lowQualScore : 1 555555555555555555
lowQualScore : 1 7 5555 33 999999999999999999 9999999 2 99 2
lowQualScore : . . .... .. .................. ....... . .. .
lowQualScore : 7 9 7777 77 999999999999999999 3333333 4 77 7
consensus : ACGATTGTAGCATTCGTCTTT----GCAGCTTC--AGA----TT--AGTCG-----GT------TCAAAATAGAACGTTCTA-TTTTTCATGGAAT-GGAAAATGGA
Reference ( gi|2 ) : ACAATTGTAGCATTCGTCTTT----GCAGCTTC--AGA-G--TTCCAGTCA-----GT------CCAAAATAGAACGTTCTA-TTTTTCATAAAAT-GGAAAATGGA
gi|4 : ACAATTGTAGCATTCGTCTTT----GCAGCTTC--ACA-AATTTCAAGTCG-----GT------CCAAAATAAAATGTTCCA-TTTTTCATAGAAT-TGAAA
gi|10 : aaACAA--GTAGCATT-GTCTTT----ACAGCTTC--AGA--------AGTTG-----AT------TCAAAATAGAACGTTCTA-GTTTTCATGGAAT-GGAAAATGGA
gi|5 : aaACTATTGCAGCATT-GTCCTT----GCAGCTTC--AGA--------AGTTG-----GT------TCAAAAAAGAACGTTCTA-TTTTTCACGGAAT-GGAAAATAG
gi|13 : gtaaaACGATTGTAGCATT-GTCTTT----GCAGCTT
gi|6 : aAATTGTAGCATT-GTCTTT----GCAGCCTC--AGA-G-------GTTG-----GT------TCCAAATAGAATGTTCTA-TTTTTCATGGAATAAAAAAATGGtgcgttatggttttcgtggaatggataatggaagt
gi|9 : aaaaaaAATAATAGCATT-GTCTTT----ACAGCTTC--AAA-TATTTCCAGTCG-----GG------CCAAAATATAACGTTCTA-TTTTTCATGGAAT-
gi|3 : aaataAAATGTAGCATTGG-CTTT----TCAGCTTC--AGA--------AGTTG-----GT------TCAAAATATAACGTTCGATTTTTTCCTGGAAT-GGAAAATAGA
gi|7 : gtaaaaaTGTAGCACT-GTCTTT----GCAGCTTC--AGA--------AGTTG-----GT------TCAAAATAGAAAGTTCTA-TTTTTCATGGAAA-AGAAAATGGA
gi|11 : aaaaaggTGTAGCAGT-ATCTTT----GCAGCTGC--AGAAG--T----GTT-------T------TCAAAATATAAC----TA-TTTTTCATAGAAT-GGAAAATGGAa
gi|1 : aaaaggGTAGTAGTCCTCTTTCTCTGCAGCTTC--AGA-AATTTACCGGCG-----AT------CCAAAACAGAACACCCTA-TTCTTCATAGAAT-GGAAAGTAGag
gi|12 : aaccaaaGTAGCATTTGTCTTT----GAAGCTTC--G------------------------------AAAATATAACGCTTTA-TTTTTCATGGAAT-TGAAATTGGA
gi|8 : TAGCATTCGTCTTT----GTAGCTCC--AAA-AATTTCAAGTTGCTTTCGTTTTTCCTCAAAAT-----GTTCTA-TTTTTCCTGGAAT-GGAagt
gi|17 : tAACATTCGTCTTC----GCAGCTTCAAAAA-A--TTCCAGTCT-----GT------CCAc
gi|16 : taaaaaaaaCATTCGTCTTT----GCAGCTT-------------CAATCG-----GT------CCAAAATAGA
gi|14 : aaaacacgtttcat----GTAGCTTC--AGA--------AATTG-----GT------TCAAAATAGAAAGTTCTA-CTTTTTGTGGAAT-GAAAAATGGA
gi|15 : AACTTT--AGA--------ACTTA-----GT------TCAAAATAGAGCGTTCTA-TGTTTCATGTAAA-GAAAAATGGAag
gi|10 : --TTCCATTCC-----AT------GAAAACTAGAACGTTCTA-TTTTag
gi|5 : aaacaagtagcattgtctttacagcttcagaagttgattc--TTCCATTCC-----GT------GAAAAATAGAACGTTCT--TTTTTaatgga
gi|18 : gtaaaactattgcagcattgtccttgcagcttcagaagttggttcA-----GT------TCAAAATAGAATGATCTA-TTTTTCATGGAAT-AGAAAATGGAaatag
gi|19 : tA-----GT------TCAAAACAGAACGTTCTA-TTTTTCATGGAAT-AGAAA
Alignments
lowQualScore : 1 5555555555555
lowQualScore : 4 6 5555 555555 6666666666666 33 1 55555 666666 2 2
lowQualScore : . . .... ...... ............. .. . ..... ...... . .
