lowQualScore : 1111111111 111111 2222
lowQualScore : 555 2222222222 6 444444 6666 3 3333 3 6
lowQualScore : ... .......... . ...... .... . .... . .
lowQualScore : 888 5555555555 0 000000 1111 6 3333 6 2
consensus : AGTTTGACACTCATGAA---TGGT----------GCATTTTTAAGTATGTG---TTTCTA----TTTAGAA-TATTGCTGCAATAAAATGAATACAAAGAAATTTAAA---GT-TTTTTTAATGGATGACT
Reference ( gi|6 ) : AGTTTGACACTCATGAA---TGGT----------GCATTTTTAAGCATGTG---CTACTA----TTTAGAA-TATTGCTGCAATAAAATGAATACAAAGAAATTTAAA---CT-TTTTTCAATGGATGACT
gi|4 : AGTTTGACACTTATGAA---TGGT----------GCATTTTTAAGTATGT-----TTCTA----TTTAGAA-TATTGCTGCAATAAAATTAATACAAAGAAATTTTAAGTTTT-TTTTTCAATGGATGACT
gi|8 : AGTTTGACACTCATGAA---TGGT----------GCAATTATAAGTATGTG---TTATTA----TTTAAAA-TATTGCTGCAATAAAATTAATACAAA-AAATTAAAA---CT-TTTTTTAATGGATGACTa
gi|2 : AGTTTGACACTCATGAA---TGGT----------GCATTTTTAAGTATGTGTTTCTATTAATACTTTAGAA-TATTACTGCAATAAAATGAATACAAAGAAATTGAAA---GT-TTTTTTACTGTATGACT
gi|3 : AGTTTGACACTCATGAAAAATGGT----------GCATTTTTAAGTATGTG---TTTCTG----TTTAGAAATATTGCTGCAATAAAATGAATACAAAGAAATTAAAA---GA-TTTAT-AACGGATGACT
gi|1 : AGTTTGACACTCATGAA---TGTTTTATTAACACTCATTTTTAAGTATGTG---TTTCTG----TTAAGAA-TATTGCTGCAATAAAATGAATACAAAGAAATGTAAA---GT-TTTTTTAATAGATGACa
gi|5 : AGTTTGACTTTTATGAA---TGGT----------GTATTTTTAAGTATCTG---TTTCTA----TTTAAAA-TATTGCAGCAATAAAATGAATACAAAGACACTTAAA---GTGTTTTTTAGTGAATGACTa
gi|13 : AGTTTGTCACTCATGAA---TGGT----------GCATTTTTAAGTATTTG---TTTCTA----TTTAGA
gi|16 : aAGTTTGATATTCATGAA---AGGT----------GCATTTTCAAGTAGGTG---TTGCT
gi|14 : aAATTTGACATTCATGAT---TAGT----------GCATTTTTAAGTATGGG---TTTCTA----
gi|7 : GTTTGACACTCATGAA---TGGT----------GTGTTTTTAAGTATGTG---TTTCTT----TTTACAA-TATTGCTGCAATAAAATGAATACAAAGAAATTTAAA---GT-TTTTTTAATGGATGACTgt
gi|15 : TTGACATTCATGAG---TGGT----------GCAATTTCAAGTAGGAG---TTTCTA----TTT
gi|9 : aGACACTCATGAA---CGGT----------GCATTTTTAAGTATGTG---TTTCTG----TTTAGAA-TATTGCTGTAATAAAATGAATACAAAGAAATTTAAA---GT-TTTTTCAATGGATGAC
gi|10 : T----------GCATTTAT--GTATGTG---TTTCTA----TTTAAAA-TATTGCTGCAATAAAATAAATACAAAGAAACTTAAA---GT-TTTTTTAATGGATGACTa
gi|11 : T----------GCATTTTTAAGTATGTG---TTTCTA----TTTATAA-TATATATGCAACAAAATAAATACAAAGAAATTTAAA---GT-TTTTTTAATGGATG
gi|12 : CTA----TTTAGAA-TATTGCTGCAATAAAATGAATACAAAG-GATTTAAAGT-GT-TTTTTTAATGGATGACT
Alignments
lowQualScore : 1111111111
lowQualScore : 555 1111111111 9999999 3 44 3 555
lowQualScore : ... .......... ....... . .. . ...
