lowQualScore : 1111 444444444444444 11 11 11
lowQualScore : 5 2222 5 5 77777 222222222222222 0 2 22 2 2 2 3 33 55 3 99 11 8
lowQualScore : . .... . . ..... ............... . . .. . . . . .. .. . .. .. .
lowQualScore : 0 1111 7 0 88888 555555555555555 4 7 55 7 9 9 1 22 55 6 22 00 2
consensus : CACCCCGG----TC-AAG-A--T--GG-G---CACAA-T-AGGGAGATAAAGTTTAGG-GTCG-NA-ACTGTTC-T-TA-CG-CAG-GAT-GGTCT--AATAT--CTTGTAAACTATT
Reference ( gi|5 ) : CACCCCCG----TC-AAG-A--T--GG-G---CACAAAT-ATGGAGATAAAGTTTAGG-GTCG-AA-ACTGTTC-T-TA-CA-TAG-AAT-GGTCT--AATAT--CGTGTAAACTATTCA
gi|1 : CACCCCGGGAGGTT-AAG-A--T--GG-GAGCCACAA-T-AGGGAAATAAAGTTTAGT-GCCG-TA-ACTGTTC-T-TA-
gi|12 : caggcttgggatcgttcttggcggagttggatggggccacaataggggaccaaaatttagcaaagttttatataggaaaatatattttgaacagtcattgttcagtttgtcaaattaacatgaaagcattcaagtttgtttaaatgatagcaaccctccaccccCACCGCGG----TC-AAG-A--T--GG-GGC-CACA---------------GTTTAGG-GTCG-AA-ACTATTC-T-TA-CG-CAG-GAT-Gggcagga
gi|7 : ccaccACCCCCG---------G-G--G--GG-G---T-CAA-T-AGCGAGATTAAGTCTAGG-GTCG--A-ACTGTTC-T-TA-CG-CAG-GAT-G
gi|4 : ccccacccaaCCCCCG----TC-AAATA--T--GGCC---CACCAAT-AGGGAAATTAA--------GTCA-CA-ACTGTTC-TATA-CA-CGG-AAT-GG
gi|9 : aattaaatgaaagcaccacaagatttgtatacatgaatagttcttacaccCCCGG----TCCAAA-A--T--GG-A---TCCAATT-AGGGAGATAAAGTTTAGG-GTCGTAA-ACTGat
gi|13 : ccccccccctccaG----TC-AGG-A--TTGGG-G---C-CACATTAGAGAGATAAACTTTAGG-GTTG-TA-AATGTTC-T-T
gi|6 : gggagg----TC-AAG-AGGT--GA-C---CACAAAT-G-GGAGAAAAA--TTAGGCGTCG-TA-GCTGTTC-T-TA-CG-GAG-AAT-GATCT--AATAT--CTTGTAAACTATT
gi|15 : gggaAA-A--T--GG-GAGCCACGA-T-AGGGAGATAAAGTTTAGG-GTAA-AA-AATATTC-T-TA-CA-ga
gi|18 : atggGAGATAAAGTTTAGG-GTCG-TA-ATTATTC-A-TA-TG-CAG-GAT-Gc
gi|8 : AGATAAAGTTTAGG-GTCG-CA-ACTGTTC-T-AA-CG-CAG-GAT-GGTCT--AATA
gi|19 : AGATAAAGTTTAGG-GTCG-TA-AATGTTC-T-TA-CG-CAG-GAT-Gcttcatattttcttgatcct
gi|10 : TAAAGTT-AAG-GTCG-AA-A-TGTTC-T-TA-CA-CAG-GAT-GGTCT--AATAC--CA
gi|11 : agccacaataggcatatGG-GTCG-AA-ACAGTTC-T-TA-CA--AG-GAT-GGTCT--ATTAT--CTTGTAAACCATTa
gi|16 : GG-TTCG-AACACTGTTC-T-TAACA-CAG-GATCAGTCTTGAATAT--CGTGTAAACTATTgaagaccatgcttgt
gi|14 : GG-GTCATGA-ACTATTCAT-CA-CGGCAGGAAT-GGTCT--AATATATCTTGTAAACTATTgat
3 sequences could not be aligned to this particular reference sequence:
Unaligned ( gi|2 ): GTACAATTTGTCAATTAAACATAGAGGCATCAATAGCTAGTGTAAATTCCTTTTTTGAAATGGTAGTGCCTCTCTCATCCACCTCCACCCCCGGAGTCCAGATGTAAACCATAATAAGGCGATTAAGTT
Unaligned ( gi|3 ): GTACAATTTGTCAATTAAAACATAGAGGCATCAATAGCTAGTGTAAATTCCTTTTTGAAATGGTAGTGCCTCTCTCATCCACCTCCACCCCCGGAGTCCAGATGTTAAACCATAATAAGGCGATTAAGT
Unaligned ( gi|17 ): ATGGGACTACAATAGGGGACCAAAGGTTAACAAAGGTTTATATA
Alignments
lowQualScore : 1111 22222
lowQualScore : 2222 5 5 66 66 22222 4 4 4 3 2 888 2 2 2 2 2 3 3 77 888
lowQualScore : .... . . .. .. ..... . . . . . ... . . . . . . . .. ...