lowQualScore : 2 1 3333 000000 0000000000000 22 9 33333 111111 4 4
consensus : ACGATTGTAGCATTCGTCTTT----GCAGCTTC---A--GA-------------A--GTCG-----GTT------CAAAATAGAACGTTCTA-TTTTTCATGGAAT-GGAAAATGGA
Reference ( family-1455 ) : ACGATTGTAGCATTCGTCTTT----GCAGCTTC---A--GA---T-----T---A--GTCG-----GTT------CAAAATAGAACGTTCTA-TTTTTCATGGAAT-GGAAAATGGA
gi|1 : GTAGTAGTCCTCTTTCTCTGCAGCTTC---A--GAAATT-----T---ACCGGCG-----ATC------CAAAACAGAACACCCTA-TTCTTCATAGAAT-GGAAAGTAG
gi|10 : aaccaaaGTAGCATT-GTCTTT----ACAGCTTC---A--GA-------------A--GTTG-----ATT------CAAAATAGAACGTTCTA-GTTTTCATGGAAT-GGAAAATGGA
gi|11 : aaacaaTGTAGCAGT-ATCTTT----GCAGCTGC---A--GA-------------A--GTGT-----TTT------CAAAATATAAC----TA-TTTTTCATAGAAT-GGAAAATGGA
gi|12 : aaaaggGTAGCATTTGTCTTT----GAAGCTTC---G---------------------------------------AAAATATAACGCTTTA-TTTTTCATGGAAT-TGAAATTGGAag
gi|13 : ACGATTGTAGCATT-GTCTTT----GCAGCTTT---------------------------------------------------GCGTTATG-GTTTTCGTGGAAT-GGATAATGGAagt
gi|14 : a----GTAGCTTC---A--GA-------------A--ATTG-----GTT------CAAAATAGAAAGTTCTA-CTTTTTGTGGAAT-GAAAAATGGAagt
gi|15 : AACTTT---A--GA-------------A--CTTA-----GTT------CAAAATAGAGCGTTCTA-TGTTTCATGTAAA-GAAAAATGGAag
gi|16 : CATTCGTCTTT----GCAGCTTC---------------------A--ATCG-----GTC------CAAAATAGAag
gi|17 : aaaacacgtttcatAACATTCGTCTTC----GCAGCTTCAAAA--AA---T-----TCC-A--GTCT-----GTC------CA
gi|18 : taaaaaaaa-----GTT------CAAAATAGAATGATCTA-TTTTTCATGGAAT-AGAAAATGGA
gi|19 : ta-----GTT------CAAAACAGAACGTTCTA-TTTTTCATGGAAT-AGAAA
gi|2 : aACAATTGTAGCATTCGTCTTT----GCAGCTTC---A--GAG--T-----TCC-A--GTCA-----GTC------CAAAATAGAACGTTCTA-TTTTTCATAAAAT-GGAAAATGGA
gi|3 : TGTAGCATTGG-CTTT----TCAGCTTC---A--GA-------------A--GTTG-----GTT------CAAAATATAACGTTCGATTTTTTCCTGGAAT-GGAAAATAGA
gi|4 : gtaaaaaaaaACAATTGTAGCATTCGTCTTT----GCAGCTTC---ACAAA---T-----TTCAA--GTCG-----GTC------CAAAATAAAATGTTCCA-TTTTTCATAGAAT-TGAAA
gi|5 : aaACTATTGCAGCATT-GTCCTT----GCAGCTTC---A--GA-------------A--GTTG-----GTT------CAAAAAAGAACGTTCTA-TTTTTCACGGAAT-GGAAAATAG
gi|6 : gtaaaATTGTAGCATT-GTCTTT----GCAGCCTC---A--GA-------------G--GTTG-----GTT------CCAAATAGAATGTTCTA-TTTTTCATGGAATAAAAAAATGG
gi|7 : aaaaaaaTGTAGCACT-GTCTTT----GCAGCTTC---A--GA-------------A--GTTG-----GTT------CAAAATAGAAAGTTCTA-TTTTTCATGGAAA-AGAAAATGGA
