lowQualScore : 111111111111111111111 111111111111111111111 111111111111111 111111
lowQualScore : 666666666666666666666 555555555555555555555 1 333 000000000000000 55555 333 888888 0 2
lowQualScore : ..................... ..................... . ... ............... ..... ... ...... . .
lowQualScore : 222222222222222222222 555555555555555555555 7 222 555555555555555 33333 777 000000 2 7
consensus : CTTCCATTTTCCATTCCATGAAAAATAG---------------------AACGT---------------------T-CTATTT---TGG------A-------C-----CGA---CT--GG-AAATTTCTGAAGCTGC-AAAGACGAATGCTACAT
Reference ( gi|6 ) : CTTCCATTTTCCATTCCATGAAAAATAG---------------------AACGT---------------------T-CTATTT---TGA------A-------C-----CGA---CT--TG-AAATTTCTGAAGCTGC-AAAGACGAATGCTACAT
gi|10 : CTTCCATTTCCCACTCCATAAAAAGTAG---------------------AACGT---------------------T-CTATTT---TGG------A-------C-----AAA---CT--GG-AAATTTCTGAAGCTGC-AAAAAC
gi|11 : CTTCCATTTTCCATTCCATGAAAAATAA---------------------AACAT---------------------T-CTTTTT---TGA------A-------C-----C-------------AATTTCTGAATTTGT-AAAGACAA
gi|13 : aCTTCTATTTTCCATTCTATGAAAAATAT---------------------AACGT---------------------T-CTATTT---TGA------A-------C-----CAA---C----------TTCTGAAGCTGggc
gi|8 : CTTCCATTTTCGTTTTCTTGTAAAATAG---------------------AACGT---------------------TCCTA-TT---TGA------A-------C-----TAA---CTTCTG-AAG---CTGAAGCTGC-AAAGACG-ATGCTACga
gi|12 : CTTTCATTTGTCATTGAATGAAAAATAG---------------------AACGT---------------------T-TTACTT---AGG------A-------C-----CGA---CT--GG-AAACTTCTGAAGCTGC-
gi|15 : CTTCCATTTTCCATTCCATGAAAAATAC---------------------AACGT---------------------T-CTATTT---TAT------A-------C-----CAA---C----------TTCTAAAGCTG
gi|14 : CTTCCATTTTCCATTCCATGAAAAATAC---------------------AACGT---------------------T-CTATTT---TAT------A-------C-----CAA---C----------TTCTAAAGCTGtc
gi|3 : TTCCATTTTCCGTTGCATGGAAAATAG---------------------AACGTACTTTTTTGCATGTTGAACGTT-CTTTTT---TGA--------------C-----CGA---CT--GG-AAATTTCTGAAGCTGC-AAAGACGATTGCTtc
gi|19 : TTCCATTTTCTATTCCATAGAAAATAG---------------------AATGT---------------------T-CTA
gi|9 : atTCCATTTTCCATTCCATGAAAAATAG---------------------AACGT---------------------T-CTATTT---TGG------A-------C-----CGA---CT--TG-AAATTTCTGAAGCTGC-AAAGACGAAT
gi|7 : TTCATTTTCCATTCCATGAAAAATAG---------------------AACGT---------------------T-CTATTT---TGG------G-------C-----CGA---CT--GG-AAATTTCTGAAGCTGC-AAAAACGAATGCTTCA
gi|5 : gTCCATTTTCCATTCCATGAAAATTAG---------------------AACAT---------------------T-ATATTT---TGG------A-------C-----CGA---CT--GG-AAACTTCTGAAACTGCAAAAAACGAATGCTACAT
gi|2 : caCCACCTTTCATT------AAAATAG---------------------AACGT---------------------T-CTATTT---Tttttt
gi|1 : attgtttccattccatgaATTTTCAATTCCATGAAAAATAGAACTTTCTATTTTGTAGGGATAACGT---------------------T-CTATTT---TGG------A-------T-----CAA---C---TA-AAATTTTTT--GCAGC-AATGACGAATGCtgtgaagtctaatgaaaatttctgaagttccaaagacgaatgccacataatgtttaaatttaatc
gi|7 : TTTCCAGTCGGCCCAAAATAG---------------------AACGT---------------------T-CTATTT---Taccaaaatgttttaatatgaaatcc