lowQualScore : 444 7777777777 3333333 3 66 3 888
consensus : AGTTTGACACTCATGAA---TGGT----------GCATTTTTAAGTATGTGTTTCTATT-------TAGAA-TATTGCTGCAATAAAATGAATACAAAGAAATTTAAA--GT-TTTTTT---AATGGATGACT
Reference ( family-1641 ) : AGTTTGACACTCATGAA---TGGT----------GCATTTTTAAGTATGTGTTTCTATT-------TAGAA-TATTGCTGCAATAAAATGAATACAAAGAAATTTAAA--GT-TTTTTT---AATGGATGACT
gi|1 : AGTTTGACACTCATGAA---TGTTTTATTAACACTCATTTTTAAGTATGTGTTTCTGTT-------AAGAA-TATTGCTGCAATAAAATGAATACAAAGAAATGTAAA--GT-TTTTTT---AATAGATGAC
gi|10 : T----------GCATTTAT--GTATGTGTTTCTATT-------TAAAA-TATTGCTGCAATAAAATAAATACAAAGAAACTTAAA--GT-TTTTTT---AATGGATGACTa
gi|11 : T----------GCATTTTTAAGTATGTGTTTCTATT-------TATAA-TATATATGCAACAAAATAAATACAAAGAAATTTAAA--GT-TTTTTT---AATGGATG
gi|12 : TTTCTATT-------TAGAA-TATTGCTGCAATAAAATGAATACAAAG-GATTTAAAGTGT-TTTTTT---AATGGATGACT
gi|13 : AGTTTGTCACTCATGAA---TGGT----------GCATTTTTAAGTATTTGTTTCTATT-------TAGA
gi|14 : aAATTTGACATTCATGAT---TAGT----------GCATTTTTAAGTATGGGTTTCTA
gi|15 : TTGACATTCATGAG---TGGT----------GCAATTTCAAGTAGGAGTTTCTATT-------Tgt
gi|16 : aAGTTTGATATTCATGAA---AGGT----------GCATTTTCAAGTAGGTGTTGCT
gi|2 : aAGTTTGACACTCATGAA---TGGT----------GCATTTTTAAGTATGTGTTTCTATTAATACTTTAGAA-TATTACTGCAATAAAATGAATACAAAGAAATTGAAA--GT-TTTTTT---ACTGTATGACT
gi|3 : AGTTTGACACTCATGAAAAATGGT----------GCATTTTTAAGTATGTGTTTCTGTT-------TAGAAATATTGCTGCAATAAAATGAATACAAAGAAATTAAAA--G--ATTTAT---AACGGATGACT
gi|4 : AGTTTGACACTTATGAA---TGGT----------GCATTTTTAAGTATGT--TTCTATT-------TAGAA-TATTGCTGCAATAAAATTAATACAAAGAAATTTTAA--GT-TTTTTTTTCAATGGATGACTa
gi|5 : AGTTTGACTTTTATGAA---TGGT----------GTATTTTTAAGTATCTGTTTCTATT-------TAAAA-TATTGCAGCAATAAAATGAATACAAAGACACTTAAA--GTGTTTTTT---AGTGAATGACTa
gi|6 : AGTTTGACACTCATGAA---TGGT----------GCATTTTTAAGCATGTGCTACTATT-------TAGAA-TATTGCTGCAATAAAATGAATACAAAGAAATTTAAA--CT-TTTTTC---AATGGATGACT
gi|7 : GTTTGACACTCATGAA---TGGT----------GTGTTTTTAAGTATGTGTTTCTTTT-------TACAA-TATTGCTGCAATAAAATGAATACAAAGAAATTTAAA--GT-TTTTTT---AATGGATGACT
gi|8 : AGTTTGACACTCATGAA---TGGT----------GCAATTATAAGTATGTGTTATTATT-------TAAAA-TATTGCTGCAATAAAATTAATACAAA-AAATTAAAA--CT-TTTTTT---AATGGATGACT
gi|9 : GACACTCATGAA---CGGT----------GCATTTTTAAGTATGTGTTTCTGTT-------TAGAA-TATTGCTGTAATAAAATGAATACAAAGAAATTTAAA--GT-TTTTTC---AATGGATGAC
Alignments
lowQualScore : 1111111111
lowQualScore : 555 1111111111 9999999 3 44 3 555
lowQualScore : ... .......... ....... . .. . ...
