lowQualScore : 111111111111111111111111111111 1 333333333333333333333 1 1
lowQualScore : 4 0 5 999999999999999999999999999999 0 555 2 555555555555555555555 3 2 3 3
lowQualScore : . . . .............................. . ... . ..................... . . . .
lowQualScore : 0 7 5 555555555555555555555555555555 5 000 9 999999999999999999999 7 9 3 3
consensus : GAAATGCAGGAAAAAC-GCAGGAAATGGCATCCTCGCCCA-AAAATA-ACTT-TGT---T-----G-G--AGCA---TGCCCC-CANA---T-AC-----CCC----TAGAATCGGCCTCCCTGTTTTT-TTTAA-G-TCTAGCT
Reference ( gi|2 ) : GAAATGCAGGAAAAAT-GCAGGAAATGGCACCCTCGTCCA-AAAATA-ACTT-TGT---T-----G-G--AGTA---TGCCCC-CATA---T-AC-----ATT----TAGAATCGGCCTCCCTGTTTTT-TTTAA-G-TCTAGCT
gi|12 : GAAATGCAGGAAAAAT-GCAGAATATGGCACCGTCGTCCA-AAACTA-ACTT-TGT---T-----G-G--ACCA---TGCCCCGAACA---T-AC-----CTT----TAGAAT
gi|1 : ctGAAATGCAGGAAAATC-CCAGAAAATGGAATCCTCAGCC---AAAT--TCTT-TTC---T-----G-G--ACGACATTGCTTT-CAGACCCT-AC------------TACAATGAGCTACCCTG-TTCT-TTAAA-G-TCTAGa
gi|9 : tctATGCAAGAAAAAT-GTAGGAAATGGCATCCTCGTCCA-AAAATA-ACTT-TGT---T-----G-G--AACA---TTCCCC-CACA---T-AC-----TTT----TAGAATCGGCCTCCCTGTTTTT-gcacg
gi|11 : GGAAAAAT-GCAGGAAATGGCACCCTCGTCCA-AAAA----------------------A--AG--------CCC-CACA---T-AC-----CTT----TAAAATCGGCCTCCTTG--TTT-TTTAAGG-TCTAGCTaag
gi|4 : GGAAAATC-GAAGGAAATGTCATCCTCGCCCA---------TTT-TAT---TTCT--G-GCCAGGA---TGATGT-CAGA---C-A------ATCC---TAGAAACGGCCTCCCTG-TTTT-TTAAA-A-TCTAGCTatg
gi|7 : AAAATCGAAGGAAATGGCATCCTCGCCCA---------TTT-TAT---TTCTGGGCG--AGCA---TGATGT-CATA---C-AC-----TCC----TAGAAACGGCCTCCCTGTTTTT-TTAAA-A-TCTAGCTacgg
gi|3 : AAAAC-GATGGAAATGGCATTCTCGCCTA-AAAAAA-AATTCTGA---C-----C-G--AGCA---TGACCC-CA-A---T-CCCCCCCACCCCACTAGAATCAGCATCCCTATTTTT-TTAAG-G-TCTA
gi|5 : gAAAT-GCAGGAAATGGCACCCTCGTCCA-AAAATA-ACTT-TGT---T-----G-G--AGCA---TACCCC-CACA---T-AC-----CTT----TAGAATCGATCTCCCTa
gi|6 : gAAAT-GCAGGAAATGGCACCCTCGCCCA-TATATA-ACTT-TGT---T-----G-G--AGCA---TTTCCC-CACA---T-AC-----CTT----TAGAATCGACCTCACTG---TT-TTTAAGG-TCTAGacggtcggtctagctacgagc
gi|8 : AAAT-GCAGGAAAAGGCATCCTCGCCCA-A---TT-TTTT-TTTCTGT-----GCA--AGCT---TGCCCC-CAGA---C-AC-----TAT----TAGAATCGACCTCACTGTTTTT-Tgttcgg