gi|8 : aaaaaggTAGCATTCGTCTTT----GTAGCTCC---A--AAAATT-----TCA-A--GTTGCTTTCGTTTTTCCTCAAAAT-----GTTCTA-TTTTTCCTGGAAT-GGAa
gi|9 : tTAGCATT-GTCTTT----ACAGCTTC---A--AA---TATTTCC---A--GTCG-----GGC------CAAAATATAACGTTCTA-TTTTTCATGGAAT-c
Alignments
lowQualScore : 1 2222222222222222222222222 1111111111111111
lowQualScore : 4 6 5555 0 1111111111111111111111111 4444444444444444 2 2
lowQualScore : . . .... . ......................... ................ . .
lowQualScore : 2 1 3333 2 5555555555555555555555555 7777777777777777 4 4
consensus : ACGATTGTAGCATTCGTCTTT----GCAGCTTCAGA-------A-------GT-------CGGTTCAAAAT----------------AGAACGTTCTA-TTTTTCATGGAAT-GGAAAATGGA
Reference ( family-1455 ) : ACGATTGTAGCATTCGTCTTT----GCAGCTTCAGA-------A-------GT-------CGGTTCAAAAT----------------AGAACGTTCTA-TTTTTCATGGAAT-GGAAAATGGA
gi|1 : GTAGTAGTCCTCTTTCTCTGCAGCTTCAGA-------A-------ATTTACCGGCGATCCAAAAC----------------AGAACACCCTA-TTCTTCATAGAAT-GGAAAGTAG
gi|10 : aaccaaaGTAGCATT-GTCTTT----ACAGCTTCAGA-------A-------GT-------TGATTCAAAAT----------------AGAACGTTCTA-GTTTTCATGGAAT-GGAAAATGGA
gi|11 : aaacaaTGTAGCAGT-ATCTTT----GCAGCTGCAGA-------A-------GT-------GTTTTCAAAAT----------------ATAAC----TA-TTTTTCATAGAAT-GGAAAATGGA
gi|12 : aaaaggGTAGCATTTGTCTTT----GAAGCTTCG--------------------------------AAAAT----------------ATAACGCTTTA-TTTTTCATGGAAT-TGAAATTGGAag
gi|13 : ACGATTGTAGCATT-GTCTTT----GCAGCTTT---------------------------------------------------------GCGTTATG-GTTTTCGTGGAAT-GGATAATGGAagt
gi|14 : a----GTAGCTTCAGA-------A-------AT-------TGGTTCAAAAT----------------AGAAAGTTCTA-CTTTTTGTGGAAT-GAAAAATGGAagt
gi|15 : AACTTTAGA-------A-------CT-------TAGTTCAAAAT----------------AGAGCGTTCTA-TGTTTCATGTAAA-GAAAAATGGAag
gi|16 : CATTCGTCTTT----GCAGCTTC----------A-------AT-------CGGTCCAAAAT----------------AGAag
gi|17 : aaaacacgtttcatAACATTCGTCTTC----GCAGCTTCAAA-------A-------
gi|18 : taaaaaaaaGTTCAAAAT----------------AGAATGATCTA-TTTTTCATGGAAT-AGAAAATGGAaattccagtctgtcca
gi|19 : taGTTCAAAAC----------------AGAACGTTCTA-TTTTTCATGGAAT-AGAAA
gi|2 : aACAATTGTAGCATTCGTCTTT----GCAGCTTCAGAGTTCC--A-------GT-------CAGTCCAAAAT----------------AGAACGTTCTA-TTTTTCATAAAAT-GGAAAATGGA
gi|3 : TGTAGCATTGG-CTTT----TCAGCTTCAGA-------A-------GT-------TGGTTCAAAAT----------------ATAACGTTCGATTTTTTCCTGGAAT-GGAAAATAGA