gi|10 : gttcattttccattccatgaTTTCCAGTTTGTCCAAAATAG---------------------AACGT---------------------T-CTACTT---Ttttctgaagctgcaaaaacgaatgcttca
gi|2 : cttccatttcccactccataaTTTCCATTCCATGAAAAATAG---------------------AACGT---------------------T-CTATTTTAATGA------AAGGTGGTG-----TGAAGTCTAATGAAAATTTCTGAAGTTCC-AAAGACGAATGCCACATtttctgaagctgcaaaaac
gi|4 : attgCCATTCCAGGAAAAATAG---------------------AAC---------------------------ATTT---TGAGGAAAAA-------CGAAAGCAA---CT--TG-AAATTTTTGGAGCTAC-AAAGACGAATGCTAaatgtttaaatttaatc
gi|1 : TCCCTACAAAATAG---------------------AAAGT---------------------T-CTATTT---TTC------A-------T-----GGA---AT--TG-AAAaaaaacatgttgaattaaa
gi|17 : atTCTATGTAAAATAG---------------------AACGT---------------------T-CTTTTT---TGA------A-------C------------------AAACTTCTGAAGCTGC-taacgttctattttggatcaactaaaattttttgcagcaatgacgaatgcaccaaaatgttttaatatgaaatcc
gi|9 : AAAATAG---------------------AACGT---------------------T-CTATTT---Tca
gi|16 : tccattttccattccatgaT---------------------T-CTATTT---TGG------G-------C-----TGA---CT--AG-AA-TCTCTAAAGCTTC-AAAGACGAATGCTACggaccgacttgaaatttctgaagctgcaaagacgaat
gi|18 : ct-CTATTT---TGG------A-------C-----AGA---CT--GG-AAATTTCTGTAGCTGC-AGAGACAAATGCTA
gi|20 : -------C-----CGA---CT--GT-AAATTTCTGAAGCTGC-AAAGACGAGTACT
Alignments
lowQualScore : 3333333333333333333333333333333333333333333 111111111
lowQualScore : 1111111111111111111111111111111111111111111 2 7777777 555555555 55555 1 7777 2
lowQualScore : ........................................... . ....... ......... ..... . .... .
lowQualScore : 0000000000000000000000000000000000000000000 1 2222222 333333333 33333 2 7777 5
consensus : CTTCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGAATGCTACAT
Reference ( family-395 ) : CTTCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGAATGCTACAT
gi|1 : ATTTTCAATTCCATGAAAAATAGA---------------------ACTTTCTATTTTGTAGGGATAACGTT-CTATTTT-------GG---------AT-----CAACT--AAAATTTTTTGCA---GC-AATGACGAATGC
gi|10 : CTTCCATTTCCCACTCCATAAAAAGTAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----AAACT--GGAAATTTCTGAAGCTGC-AAAAACaccaaaatgttttaatatgaaatcc
gi|11 : CTTCCATTTTCCATTCCATGAAAAATAAA---------------------A---------------------CATT-CTTTTTT-------GA---------AC-----C---------AATTTCTGAATTTGT-AAAGACAA
gi|12 : aCTTTCATTTGTCATTGAATGAAAAATAGA---------------------A---------------------CGTT-TTACTTA-------GG---------AC-----CGACT--GGAAACTTCTGAAGCTGC-ggc
gi|13 : CTTCTATTTTCCATTCTATGAAAAATATA---------------------A---------------------CGTT-CTATTTT-------GA---------AC-----CAAC---------TTCTGAAGCTG
gi|14 : CTTCCATTTTCCATTCCATGAAAAATACA---------------------A---------------------CGTT-CTATTTT-------AT---------AC-----CAAC---------TTCTAAAGCTGga
gi|15 : CTTCCATTTTCCATTCCATGAAAAATACA---------------------A---------------------CGTT-CTATTTT-------AT---------AC-----CAAC---------TTCTAAAGCTGtc
gi|16 : TT-CTATTTT-------GG---------GC-----TGACT--AGAA-TCTCTAAAGCTTC-AAAGACGAATGCTACtc