gi|10 : tgCAGGAAATTGCATCCTCG---ATAAAATACATTT-TCT---A-----G-G--CGAA---TACCC--------------------T----T-GAATCGGTCTCCATGTCTTT-TTTAG-G-TCTAGCTaggtacggg
gi|13 : GAAATGGCATCCTCGACTA-AAGA-A-ATTT-TCT---G-----G-GTAAGCA---TGCCCC-CATA---TCAC------CC----TAGAATCCGCCTCCC---TTTT-TTTAA-G-acggacct
gi|14 : -G--AGCA---TGCCTC-CTGAC--T-A------ACC----TAGAATCGGCCTCCCTG--TTT-TTTAAGG-TCTAGCTgtc
gi|16 : aggttctgtatttttatgaga-G--AGCA---TGCCAT-TAGA---C-CC-----TCC----TAGAATCAACCTCCCTGTTTTTAGGTAG-G-TCTAGCacaggcc
gi|17 : tcttttctgagc----TAGAATTGGCCTCACTGTT----TTTAA-GTTCTAGCT
gi|18 : aaccccAATCAGCCTCCCTG--TTT-TTTAAGG-TGTAGCTatgaacc
1 sequences could not be aligned to this particular reference sequence:
Unaligned ( gi|15 ): TCTGAGATGTATGAAAACGCAGGAATGGCATCCTACACCCTAAGAATCGGCCTGCTTGTTTTAAGGTCATGCTACCGG
Alignments
lowQualScore : 111111111 1 1
lowQualScore : 1 2 2 2 1 9999 3 2 666666666 5 77 33 2 2 3 2 7777777 77777 3 2 2 3
lowQualScore : . . . . . .... . . ......... . .. .. . . . . ....... ..... . . . .
lowQualScore : 6 9 9 9 6 2222 1 1 333333333 3 33 77 7 7 6 5 6666666 99999 9 7 3 1
consensus : GAAATGCAGGAAAAACGCAGGAAATGGCATCCT-C-GCCC-AAAAATA-ACTT-TGT---T-----G-G--A--GCA-TGCCCC-CANA-T-------ACCC--C--TAGAATCGGCCTCCCTGTTTTT-TTTAA-G-TCTAGCT
Reference ( family-713 ) : GAAATGCAGGAAAAACGCAGGAAATGGCATCCT-C-GCCC-AAAAATA-ACTT-TGT---T-----G-G--A--GCA-TGCCCC-CANA-T-------ACCC--C--TAGAATCGGCCTCCCTGTTTTT-TTTAA-G-TCTAGCT
gi|1 : GAAATGCAGGAAAATCCCAGAAAATGGAATCCT-CAGCC----AAAT--TCTT-TTC---T-----G-G--ACGACATTGCTTT-CAG----------ACCCTAC--TACAATGAGCTACCCTG-TTCT-TTAAA-G-TCTAG
gi|10 : tctCAGGAAATTGCATCCT-C-GAT---AAAATACATTT-TCT---A-----G-G----------------CGAA-T-------ACCC--T--T-GAATCGGTCTCCATGTCTTT-TTTAG-G-TCTAGCTgcacg
gi|11 : GGAAAAATGCAGGAAATGGCACCCT-C-GTCC-AAAAA----------------------A--A--GC------CC-CACA-T-------ACCT--T--TAAAATCGGCCTCCTTG--TTT-TTTAAGG-TCTAGCTacggacct
gi|12 : GAAATGCAGGAAAAATGCAGAATATGGCACCGT-C-GTCC-AAAACTA-ACTT-TGT---T-----G-G--A--CCA-TGCCCCGAACA-T-------ACCT--T--TAGAATatg