gi|4 : gtaaaaaaaaACAATTGTAGCATTCGTCTTT----GCAGCTTCACA-------AATTTCAAGT-------CGGTCCAAAAT----------------AAAATGTTCCA-TTTTTCATAGAAT-TGAAA
gi|5 : aaACTATTGCAGCATT-GTCCTT----GCAGCTTCAGA-------A-------GT-------TGGTTCAAAAA----------------AGAACGTTCTA-TTTTTCACGGAAT-GGAAAATAG
gi|6 : gtaaaATTGTAGCATT-GTCTTT----GCAGCCTCAGA-------G-------GT-------TGGTTCCAAAT----------------AGAATGTTCTA-TTTTTCATGGAATAAAAAAATGG
gi|7 : aaaaaaaTGTAGCACT-GTCTTT----GCAGCTTCAGA-------A-------GT-------TGGTTCAAAAT----------------AGAAAGTTCTA-TTTTTCATGGAAA-AGAAAATGGA
gi|8 : aaaaaggTAGCATTCGTCTTT----GTAGCTCCAAA-------A-------AT----------TTCAAGTTGCTTTCGTTTTTCCTCAAAATGTTCTA-TTTTTCCTGGAAT-GGAa
gi|9 : tTAGCATT-GTCTTT----ACAGCTTCAAATATTTCCA-------GT-------CGGGCCAAAAT----------------ATAACGTTCTA-TTTTTCATGGAAT-c
Alignments
lowQualScore : 1 2222222222222222222222222 1111111111111111
lowQualScore : 4 6 5555 0 1111111111111111111111111 4444444444444444 2 2
lowQualScore : . . .... . ......................... ................ . .
lowQualScore : 2 1 3333 2 5555555555555555555555555 7777777777777777 4 4
consensus : ACGATTGTAGCATTCGTCTTT----GCAGCTTCAGA-------A-------GT-------CGGTTCAAAAT----------------AGAACGTTCTA-TTTTTCATGGAAT-GGAAAATGGA
Reference ( family-1455 ) : ACGATTGTAGCATTCGTCTTT----GCAGCTTCAGA-------A-------GT-------CGGTTCAAAAT----------------AGAACGTTCTA-TTTTTCATGGAAT-GGAAAATGGA
gi|1 : GTAGTAGTCCTCTTTCTCTGCAGCTTCAGA-------A-------ATTTACCGGCGATCCAAAAC----------------AGAACACCCTA-TTCTTCATAGAAT-GGAAAGTAG
gi|10 : aaccaaaGTAGCATT-GTCTTT----ACAGCTTCAGA-------A-------GT-------TGATTCAAAAT----------------AGAACGTTCTA-GTTTTCATGGAAT-GGAAAATGGA
gi|11 : aaacaaTGTAGCAGT-ATCTTT----GCAGCTGCAGA-------A-------GT-------GTTTTCAAAAT----------------ATAAC----TA-TTTTTCATAGAAT-GGAAAATGGA
gi|12 : aaaaggGTAGCATTTGTCTTT----GAAGCTTCG--------------------------------AAAAT----------------ATAACGCTTTA-TTTTTCATGGAAT-TGAAATTGGAag
gi|13 : ACGATTGTAGCATT-GTCTTT----GCAGCTTT---------------------------------------------------------GCGTTATG-GTTTTCGTGGAAT-GGATAATGGAagt
gi|14 : a----GTAGCTTCAGA-------A-------AT-------TGGTTCAAAAT----------------AGAAAGTTCTA-CTTTTTGTGGAAT-GAAAAATGGAagt
gi|15 : AACTTTAGA-------A-------CT-------TAGTTCAAAAT----------------AGAGCGTTCTA-TGTTTCATGTAAA-GAAAAATGGAag
gi|16 : CATTCGTCTTT----GCAGCTTC----------A-------AT-------CGGTCCAAAAT----------------AGAag