lowQualScore : 444 7777777777 3333333 3 66 3 888
consensus : AGTTTGACACTCATGAA---TGGT----------GCATTTTTAAGTATGTGTTTCTATT-------TAGAA-TATTGCTGCAATAAAATGAATACAAAGAAATTTAAA--GT-TTTTTT---AATGGATGACT
Reference ( family-1641 ) : AGTTTGACACTCATGAA---TGGT----------GCATTTTTAAGTATGTGTTTCTATT-------TAGAA-TATTGCTGCAATAAAATGAATACAAAGAAATTTAAA--GT-TTTTTT---AATGGATGACT
gi|1 : AGTTTGACACTCATGAA---TGTTTTATTAACACTCATTTTTAAGTATGTGTTTCTGTT-------AAGAA-TATTGCTGCAATAAAATGAATACAAAGAAATGTAAA--GT-TTTTTT---AATAGATGAC
gi|10 : T----------GCATTTAT--GTATGTGTTTCTATT-------TAAAA-TATTGCTGCAATAAAATAAATACAAAGAAACTTAAA--GT-TTTTTT---AATGGATGACTa
gi|11 : T----------GCATTTTTAAGTATGTGTTTCTATT-------TATAA-TATATATGCAACAAAATAAATACAAAGAAATTTAAA--GT-TTTTTT---AATGGATG
gi|12 : TTTCTATT-------TAGAA-TATTGCTGCAATAAAATGAATACAAAG-GATTTAAAGTGT-TTTTTT---AATGGATGACT
gi|13 : AGTTTGTCACTCATGAA---TGGT----------GCATTTTTAAGTATTTGTTTCTATT-------TAGA
gi|14 : aAATTTGACATTCATGAT---TAGT----------GCATTTTTAAGTATGGGTTTCTA
gi|15 : TTGACATTCATGAG---TGGT----------GCAATTTCAAGTAGGAGTTTCTATT-------Tgt
gi|16 : aAGTTTGATATTCATGAA---AGGT----------GCATTTTCAAGTAGGTGTTGCT
gi|2 : aAGTTTGACACTCATGAA---TGGT----------GCATTTTTAAGTATGTGTTTCTATTAATACTTTAGAA-TATTACTGCAATAAAATGAATACAAAGAAATTGAAA--GT-TTTTTT---ACTGTATGACT
gi|3 : AGTTTGACACTCATGAAAAATGGT----------GCATTTTTAAGTATGTGTTTCTGTT-------TAGAAATATTGCTGCAATAAAATGAATACAAAGAAATTAAAA--G--ATTTAT---AACGGATGACT
gi|4 : AGTTTGACACTTATGAA---TGGT----------GCATTTTTAAGTATGT--TTCTATT-------TAGAA-TATTGCTGCAATAAAATTAATACAAAGAAATTTTAA--GT-TTTTTTTTCAATGGATGACTa
gi|5 : AGTTTGACTTTTATGAA---TGGT----------GTATTTTTAAGTATCTGTTTCTATT-------TAAAA-TATTGCAGCAATAAAATGAATACAAAGACACTTAAA--GTGTTTTTT---AGTGAATGACTa
gi|6 : AGTTTGACACTCATGAA---TGGT----------GCATTTTTAAGCATGTGCTACTATT-------TAGAA-TATTGCTGCAATAAAATGAATACAAAGAAATTTAAA--CT-TTTTTC---AATGGATGACT
gi|7 : GTTTGACACTCATGAA---TGGT----------GTGTTTTTAAGTATGTGTTTCTTTT-------TACAA-TATTGCTGCAATAAAATGAATACAAAGAAATTTAAA--GT-TTTTTT---AATGGATGACT
gi|8 : AGTTTGACACTCATGAA---TGGT----------GCAATTATAAGTATGTGTTATTATT-------TAAAA-TATTGCTGCAATAAAATTAATACAAA-AAATTAAAA--CT-TTTTTT---AATGGATGACT
gi|9 : GACACTCATGAA---CGGT----------GCATTTTTAAGTATGTGTTTCTGTT-------TAGAA-TATTGCTGTAATAAAATGAATACAAAGAAATTTAAA--GT-TTTTTC---AATGGATGAC
blockSeqs : AAA . AATACTT A GT G TTC
blockSeqs : . . . . . . .
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blockSeqs : . . . . . . .
blockSeqs : . . . . . . .
blockSeqs : . . . . . . .
blockSeqs : . . . . . . .
blockSeqs : . . . . . . .
blockSeqs : . . . . . . .
blockSeqs : . . .
blockSeqs : . .
blockSeqs : .
blockSeqCons : **********
originalCons : AGTTTGACACTCATGAA---TGGT----------GCATTTTTAAGTATGTGTTTCTATT-------TAGAA-TATTGCTGCAATAAAATGAATACAAAGAAATTTAAA--GT-TTTTTT---AATGGATGACT
finalCons : AGTTTGACACTCATGAA---TGGT----------GCATTTTTAAGTATGTGTTTCTATT-------TAGAA-TATTGCTGCAATAAAATGAATACAAAGAAATTTAAA--GT-TTTTTT---AATGGATGACT
Alignments
lowQualScore : 1111111111
lowQualScore : 555 1111111111 9999999 3 44 3 555
lowQualScore : ... .......... ....... . .. . ...