gi|13 : ctGAAATGGCATCCT-C-GACT-AAAGA-A-ATTT-TCT---G-----G-GTAA--GCA-TGCCCC-CATA-T-------CACC--C--TAGAATCCGCCTCCC---TTTT-TTTAA-G-a
gi|14 : -G--A--GCA-TGCCTC-CTGACT-------AACC-----TAGAATCGGCCTCCCTG--TTT-TTTAAGG-TCTAGCTgtc
gi|15 : aggttctgtatttttatgagaGAGATGTATGAAAA-CGCAGG-AATGGCATCCTAC-ACCCTAAGAATacaggcc
gi|15 : tctA-C-------ACCC--T--AAGAATCGGCCTGCTTGTTTTcggcctgcttgttttaaggtcatgctaccgg
gi|16 : tctgagatgtatgaaaacgcaggaatggcatcct-G--A--GCA-TGCCAT-TAGA-C-------CCTC--C--TAGAATCAACCTCCCTGTTTTTAGGTAG-G-TCTAGCaaggtcatgctaccgg
gi|17 : tcttttctgagc-------ACCC--C--TAGAATTGGCCTCACTG---TT-TTTAA-GTTCTAGCT
gi|18 : aAATCAGCCTCCCTG--TTT-TTTAAGG-TGTAGCTatgaacc
gi|2 : GAAATGCAGGAAAAATGCAGGAAATGGCACCCT-C-GTCC-AAAAATA-ACTT-TGT---T-----G-G--A--GTA-TGCCCC-CATA-T-------ACAT--T--TAGAATCGGCCTCCCTGTTTTT-TTTAA-G-TCTAGCTatggac
gi|3 : AAAACGATGGAAATGGCATTCT-C-GCCT-AAAAAAA-AATTCTGA---C-----C-G--A--GCA-TGACCC-CA-A-TCCCCCCCACCC--CACTAGAATCAGCATCCCTATTTTT-TTAAG-G-TCTA
gi|4 : gGGAAAATCGAAGGAAATGTCATCCT-C-GCCC-A--------TTT-TAT---TTCT--G-GCCA--GGA-TGATGT-CAGA-C-------AATC--C--TAGAAACGGCCTCCCTG-TTTT-TTAAA-A-TCTAGCTa
gi|5 : AAATGCAGGAAATGGCACCCT-C-GTCC-AAAAATA-ACTT-TGT---T-----G-G--A--GCA-TACCCC-CACA-T-------ACCT--T--TAGAATCGATCTCCCTacgg
gi|6 : gAAATGCAGGAAATGGCACCCT-C-GCCC-ATATATA-ACTT-TGT---T-----G-G--A--GCA-TTTCCC-CACA-T-------ACCT--T--TAGAATCGACCTCACTG---TT-TTTAAGG-TCTAGacggtcggtctagctacgagc
gi|7 : AAAATCGAAGGAAATGGCATCCT-C-GCCC-A--------TTT-TAT---TTCTGGGCG--A--GCA-TGATGT-CATA-C-------ACTC--C--TAGAAACGGCCTCCCTGTTTTT-TTAAA-A-TCTAGCTgttcgg
gi|8 : AAATGCAGGAAAAGGCATCCT-C-GCCC-AA---TT-TTTT-TTTCTGT-----GCA--A--GCT-TGCCCC-CAGA-C-------ACTA--T--TAGAATCGACCTCACTGTTTTT-T
gi|9 : tgATGCAAGAAAAATGTAGGAAATGGCATCCT-C-GTCC-AAAAATA-ACTT-TGT---T-----G-G--A--ACA-TTCCCC-CACA-T-------ACTT--T--TAGAATCGGCCTCCCTGTTTTT-aggtacggg
Alignments
lowQualScore : 111111111 1 1
lowQualScore : 1 2 2 2 1 9999 3 2 666666666 5 77 33 2 2 3 2 7777777 77777 3 2 2 3
lowQualScore : . . . . . .... . . ......... . .. .. . . . . ....... ..... . . . .