gi|17 : ctTCTATGTAAAATAGA---------------------A---------------------CGTT-CTTTTTT-------GA---------AC--------------AAACTTCTGAAGCTGC-
gi|18 : -CTATTTT-------GG---------AC-----AGACT--GGAAATTTCTGTAGCTGC-AGAGACAAATGCTAca
gi|19 : TTCCATTTTCTATTCCATAGAAAATAGA---------------------A---------------------TGTT-CTA
gi|2 : atTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTTAATGAAAGGTGGTGTGAAGT-----CTAAT--GAAAATTTCTGAAGTTCC-AAAGACGAATGCCACAT
gi|20 : attgC-----CGACT--GTAAATTTCTGAAGCTGC-AAAGACGAGTACTaatgtttaaatttaatc
gi|3 : TTCCATTTTCCGTTGCATGGAAAATAGAACGTACTTTTTTGCATGTTGAA---------------------CGTT-CT-TTTT-------TG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGATTGCT
gi|4 : CCATTCCAGGAAAAATAGA---------------------A---------------------C------ATTTT-------GAGGAAAA---ACGAAAGCAACT--TGAAATTTTTGGAGCTAC-AAAGACGAATGCTA
gi|5 : TCCATTTTCCATTCCATGAAAATTAGA---------------------A---------------------CATT-ATATTTT-------GG---------AC-----CGACT--GGAAACTTCTGAAACTGCAAAAAACGAATGCTACATaaaaacatgttgaattaaa
gi|6 : caCTTCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GA---------AC-----CGACT--TGAAATTTCTGAAGCTGC-AAAGACGAATGCTACATttttt
gi|7 : TTCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------GC-----CGACT--GGAAATTTCTGAAGCTGC-AAAAACGAATGCTTCA
gi|8 : gCTTCCATTTTCGTTTTCTTGTAAAATAGA---------------------A---------------------CGTTCCTA-TTT-------GA---------AC-----TAACTTCTGAAG---CTGAAGCTGC-AAAGACG-ATGCTAC
gi|9 : TCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----CGACT--TGAAATTTCTGAAGCTGC-AAAGACGAAT
Alignments
lowQualScore : 3333333333333333333333333333333333333333333 111111111
lowQualScore : 1111111111111111111111111111111111111111111 2 7777777 555555555 55555 1 7777 2
lowQualScore : ........................................... . ....... ......... ..... . .... .
lowQualScore : 0000000000000000000000000000000000000000000 1 2222222 333333333 33333 2 7777 5
consensus : CTTCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGAATGCTACAT
Reference ( family-395 ) : CTTCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGAATGCTACAT
gi|1 : ATTTTCAATTCCATGAAAAATAGA---------------------ACTTTCTATTTTGTAGGGATAACGTT-CTATTTT-------GG---------AT-----CAACT--AAAATTTTTTGCA---GC-AATGACGAATGC
gi|10 : CTTCCATTTCCCACTCCATAAAAAGTAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----AAACT--GGAAATTTCTGAAGCTGC-AAAAACaccaaaatgttttaatatgaaatcc
gi|11 : CTTCCATTTTCCATTCCATGAAAAATAAA---------------------A---------------------CATT-CTTTTTT-------GA---------AC-----C---------AATTTCTGAATTTGT-AAAGACAA
gi|12 : aCTTTCATTTGTCATTGAATGAAAAATAGA---------------------A---------------------CGTT-TTACTTA-------GG---------AC-----CGACT--GGAAACTTCTGAAGCTGC-ggc
gi|13 : CTTCTATTTTCCATTCTATGAAAAATATA---------------------A---------------------CGTT-CTATTTT-------GA---------AC-----CAAC---------TTCTGAAGCTG
gi|14 : CTTCCATTTTCCATTCCATGAAAAATACA---------------------A---------------------CGTT-CTATTTT-------AT---------AC-----CAAC---------TTCTAAAGCTGga