lowQualScore : 1111 7 0 99 99 33333 0 0 0 1 5 444 5 7 7 9 9 1 3 99 000
consensus : CACCCCGG----TC-AAG-A--T--GGG---C-AC-AA-T-AGGGAGAT-AAAGTTTAGG-GTCG-N-A-ACTGTTC-T-TA-CG-CAGGA-T-GGTCT--AATAT--CTTGTAAACTATT
Reference ( family-2788 ) : CACCCCGG----TC-AAG-A--T--GGG---C-AC-AA-T-AGGGAGAT-AAAGTTTAGG-GTCG-N-A-ACTGTTC-T-TA-CG-CAGGA-T-GGTCT--AATAT--CTTGTAAACTATT
gi|1 : CACCCCGGGAGGTT-AAG-A--T--GGGAGCC-AC-AA-T-AGGGAAAT-AAAGTTTAGT-GCCG-T-A-ACTGTTC-T-TA-GG-CAGGA-
gi|10 : caggcttgggatcgttcttggcggagttggatggggccacaataggggaccaaaatttagcaaagttttatataggaaaatatattttgaacagtcattgttcagtttgtcaaattaacatgaaagcattcaagtttgtttaaatgatagcaaccctccacccc---C-AC-AA-T-AGGCATATTAAAGTT-AAG-GTCG-A-A-A-TGTTC-T-TA-CA-CAGGA-T-GGTCT--AATAC--
gi|11 : agcGG-GTCG-A-A-ACAGTTC-T-TA-CA--AGGA-T-GGTCT--ATTAT--CTTGTAAACCATTata
gi|12 : CACCGCGG----TC-AAG-A--T--GGGGC-C-AC-A----------------GTTTAGG-GTCG-A-A-ACTATTC-T-TA-CG-CAGGA-T-Ggaagaccatgcttgt
gi|13 : ccaccGG----TC-AGG-A--TTGGGG---CCAC-AT-T-AGAGAGAT-AAACTTTAGG-GTTG-T-A-AATGTTC-T-T
gi|14 : gggagGG-GTCA-TGA-ACTATTCAT-CA-CGGCAGGAAT-GGTCT--AATATATCTTGTAAACTATT
gi|15 : AA-A--T--GGGAGCC-AC-GA-T-AGGGAGAT-AAAGTTTAGG-GTAA-A-A-AATATTC-T-TA-CA-Cgaga
gi|16 : atggGG-TTCG-A-ACACTGTTC-T-TAACA-CAGGA-TCAGTCTTGAATAT--CGTGTAAACTATT
gi|18 : GAGAT-AAAGTTTAGG-GTCG-T-A-ATTATTC-A-TA-TG-CAGGA-T-Ggat
gi|19 : AGAT-AAAGTTTAGG-GTCG-T-A-AATGTTC-T-TA-CG-CAGGA-T-G
gi|4 : CCCCCG----TC-AAATA--T--GGC---CCACCAA-T-AGGGAAAT-TAA--------GTCA-C-A-ACTGTTC-TATA-CA-CGGAA-T-GG
gi|5 : aattaaatgaaagcaccacaagatttgtatacatgaatagttcttacaccCACCCCCG----TC-AAG-A--T--GGG---C-AC-AAAT-ATGGAGAT-AAAGTTTAGG-GTCG-A-A-ACTGTTC-T-TA-CA-TAGAA-T-GGTCT--AATAT--CGTGTAAACTATTat
gi|6 : GA----TC-AAG-AGGT--GAC---C-AC-AA-A-TGGGAGAA-AAA--TTAGGCGTCG-T-A-GCTGTTC-T-TA-CG-GAGAA-T-GATCT--AATAT--CTTGTAAACTATTca
gi|7 : ggC-AA-T-AGCGAGAT-TAAGTCTAGG-GTCG---A-ACTGTTC-T-TA-CG-CAGGA-T-Gga
gi|8 : ccccacccaaacccccgggggggtAGAT-AAAGTTTAGG-GTCG-C-A-ACTGTTC-T-AA-CG-CAGGA-T-GGTCT--AATA---CTT
gi|9 : CCCGG----TCCAAA-A--T--GGA---T-CC-AA-TTAGGGAGAT-AAAGTTTAGG-GTCGTA-A-ACTGcatattttcttgatcct
3 sequences could not be aligned to this reference sequence:
Unaligned ( gi|2 ): GTACAATTTGTCAATTAAACATAGAGGCATCAATAGCTAGTGTAAATTCCTTTTTTGAAATGGTAGTGCCTCTCTCATCCACCTCCACCCCCGGAGTCCAGATGTAAACCATAATAAGGCGATTAAGTT
Unaligned ( gi|3 ): GTACAATTTGTCAATTAAAACATAGAGGCATCAATAGCTAGTGTAAATTCCTTTTTGAAATGGTAGTGCCTCTCTCATCCACCTCCACCCCCGGAGTCCAGATGTTAAACCATAATAAGGCGATTAAGT
Unaligned ( gi|17 ): ATGGGACTACAATAGGGGACCAAAGGTTAACAAAGGTTTATATA
Alignments
lowQualScore : 1111 22222
lowQualScore : 2222 5 5 66 66 22222 4 4 4 3 2 888 2 2 2 2 2 3 3 77 888
lowQualScore : .... . . .. .. ..... . . . . . ... . . . . . . . .. ...
lowQualScore : 1111 7 0 99 99 33333 0 0 0 1 5 444 5 7 7 9 9 1 3 99 000
consensus : CACCCCGG----TC-AAG-A--T--GGG---C-AC-AA-T-AGGGAGAT-AAAGTTTAGG-GTCG-N-A-ACTGTTC-T-TA-CG-CAGGA-T-GGTCT--AATAT--CTTGTAAACTATT
Reference ( family-2788 ) : CACCCCGG----TC-AAG-A--T--GGG---C-AC-AA-T-AGGGAGAT-AAAGTTTAGG-GTCG-N-A-ACTGTTC-T-TA-CG-CAGGA-T-GGTCT--AATAT--CTTGTAAACTATT
gi|1 : CACCCCGGGAGGTT-AAG-A--T--GGGAGCC-AC-AA-T-AGGGAAAT-AAAGTTTAGT-GCCG-T-A-ACTGTTC-T-TA-GG-CAGGA-
gi|10 : caggcttgggatcgttcttggcggagttggatggggccacaataggggaccaaaatttagcaaagttttatataggaaaatatattttgaacagtcattgttcagtttgtcaaattaacatgaaagcattcaagtttgtttaaatgatagcaaccctccacccc---C-AC-AA-T-AGGCATATTAAAGTT-AAG-GTCG-A-A-A-TGTTC-T-TA-CA-CAGGA-T-GGTCT--AATAC--
gi|11 : agcGG-GTCG-A-A-ACAGTTC-T-TA-CA--AGGA-T-GGTCT--ATTAT--CTTGTAAACCATTata
gi|12 : CACCGCGG----TC-AAG-A--T--GGGGC-C-AC-A----------------GTTTAGG-GTCG-A-A-ACTATTC-T-TA-CG-CAGGA-T-Ggaagaccatgcttgt
gi|13 : ccaccGG----TC-AGG-A--TTGGGG---CCAC-AT-T-AGAGAGAT-AAACTTTAGG-GTTG-T-A-AATGTTC-T-T
gi|14 : gggagGG-GTCA-TGA-ACTATTCAT-CA-CGGCAGGAAT-GGTCT--AATATATCTTGTAAACTATT
gi|15 : AA-A--T--GGGAGCC-AC-GA-T-AGGGAGAT-AAAGTTTAGG-GTAA-A-A-AATATTC-T-TA-CA-Cgaga
gi|16 : atggGG-TTCG-A-ACACTGTTC-T-TAACA-CAGGA-TCAGTCTTGAATAT--CGTGTAAACTATT
gi|18 : GAGAT-AAAGTTTAGG-GTCG-T-A-ATTATTC-A-TA-TG-CAGGA-T-Ggat
gi|19 : AGAT-AAAGTTTAGG-GTCG-T-A-AATGTTC-T-TA-CG-CAGGA-T-G
gi|4 : CCCCCG----TC-AAATA--T--GGC---CCACCAA-T-AGGGAAAT-TAA--------GTCA-C-A-ACTGTTC-TATA-CA-CGGAA-T-GG