lowQualScore : 6 9 9 9 6 2222 1 1 333333333 3 33 77 7 7 6 5 6666666 99999 9 7 3 1
consensus : GAAATGCAGGAAAAACGCAGGAAATGGCATCCT-C-GCCC-AAAAATA-ACTT-TGT---T-----G-G--A--GCA-TGCCCC-CANA-T-------ACCC--C--TAGAATCGGCCTCCCTGTTTTT-TTTAA-G-TCTAGCT
Reference ( family-713 ) : GAAATGCAGGAAAAACGCAGGAAATGGCATCCT-C-GCCC-AAAAATA-ACTT-TGT---T-----G-G--A--GCA-TGCCCC-CANA-T-------ACCC--C--TAGAATCGGCCTCCCTGTTTTT-TTTAA-G-TCTAGCT
gi|1 : GAAATGCAGGAAAATCCCAGAAAATGGAATCCT-CAGCC----AAAT--TCTT-TTC---T-----G-G--ACGACATTGCTTT-CAG----------ACCCTAC--TACAATGAGCTACCCTG-TTCT-TTAAA-G-TCTAG
gi|10 : tctCAGGAAATTGCATCCT-C-GAT---AAAATACATTT-TCT---A-----G-G----------------CGAA-T-------ACCC--T--T-GAATCGGTCTCCATGTCTTT-TTTAG-G-TCTAGCTgcacg
gi|11 : GGAAAAATGCAGGAAATGGCACCCT-C-GTCC-AAAAA----------------------A--A--GC------CC-CACA-T-------ACCT--T--TAAAATCGGCCTCCTTG--TTT-TTTAAGG-TCTAGCTacggacct
gi|12 : GAAATGCAGGAAAAATGCAGAATATGGCACCGT-C-GTCC-AAAACTA-ACTT-TGT---T-----G-G--A--CCA-TGCCCCGAACA-T-------ACCT--T--TAGAATatg
gi|13 : ctGAAATGGCATCCT-C-GACT-AAAGA-A-ATTT-TCT---G-----G-GTAA--GCA-TGCCCC-CATA-T-------CACC--C--TAGAATCCGCCTCCC---TTTT-TTTAA-G-a
gi|14 : -G--A--GCA-TGCCTC-CTGACT-------AACC-----TAGAATCGGCCTCCCTG--TTT-TTTAAGG-TCTAGCTgtc
gi|15 : aggttctgtatttttatgagaGAGATGTATGAAAA-CGCAGG-AATGGCATCCTAC-ACCCTAAGAATacaggcc
gi|15 : tctA-C-------ACCC--T--AAGAATCGGCCTGCTTGTTTTcggcctgcttgttttaaggtcatgctaccgg
gi|16 : tctgagatgtatgaaaacgcaggaatggcatcct-G--A--GCA-TGCCAT-TAGA-C-------CCTC--C--TAGAATCAACCTCCCTGTTTTTAGGTAG-G-TCTAGCaaggtcatgctaccgg
gi|17 : tcttttctgagc-------ACCC--C--TAGAATTGGCCTCACTG---TT-TTTAA-GTTCTAGCT
gi|18 : aAATCAGCCTCCCTG--TTT-TTTAAGG-TGTAGCTatgaacc
gi|2 : GAAATGCAGGAAAAATGCAGGAAATGGCACCCT-C-GTCC-AAAAATA-ACTT-TGT---T-----G-G--A--GTA-TGCCCC-CATA-T-------ACAT--T--TAGAATCGGCCTCCCTGTTTTT-TTTAA-G-TCTAGCTatggac
gi|3 : AAAACGATGGAAATGGCATTCT-C-GCCT-AAAAAAA-AATTCTGA---C-----C-G--A--GCA-TGACCC-CA-A-TCCCCCCCACCC--CACTAGAATCAGCATCCCTATTTTT-TTAAG-G-TCTA
gi|4 : gGGAAAATCGAAGGAAATGTCATCCT-C-GCCC-A--------TTT-TAT---TTCT--G-GCCA--GGA-TGATGT-CAGA-C-------AATC--C--TAGAAACGGCCTCCCTG-TTTT-TTAAA-A-TCTAGCTa
gi|5 : AAATGCAGGAAATGGCACCCT-C-GTCC-AAAAATA-ACTT-TGT---T-----G-G--A--GCA-TACCCC-CACA-T-------ACCT--T--TAGAATCGATCTCCCTacgg
gi|6 : gAAATGCAGGAAATGGCACCCT-C-GCCC-ATATATA-ACTT-TGT---T-----G-G--A--GCA-TTTCCC-CACA-T-------ACCT--T--TAGAATCGACCTCACTG---TT-TTTAAGG-TCTAGacggtcggtctagctacgagc
gi|7 : AAAATCGAAGGAAATGGCATCCT-C-GCCC-A--------TTT-TAT---TTCTGGGCG--A--GCA-TGATGT-CATA-C-------ACTC--C--TAGAAACGGCCTCCCTGTTTTT-TTAAA-A-TCTAGCTgttcgg
gi|8 : AAATGCAGGAAAAGGCATCCT-C-GCCC-AA---TT-TTTT-TTTCTGT-----GCA--A--GCT-TGCCCC-CAGA-C-------ACTA--T--TAGAATCGACCTCACTGTTTTT-T
gi|9 : tgATGCAAGAAAAATGTAGGAAATGGCATCCT-C-GTCC-AAAAATA-ACTT-TGT---T-----G-G--A--ACA-TTCCCC-CACA-T-------ACTT--T--TAGAATCGGCCTCCCTGTTTTT-aggtacggg
blockSeqs : A A . T A TACA C C TTCTGG C TA . . G A C CCCCCCC CAC T A G T
blockSeqs : A . . . A TAA . G TTCT C CC . . . C . . T T . G .