gi|15 : CTTCCATTTTCCATTCCATGAAAAATACA---------------------A---------------------CGTT-CTATTTT-------AT---------AC-----CAAC---------TTCTAAAGCTGtc
gi|16 : TT-CTATTTT-------GG---------GC-----TGACT--AGAA-TCTCTAAAGCTTC-AAAGACGAATGCTACtc
gi|17 : ctTCTATGTAAAATAGA---------------------A---------------------CGTT-CTTTTTT-------GA---------AC--------------AAACTTCTGAAGCTGC-
gi|18 : -CTATTTT-------GG---------AC-----AGACT--GGAAATTTCTGTAGCTGC-AGAGACAAATGCTAca
gi|19 : TTCCATTTTCTATTCCATAGAAAATAGA---------------------A---------------------TGTT-CTA
gi|2 : atTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTTAATGAAAGGTGGTGTGAAGT-----CTAAT--GAAAATTTCTGAAGTTCC-AAAGACGAATGCCACAT
gi|20 : attgC-----CGACT--GTAAATTTCTGAAGCTGC-AAAGACGAGTACTaatgtttaaatttaatc
gi|3 : TTCCATTTTCCGTTGCATGGAAAATAGAACGTACTTTTTTGCATGTTGAA---------------------CGTT-CT-TTTT-------TG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGATTGCT
gi|4 : CCATTCCAGGAAAAATAGA---------------------A---------------------C------ATTTT-------GAGGAAAA---ACGAAAGCAACT--TGAAATTTTTGGAGCTAC-AAAGACGAATGCTA
gi|5 : TCCATTTTCCATTCCATGAAAATTAGA---------------------A---------------------CATT-ATATTTT-------GG---------AC-----CGACT--GGAAACTTCTGAAACTGCAAAAAACGAATGCTACATaaaaacatgttgaattaaa
gi|6 : caCTTCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GA---------AC-----CGACT--TGAAATTTCTGAAGCTGC-AAAGACGAATGCTACATttttt
gi|7 : TTCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------GC-----CGACT--GGAAATTTCTGAAGCTGC-AAAAACGAATGCTTCA
gi|8 : gCTTCCATTTTCGTTTTCTTGTAAAATAGA---------------------A---------------------CGTTCCTA-TTT-------GA---------AC-----TAACTTCTGAAG---CTGAAGCTGC-AAAGACG-ATGCTAC
gi|9 : TCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----CGACT--TGAAATTTCTGAAGCTGC-AAAGACGAAT
blockSeqs : ACGTACTTTTTTGCATGTTGAA C AATGAAA TGGTGTGAA GAAAG A TTCT A
blockSeqs : A . . GGAAAA . G TG .
blockSeqs : A . . . . A TG .
blockSeqs : A . . . . A TA .
blockSeqs : A . . . . A TG .
blockSeqs : A . . . . G TG .
blockSeqs : A . . . . G TG .
blockSeqs : A . . . . T TG .
blockSeqs : A . . . . G TT .
blockSeqs : A . . . . G TG .
blockSeqs : A . . . . A TT .
blockSeqs : A . . . . G TG .
blockSeqs : A . . . . G TT .
blockSeqs : A . . . . G . .
blockSeqs : A . . . . A . .
blockSeqs : A . . . . G .
blockSeqs : . . . . . .
blockSeqs : . . . .
blockSeqCons : A******************************************
originalCons : CTTCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGAATGCTACAT
finalCons : CTTCCATTTTCCATTCCATGAAAAATAGAA------------------------------------------CGTT-CTATTTT-------GG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGAATGCTACAT
Alignments
lowQualScore : 3333333333333333333333333333333333333333333 111111111
lowQualScore : 1111111111111111111111111111111111111111111 2 7777777 555555555 55555 1 7777 2
lowQualScore : ........................................... . ....... ......... ..... . .... .