gi|5 : aattaaatgaaagcaccacaagatttgtatacatgaatagttcttacaccCACCCCCG----TC-AAG-A--T--GGG---C-AC-AAAT-ATGGAGAT-AAAGTTTAGG-GTCG-A-A-ACTGTTC-T-TA-CA-TAGAA-T-GGTCT--AATAT--CGTGTAAACTATTat
gi|6 : GA----TC-AAG-AGGT--GAC---C-AC-AA-A-TGGGAGAA-AAA--TTAGGCGTCG-T-A-GCTGTTC-T-TA-CG-GAGAA-T-GATCT--AATAT--CTTGTAAACTATTca
gi|7 : ggC-AA-T-AGCGAGAT-TAAGTCTAGG-GTCG---A-ACTGTTC-T-TA-CG-CAGGA-T-Gga
gi|8 : ccccacccaaacccccgggggggtAGAT-AAAGTTTAGG-GTCG-C-A-ACTGTTC-T-AA-CG-CAGGA-T-GGTCT--AATA---CTT
gi|9 : CCCGG----TCCAAA-A--T--GGA---T-CC-AA-TTAGGGAGAT-AAAGTTTAGG-GTCGTA-A-ACTGcatattttcttgatcct
blockSeqs : . C T GG TG AGCC C A T T C TG C A A A G A C TG TAT
blockSeqs : . . . . . GCC . . . . . TA . . . . . . . . T
blockSeqs : . . . . . CC . . . . . A . . . . . . . . T
blockSeqs : . . . . . CC . . . . . A . . . . . . . . T
blockSeqs : . . . . . C . . . . . A . . . . . . . . T
blockSeqs : . . . . . C . . . . . T . . . . . . . . .
blockSeqs : . . . C . . . . . A . . . . . . .
blockSeqs : T . . . . . A . . . . . . .
blockSeqs : . . . . . T . . . . . . .
blockSeqs : . . T . . . . . . .
blockSeqs : . . C . . . . . . .
blockSeqs : . . A . . . . . .
blockSeqs : . T . . . . .
blockSeqs : . C . . .
blockSeqs : . . .
blockSeqCons : **** C****
originalCons : CACCCCGG----TC-AAG-A--T--GGG---C-AC-AA-T-AGGGAGAT-AAAGTTTAGG-GTCG-N-A-ACTGTTC-T-TA-CG-CAGGA-T-GGTCT--AATAT--CTTGTAAACTATT
finalCons : CACCCCGG----TC-AAG-A--T--GGGC----AC-AA-T-AGGGAGAT-AAAGTTTAGG-GTCG-N-A-ACTGTTC-T-TA-CG-CAGGA-T-GGTCT--AATAT--CTTGTAAACTATT
3 sequences could not be aligned to this reference sequence:
Unaligned ( gi|2 ): GTACAATTTGTCAATTAAACATAGAGGCATCAATAGCTAGTGTAAATTCCTTTTTTGAAATGGTAGTGCCTCTCTCATCCACCTCCACCCCCGGAGTCCAGATGTAAACCATAATAAGGCGATTAAGTT
Unaligned ( gi|3 ): GTACAATTTGTCAATTAAAACATAGAGGCATCAATAGCTAGTGTAAATTCCTTTTTGAAATGGTAGTGCCTCTCTCATCCACCTCCACCCCCGGAGTCCAGATGTTAAACCATAATAAGGCGATTAAGT
Unaligned ( gi|17 ): ATGGGACTACAATAGGGGACCAAAGGTTAACAAAGGTTTATATA
Alignments
lowQualScore : 1111 22222
lowQualScore : 2222 5 5 66 66 22222 4 4 4 3 2 888 2 2 2 2 2 3 3 77 888
lowQualScore : .... . . .. .. ..... . . . . . ... . . . . . . . .. ...