lowQualScore : 444 7777777777 3333333 3 66 3 888
consensus : AGTTTGACACTCATGAA---TGGT----------GCATTTTTAAGTATGTGTTTCTATT-------TAGAA-TATTGCTGCAATAAAATGAATACAAAGAAATTTAAA--GT-TTTTTT---AATGGATGACT
Reference ( family-1641 ) : AGTTTGACACTCATGAA---TGGT----------GCATTTTTAAGTATGTGTTTCTATT-------TAGAA-TATTGCTGCAATAAAATGAATACAAAGAAATTTAAA--GT-TTTTTT---AATGGATGACT
gi|1 : AGTTTGACACTCATGAA---TGTTTTATTAACACTCATTTTTAAGTATGTGTTTCTGTT-------AAGAA-TATTGCTGCAATAAAATGAATACAAAGAAATGTAAA--GT-TTTTTT---AATAGATGAC
gi|10 : T----------GCATTTAT--GTATGTGTTTCTATT-------TAAAA-TATTGCTGCAATAAAATAAATACAAAGAAACTTAAA--GT-TTTTTT---AATGGATGACTa
gi|11 : T----------GCATTTTTAAGTATGTGTTTCTATT-------TATAA-TATATATGCAACAAAATAAATACAAAGAAATTTAAA--GT-TTTTTT---AATGGATG
gi|12 : TTTCTATT-------TAGAA-TATTGCTGCAATAAAATGAATACAAAG-GATTTAAAGTGT-TTTTTT---AATGGATGACT
gi|13 : AGTTTGTCACTCATGAA---TGGT----------GCATTTTTAAGTATTTGTTTCTATT-------TAGA
gi|14 : aAATTTGACATTCATGAT---TAGT----------GCATTTTTAAGTATGGGTTTCTA
gi|15 : TTGACATTCATGAG---TGGT----------GCAATTTCAAGTAGGAGTTTCTATT-------Tgt
gi|16 : aAGTTTGATATTCATGAA---AGGT----------GCATTTTCAAGTAGGTGTTGCT
gi|2 : aAGTTTGACACTCATGAA---TGGT----------GCATTTTTAAGTATGTGTTTCTATTAATACTTTAGAA-TATTACTGCAATAAAATGAATACAAAGAAATTGAAA--GT-TTTTTT---ACTGTATGACT
gi|3 : AGTTTGACACTCATGAAAAATGGT----------GCATTTTTAAGTATGTGTTTCTGTT-------TAGAAATATTGCTGCAATAAAATGAATACAAAGAAATTAAAA--G--ATTTAT---AACGGATGACT
gi|4 : AGTTTGACACTTATGAA---TGGT----------GCATTTTTAAGTATGT--TTCTATT-------TAGAA-TATTGCTGCAATAAAATTAATACAAAGAAATTTTAA--GT-TTTTTTTTCAATGGATGACTa
gi|5 : AGTTTGACTTTTATGAA---TGGT----------GTATTTTTAAGTATCTGTTTCTATT-------TAAAA-TATTGCAGCAATAAAATGAATACAAAGACACTTAAA--GTGTTTTTT---AGTGAATGACTa
gi|6 : AGTTTGACACTCATGAA---TGGT----------GCATTTTTAAGCATGTGCTACTATT-------TAGAA-TATTGCTGCAATAAAATGAATACAAAGAAATTTAAA--CT-TTTTTC---AATGGATGACT
gi|7 : GTTTGACACTCATGAA---TGGT----------GTGTTTTTAAGTATGTGTTTCTTTT-------TACAA-TATTGCTGCAATAAAATGAATACAAAGAAATTTAAA--GT-TTTTTT---AATGGATGACT
gi|8 : AGTTTGACACTCATGAA---TGGT----------GCAATTATAAGTATGTGTTATTATT-------TAAAA-TATTGCTGCAATAAAATTAATACAAA-AAATTAAAA--CT-TTTTTT---AATGGATGACT
gi|9 : GACACTCATGAA---CGGT----------GCATTTTTAAGTATGTGTTTCTGTT-------TAGAA-TATTGCTGTAATAAAATGAATACAAAGAAATTTAAA--GT-TTTTTC---AATGGATGAC