lowQualScore : 0000000000000000000000000000000000000000000 1 2222222 333333333 33333 2 7777 5
consensus : CTTCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGAATGCTACAT
Reference ( family-395 ) : CTTCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGAATGCTACAT
gi|1 : ATTTTCAATTCCATGAAAAATAGA---------------------ACTTTCTATTTTGTAGGGATAACGTT-CTATTTT-------GG---------AT-----CAACT--AAAATTTTTTGCA---GC-AATGACGAATGC
gi|10 : CTTCCATTTCCCACTCCATAAAAAGTAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----AAACT--GGAAATTTCTGAAGCTGC-AAAAACaccaaaatgttttaatatgaaatcc
gi|11 : CTTCCATTTTCCATTCCATGAAAAATAAA---------------------A---------------------CATT-CTTTTTT-------GA---------AC-----C---------AATTTCTGAATTTGT-AAAGACAA
gi|12 : aCTTTCATTTGTCATTGAATGAAAAATAGA---------------------A---------------------CGTT-TTACTTA-------GG---------AC-----CGACT--GGAAACTTCTGAAGCTGC-ggc
gi|13 : CTTCTATTTTCCATTCTATGAAAAATATA---------------------A---------------------CGTT-CTATTTT-------GA---------AC-----CAAC---------TTCTGAAGCTG
gi|14 : CTTCCATTTTCCATTCCATGAAAAATACA---------------------A---------------------CGTT-CTATTTT-------AT---------AC-----CAAC---------TTCTAAAGCTGga
gi|15 : CTTCCATTTTCCATTCCATGAAAAATACA---------------------A---------------------CGTT-CTATTTT-------AT---------AC-----CAAC---------TTCTAAAGCTGtc
gi|16 : TT-CTATTTT-------GG---------GC-----TGACT--AGAA-TCTCTAAAGCTTC-AAAGACGAATGCTACtc
gi|17 : ctTCTATGTAAAATAGA---------------------A---------------------CGTT-CTTTTTT-------GA---------AC--------------AAACTTCTGAAGCTGC-
gi|18 : -CTATTTT-------GG---------AC-----AGACT--GGAAATTTCTGTAGCTGC-AGAGACAAATGCTAca
gi|19 : TTCCATTTTCTATTCCATAGAAAATAGA---------------------A---------------------TGTT-CTA
gi|2 : atTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTTAATGAAAGGTGGTGTGAAGT-----CTAAT--GAAAATTTCTGAAGTTCC-AAAGACGAATGCCACAT
gi|20 : attgC-----CGACT--GTAAATTTCTGAAGCTGC-AAAGACGAGTACTaatgtttaaatttaatc
gi|3 : TTCCATTTTCCGTTGCATGGAAAATAGAACGTACTTTTTTGCATGTTGAA---------------------CGTT-CT-TTTT-------TG---------AC-----CGACT--GGAAATTTCTGAAGCTGC-AAAGACGATTGCT
gi|4 : CCATTCCAGGAAAAATAGA---------------------A---------------------C------ATTTT-------GAGGAAAA---ACGAAAGCAACT--TGAAATTTTTGGAGCTAC-AAAGACGAATGCTA
gi|5 : TCCATTTTCCATTCCATGAAAATTAGA---------------------A---------------------CATT-ATATTTT-------GG---------AC-----CGACT--GGAAACTTCTGAAACTGCAAAAAACGAATGCTACATaaaaacatgttgaattaaa
gi|6 : caCTTCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GA---------AC-----CGACT--TGAAATTTCTGAAGCTGC-AAAGACGAATGCTACATttttt
gi|7 : TTCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------GC-----CGACT--GGAAATTTCTGAAGCTGC-AAAAACGAATGCTTCA
gi|8 : gCTTCCATTTTCGTTTTCTTGTAAAATAGA---------------------A---------------------CGTTCCTA-TTT-------GA---------AC-----TAACTTCTGAAG---CTGAAGCTGC-AAAGACG-ATGCTAC
gi|9 : TCCATTTTCCATTCCATGAAAAATAGA---------------------A---------------------CGTT-CTATTTT-------GG---------AC-----CGACT--TGAAATTTCTGAAGCTGC-AAAGACGAAT