blockSeqs : A . . . A TAA . C CTGT . . . . . C . . T T . G .
blockSeqs : A . . . A AAA . G A . . . . . T . . T T . G .
blockSeqs : T . . . A TAA . G T . . . . . G . . C T . . .
blockSeqs : A . . . A TAA . A G . . . . . G . . T T . . .
blockSeqs : A . . . A TTT . G T . . . . . T . . C T . . .
blockSeqs : T . . . A TAA . G C . . . . . G . . C T . . .
blockSeqs : A . . . T AA . A T . . . . . C . . T . . . .
blockSeqs : A . . . A . . T T . . . . . C . . C . . . .
blockSeqs : . . . . A . . G T . . . . . T . . T . . . .
blockSeqs : . . . . . . . . . . . . . G . . T . . . .
blockSeqs : . . . . . . . . . C . . C . .
blockSeqs : . . . . . . . . T . .
blockSeqs : . . T .
blockSeqs : . .
blockSeqCons : TAA* ** T****
originalCons : GAAATGCAGGAAAAACGCAGGAAATGGCATCCT-C-GCCC-AAAAATA-ACTT-TGT---T-----G-G--A--GCA-TGCCCC-CANA-T-------ACCC--C--TAGAATCGGCCTCCCTGTTTTT-TTTAA-G-TCTAGCT
finalCons : GAAATGCAGGAAAAACGCAGGAAATGGCATCCT-C-GCCC-AAAAATAA-CTT-TGT---T-----G-G--A--GCA-TGCCCC-CANA-T-------ACCCT----TAGAATCGGCCTCCCTGTTTTT-TTTAA-G-TCTAGCT
Alignments
lowQualScore : 111111111 1111111 1 1
lowQualScore : 1 2 2 2 1 9999 3 2 666666666 5 77 33 2 2 3 2 0000000 44444 0 2 2 3
lowQualScore : . . . . . .... . . ......... . .. .. . . . . ....... ..... . . . .
lowQualScore : 6 9 9 9 6 2222 1 1 333333333 3 33 77 7 7 6 5 0000000 88888 9 7 3 1
consensus : GAAATGCAGGAAAAACGCAGGAAATGGCATCCT-C-GCCC-AAAAATA-ACTT-TGT---T-----G-G--A--GCA-TGCCCC-CANA-T-------ACCC--T--TAGAATCGGCCTCCCTGTTTTT-TTTAA-G-TCTAGCT
Reference ( family-713 ) : GAAATGCAGGAAAAACGCAGGAAATGGCATCCT-C-GCCC-AAAAATA-ACTT-TGT---T-----G-G--A--GCA-TGCCCC-CANA-T-------ACCC--T--TAGAATCGGCCTCCCTGTTTTT-TTTAA-G-TCTAGCT
gi|1 : GAAATGCAGGAAAATCCCAGAAAATGGAATCCT-CAGCC----AAAT--TCTT-TTC---T-----G-G--ACGACATTGCTTT-CAG----------ACCC--TACTACAATGAGCTACCCTG-TTCT-TTAAA-G-TCTAG
gi|10 : tctCAGGAAATTGCATCCT-C-GAT---AAAATACATTT-TCT---A-----G-G----------------CGAA-T-------ACCC--T--T-GAATCGGTCTCCATGTCTTT-TTTAG-G-TCTAGCTgcacg