gi|17 : aaaacacgtttcatAACATTCGTCTTC----GCAGCTTCAAA-------A-------
gi|18 : taaaaaaaaGTTCAAAAT----------------AGAATGATCTA-TTTTTCATGGAAT-AGAAAATGGAaattccagtctgtcca
gi|19 : taGTTCAAAAC----------------AGAACGTTCTA-TTTTTCATGGAAT-AGAAA
gi|2 : aACAATTGTAGCATTCGTCTTT----GCAGCTTCAGAGTTCC--A-------GT-------CAGTCCAAAAT----------------AGAACGTTCTA-TTTTTCATAAAAT-GGAAAATGGA
gi|3 : TGTAGCATTGG-CTTT----TCAGCTTCAGA-------A-------GT-------TGGTTCAAAAT----------------ATAACGTTCGATTTTTTCCTGGAAT-GGAAAATAGA
gi|4 : gtaaaaaaaaACAATTGTAGCATTCGTCTTT----GCAGCTTCACA-------AATTTCAAGT-------CGGTCCAAAAT----------------AAAATGTTCCA-TTTTTCATAGAAT-TGAAA
gi|5 : aaACTATTGCAGCATT-GTCCTT----GCAGCTTCAGA-------A-------GT-------TGGTTCAAAAA----------------AGAACGTTCTA-TTTTTCACGGAAT-GGAAAATAG
gi|6 : gtaaaATTGTAGCATT-GTCTTT----GCAGCCTCAGA-------G-------GT-------TGGTTCCAAAT----------------AGAATGTTCTA-TTTTTCATGGAATAAAAAAATGG
gi|7 : aaaaaaaTGTAGCACT-GTCTTT----GCAGCTTCAGA-------A-------GT-------TGGTTCAAAAT----------------AGAAAGTTCTA-TTTTTCATGGAAA-AGAAAATGGA
gi|8 : aaaaaggTAGCATTCGTCTTT----GTAGCTCCAAA-------A-------AT----------TTCAAGTTGCTTTCGTTTTTCCTCAAAATGTTCTA-TTTTTCCTGGAAT-GGAa
gi|9 : tTAGCATT-GTCTTT----ACAGCTTCAAATATTTCCA-------GT-------CGGGCCAAAAT----------------ATAACGTTCTA-TTTTTCATGGAAT-c
blockSeqs : A T . AATTTCAAGTC GCTTTCGTTTTTCCTC T A
blockSeqs : A C . TATTTCCAGTC . . .
blockSeqs : T C . GTTCCAGTC . . .
blockSeqs : C . AGTT . . .
blockSeqs : G . AGTG . . .
blockSeqs : C . AATT . . .
blockSeqs : C . ACTT . . .
blockSeqs : . . AATC . . .
blockSeqs : . . AGTT . . .
blockSeqs : . . AGTT . . .
blockSeqs : . . GGTT . . .
blockSeqs : . . AGTT . . .
blockSeqs : . . AAT . . .
blockSeqs : . . . . . .
blockSeqs : . . . . .
blockSeqs : . . .
blockSeqs : .
blockSeqCons : **** AGTT*********************
originalCons : ACGATTGTAGCATTCGTCTTT----GCAGCTTCAGA-------A-------GT-------CGGTTCAAAAT----------------AGAACGTTCTA-TTTTTCATGGAAT-GGAAAATGGA
finalCons : ACGATTGTAGCATTCGTCTTT----GCAGCTTCAGAAGTT---------------------GGTTCAAAAT----------------AGAACGTTCTA-TTTTTCATGGAAT-GGAAAATGGA
Alignments
lowQualScore : 1 111111111111111111111111
lowQualScore : 4 6 5555 888888888888888888888888 9999999999999 666666 2 2
lowQualScore : . . .... ........................ ............. ...... . .