lowQualScore : 1111 7 0 99 99 33333 0 0 0 1 5 444 5 7 7 9 9 1 3 99 000
consensus : CACCCCGG----TC-AAG-A--T--GGG---C-AC-AA-T-AGGGAGAT-AAAGTTTAGG-GTCG-N-A-ACTGTTC-T-TA-CG-CAGGA-T-GGTCT--AATAT--CTTGTAAACTATT
Reference ( family-2788 ) : CACCCCGG----TC-AAG-A--T--GGG---C-AC-AA-T-AGGGAGAT-AAAGTTTAGG-GTCG-N-A-ACTGTTC-T-TA-CG-CAGGA-T-GGTCT--AATAT--CTTGTAAACTATT
gi|1 : CACCCCGGGAGGTT-AAG-A--T--GGGAGCC-AC-AA-T-AGGGAAAT-AAAGTTTAGT-GCCG-T-A-ACTGTTC-T-TA-GG-CAGGA-
gi|10 : caggcttgggatcgttcttggcggagttggatggggccacaataggggaccaaaatttagcaaagttttatataggaaaatatattttgaacagtcattgttcagtttgtcaaattaacatgaaagcattcaagtttgtttaaatgatagcaaccctccacccc---C-AC-AA-T-AGGCATATTAAAGTT-AAG-GTCG-A-A-A-TGTTC-T-TA-CA-CAGGA-T-GGTCT--AATAC--
gi|11 : agcGG-GTCG-A-A-ACAGTTC-T-TA-CA--AGGA-T-GGTCT--ATTAT--CTTGTAAACCATTata
gi|12 : CACCGCGG----TC-AAG-A--T--GGGGC-C-AC-A----------------GTTTAGG-GTCG-A-A-ACTATTC-T-TA-CG-CAGGA-T-Ggaagaccatgcttgt
gi|13 : ccaccGG----TC-AGG-A--TTGGGG---CCAC-AT-T-AGAGAGAT-AAACTTTAGG-GTTG-T-A-AATGTTC-T-T
gi|14 : gggagGG-GTCA-TGA-ACTATTCAT-CA-CGGCAGGAAT-GGTCT--AATATATCTTGTAAACTATT
gi|15 : AA-A--T--GGGAGCC-AC-GA-T-AGGGAGAT-AAAGTTTAGG-GTAA-A-A-AATATTC-T-TA-CA-Cgaga
gi|16 : atggGG-TTCG-A-ACACTGTTC-T-TAACA-CAGGA-TCAGTCTTGAATAT--CGTGTAAACTATT
gi|18 : GAGAT-AAAGTTTAGG-GTCG-T-A-ATTATTC-A-TA-TG-CAGGA-T-Ggat
gi|19 : AGAT-AAAGTTTAGG-GTCG-T-A-AATGTTC-T-TA-CG-CAGGA-T-G
gi|4 : CCCCCG----TC-AAATA--T--GGC---CCACCAA-T-AGGGAAAT-TAA--------GTCA-C-A-ACTGTTC-TATA-CA-CGGAA-T-GG
gi|5 : aattaaatgaaagcaccacaagatttgtatacatgaatagttcttacaccCACCCCCG----TC-AAG-A--T--GGG---C-AC-AAAT-ATGGAGAT-AAAGTTTAGG-GTCG-A-A-ACTGTTC-T-TA-CA-TAGAA-T-GGTCT--AATAT--CGTGTAAACTATTat
gi|6 : GA----TC-AAG-AGGT--GAC---C-AC-AA-A-TGGGAGAA-AAA--TTAGGCGTCG-T-A-GCTGTTC-T-TA-CG-GAGAA-T-GATCT--AATAT--CTTGTAAACTATTca
gi|7 : ggC-AA-T-AGCGAGAT-TAAGTCTAGG-GTCG---A-ACTGTTC-T-TA-CG-CAGGA-T-Gga
gi|8 : ccccacccaaacccccgggggggtAGAT-AAAGTTTAGG-GTCG-C-A-ACTGTTC-T-AA-CG-CAGGA-T-GGTCT--AATA---CTT
gi|9 : CCCGG----TCCAAA-A--T--GGA---T-CC-AA-TTAGGGAGAT-AAAGTTTAGG-GTCGTA-A-ACTGcatattttcttgatcct
3 sequences could not be aligned to this reference sequence:
Unaligned ( gi|2 ): GTACAATTTGTCAATTAAACATAGAGGCATCAATAGCTAGTGTAAATTCCTTTTTTGAAATGGTAGTGCCTCTCTCATCCACCTCCACCCCCGGAGTCCAGATGTAAACCATAATAAGGCGATTAAGTT
Unaligned ( gi|3 ): GTACAATTTGTCAATTAAAACATAGAGGCATCAATAGCTAGTGTAAATTCCTTTTTGAAATGGTAGTGCCTCTCTCATCCACCTCCACCCCCGGAGTCCAGATGTTAAACCATAATAAGGCGATTAAGT
Unaligned ( gi|17 ): ATGGGACTACAATAGGGGACCAAAGGTTAACAAAGGTTTATATA