gi|11 : GGAAAAATGCAGGAAATGGCACCCT-C-GTCC-AAAAA----------------------A--A--GC------CC-CACA-T-------ACCT--T--TAAAATCGGCCTCCTTG--TTT-TTTAAGG-TCTAGCTacggacct
gi|12 : GAAATGCAGGAAAAATGCAGAATATGGCACCGT-C-GTCC-AAAACTA-ACTT-TGT---T-----G-G--A--CCA-TGCCCCGAACA-T-------ACCT--T--TAGAATatg
gi|13 : ctGAAATGGCATCCT-C-GACT-AAAGA-A-ATTT-TCT---G-----G-GTAA--GCA-TGCCCC-CATA-TC------ACCC-----TAGAATCCGCCTCCC---TTTT-TTTAA-G-a
gi|14 : -G--A--GCA-TGCCTC-CTGACT-------AACC--T---AGAATCGGCCTCCCTG--TTT-TTTAAGG-TCTAGCTgtc
gi|15 : aggttctgtatttttatgagaGAGATGTATGAAAA-CGCAGG-AATGGCATCCTAC-ACCCTAAGAATacaggcc
gi|15 : tctA-C-------ACCC--T--AAGAATCGGCCTGCTTGTTTTcggcctgcttgttttaaggtcatgctaccgg
gi|16 : tctgagatgtatgaaaacgcaggaatggcatcct-G--A--GCA-TGCCAT-TAGA-C-------CCTC--C--TAGAATCAACCTCCCTGTTTTTAGGTAG-G-TCTAGCaaggtcatgctaccgg
gi|17 : tcttttctgagc-------ACCC--C--TAGAATTGGCCTCACTGTT----TTTAA-GTTCTAGCT
gi|18 : aAATCAGCCTCCCTG--TTT-TTTAAGG-TGTAGCTatgaacc
gi|2 : GAAATGCAGGAAAAATGCAGGAAATGGCACCCT-C-GTCC-AAAAATA-ACTT-TGT---T-----G-G--A--GTA-TGCCCC-CATA-T-------ACAT--T--TAGAATCGGCCTCCCTGTTTTT-TTTAA-G-TCTAGCTatggac
gi|3 : AAAACGATGGAAATGGCATTCT-C-GCCT-AAAAAAA-AATTCTGA---C-----C-G--A--GCA-TGACCC-CA-A-TCCCCCCCACCCCAC--TAGAATCAGCATCCCTATTTTT-TTAAG-G-TCTA
gi|4 : gGGAAAATCGAAGGAAATGTCATCCT-C-GCCC-A--------TTT-TAT---TTCT--G-GCCA--GGA-TGATGT-CAGA-C-------AATC--C--TAGAAACGGCCTCCCTG-TTTT-TTAAA-A-TCTAGCTa
gi|5 : AAATGCAGGAAATGGCACCCT-C-GTCC-AAAAATA-ACTT-TGT---T-----G-G--A--GCA-TACCCC-CACA-T-------ACCT--T--TAGAATCGATCTCCCTacgg
gi|6 : gAAATGCAGGAAATGGCACCCT-C-GCCC-ATATATA-ACTT-TGT---T-----G-G--A--GCA-TTTCCC-CACA-T-------ACCT--T--TAGAATCGACCTCACTG---TT-TTTAAGG-TCTAGacggtcggtctagctacgagc
gi|7 : AAAATCGAAGGAAATGGCATCCT-C-GCCC-A--------TTT-TAT---TTCTGGGCG--A--GCA-TGATGT-CATA-C-------ACTC--C--TAGAAACGGCCTCCCTGTTTTT-TTAAA-A-TCTAGCTgttcgg
gi|8 : AAATGCAGGAAAAGGCATCCT-C-GCCC-AA---TT-TTTT-TTTCTGT-----GCA--A--GCT-TGCCCC-CAGA-C-------ACTA--T--TAGAATCGACCTCACTGTTTTT-T
gi|9 : tgATGCAAGAAAAATGTAGGAAATGGCATCCT-C-GTCC-AAAAATA-ACTT-TGT---T-----G-G--A--ACA-TTCCCC-CACA-T-------ACTT--T--TAGAATCGGCCTCCCTGTTTTT-aggtacggg