lowQualScore : 2 1 3333 999999999999999999999999 0000000000000 444444 4 4
consensus : ACGATTGTAGCATTCGTCTTT----GCAGCTTCAG-------A-------A-------GTT-------G-----GT------TCAAAATAGAACGTTCTA-TTTTTCATGGAAT-GGAAAATGGA
Reference ( family-1455 ) : ACGATTGTAGCATTCGTCTTT----GCAGCTTCAG-------A-------A-------GTT-------G-----GT------TCAAAATAGAACGTTCTA-TTTTTCATGGAAT-GGAAAATGGA
gi|1 : GTAGTAGTCCTCTTTCTCTGCAGCTTCAG-------A-------A-------ATTTACCGGCG-----AT------CCAAAACAGAACACCCTA-TTCTTCATAGAAT-GGAAAGTAG
gi|10 : aaccaaaGTAGCATT-GTCTTT----ACAGCTTCAG-------A-------A-------GTT-------G-----AT------TCAAAATAGAACGTTCTA-GTTTTCATGGAAT-GGAAAATGGA
gi|11 : aaacaaTGTAGCAGT-ATCTTT----GCAGCTGCAG-------A-------A-------GTG-------T-----TT------TCAAAATATAAC----TA-TTTTTCATAGAAT-GGAAAATGGA
gi|12 : aaaaggGTAGCATTTGTCTTT----GAAGCTTCG--------------------------------------------------AAAATATAACGCTTTA-TTTTTCATGGAAT-TGAAATTGGAag
gi|13 : ACGATTGTAGCATT-GTCTTT----GCAGCT----------------------------TT-------G------------------------CGTTATG-GTTTTCGTGGAAT-GGATAATGGAagt
gi|14 : a----GTAGCTTCAG-------A-------A-------ATT-------G-----GT------TCAAAATAGAAAGTTCTA-CTTTTTGTGGAAT-GAAAAATGGAagt
gi|15 : AACTTTAG-------A-------A-------CTT-------A-----GT------TCAAAATAGAGCGTTCTA-TGTTTCATGTAAA-GAAAAATGGAag
gi|16 : CATTCGTCTTT----GCAGCTTC-----------------A-------ATC-------G-----GT------CCAAAATAGAag
gi|17 : aaaacacgtttcatAACATTCGTCTTC----GCAGCTTCAA-------A-------A-------
gi|18 : taaaaaaaaT-------A-----GT------TCAAAATAGAATGATCTA-TTTTTCATGGAAT-AGAAAATGGAaattccagtctgtcca
gi|19 : -----GT------TCAAAACAGAACGTTCTA-TTTTTCATGGAAT-AGAAA
gi|2 : aACAATTGTAGCATTCGTCTTT----GCAGCTTCAG-------AGTTCC--A-------GTC-------A-----GT------CCAAAATAGAACGTTCTA-TTTTTCATAAAAT-GGAAAATGGA
gi|3 : TGTAGCATTGG-CTTT----TCAGCTTCAG-------A-------A-------GTT-------G-----GT------TCAAAATATAACGTTCGATTTTTTCCTGGAAT-GGAAAATAGA
gi|4 : gtaaaaaaaaACAATTGTAGCATTCGTCTTT----GCAGCTTCAC-------A-------AATTTCAAGTC-------G-----GT------CCAAAATAAAATGTTCCA-TTTTTCATAGAAT-TGAAA
gi|5 : aaACTATTGCAGCATT-GTCCTT----GCAGCTTCAG-------A-------A-------GTT-------G-----GT------TCAAAAAAGAACGTTCTA-TTTTTCACGGAAT-GGAAAATAG
gi|6 : gtaaaATTGTAGCATT-GTCTTT----GCAGCCTCAG-------A-------G-------GTT-------G-----GT------TCCAAATAGAATGTTCTA-TTTTTCATGGAATAAAAAAATGG
gi|7 : aaaaaaaTGTAGCACT-GTCTTT----GCAGCTTCAG-------A-------A-------GTT-------G-----GT------TCAAAATAGAAAGTTCTA-TTTTTCATGGAAA-AGAAAATGGA
gi|8 : aaaaaggTAGCATTCGTCTTT----GTAGCTCCAAAAATTTCA-------A-------GTT-------GCTTTCGTTTTTCCTCAAAAT-----GTTCTA-TTTTTCCTGGAAT-GGAa
gi|9 : tTAGCATT-GTCTTT----ACAGCTTCAA-------ATATTTCCA-------GTC-------G-----GG------CCAAAATATAACGTTCTA-TTTTTCATGGAAT-c