-----TT-TTAGTTGATCTTC-CTC----T-A--------AAAAGGGGCTAGTCTCACCCTTATTACGGCAATTAAATGAGAC
gi|10 : CTAGTCCCACCCTTATTACGGCGATTAAATGAGAC
gi|11 : cgtcct---GGGTTAGTCTCATACCTATTACGGTAATTAAATGAGACt
gi|12 : g---GGGTTAGTCTCACCCCTATTACGGCGATTAAATGAGACt
gi|13 : g---GGGCTAGTCTCACCCCTATTACGGCGATTAAATGAGACt
gi|14 : g---GGGCTAGTCTCACCCCTATTATGGCGATTAAATGAGACt
gi|15 : gGCTAGTCTCACACCTATCACGGCGATTAAATGAGACt
gi|16 : gaaAATCTCACCCTTATTACGGCGATTAAATGAGAt
gi|17 : ccgcGGCTTATCTCACTCCTATTACAGCAATTAAATGAGACt
gi|18 : GTCTCACCCCTATTACGGCGATTAAATGAGAC
gi|19 : ttTAGTCTCACCCCTATTACAGTAATTAAATGAGACta
gi|2 : CACATCAAAGCATGTTG---TCAAACGATT---AT-----GTAT-----TT-T-AGTTGATCGTC-TGC----T-ACGATGTAAAG---GGGCTTGTCTCACCATTATAACGGCGAATAAATGAGAt
gi|20 : GTCTCACCCCTATTACGGCGATTAAATGAGACt
gi|21 : tCTATTACGGCGATTAAATGAGACt
gi|3 : CATATCAAAGCATATTG---TCAAGCGATTTG-AT-----TTTT-----TTAT-ATTTGATT-TC-TGC----T-ACGTA----AAT--GGGCTAGTCTCGCCCCTATAACGTCGATTAAATGAGACtac
gi|4 : CATATCAAAGCATGTTG---TCAATTGATTTG-AT-----ATTT-----TT-T-ATTTGATCATC-TGTTTAAT-A--------AT---GGGCTAGTCTCATCCCTATTATGGTGATTAAATGAGA
gi|5 : gCATATCAAAGCACGTTG---ACAAACAATTTA-AA-----A---AAAAATT-T-ATTTGATCGTC-TGC----TGA--------AG---GGGCTAATCTCACCCCTATCACAGCAATTAAATGAGAC
gi|6 : gTTAAGGCACGTTG---TCGAATTATTTG-ATTTTTGATTC-----TA-T-ATTCAATGGTC-CGC----T-A-------------------GTTTCACCCGTATTACGACGATTTTATGAGAC
gi|7 : ATTTCAAGGCATGTTG---TCGGACTATTCG-AT-----ATTT-----TT-A-ATTTGGTCGTCGGGC--------------------GGGCTAGTCTCGTCCCTATTACGGCGAATAAATG
gi|8 : ATATCAATGTGCATTG---TCAAACAATTTA-AT-----AAAT-----TT-A-ATTTGATCGTC-TGC----------------A--------AGTCTCACCCCTATTATAGCGATTAAATGAGAC
gi|9 : CATATCAAAGCACGTTG---TTGAACAATTTG-AT-----ACTT-----TT-TAAGTTGATTGTT-TGT----T-A--------