lowQualScore : 111111111111111111111111111111111111111111111 33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333 2222222222222222222222222222222222222222222222222222222222222
lowQualScore : 1111 4444444444444444444444444444444444444444 111 11111 666666666666666666 11 111111 333 222222 1111 111111111 1 11 111 222222 22222222 11 11 1 1 1 1 11 444 1 1 1111111 1 66666666666 111 111 1 22 111 1 1 11 1 11 11 11 1 11 555555555 333333333333333333333333333333333333333333333 1111 1 2222 22222 111 1 111 11 1 22222 1 11 22222 00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 1 11 1 11 222 2222 22 11 7777777777777 1 1 222 22 88888888888888888888888 1 1 1111111111111111111111111111111111111111111111111111111111111 44444 2
lowQualScore : 888 66 66 4 66 66 2 44 0 44 66 5 5 4444 3333333333333333333333333333333333333333 4 0 66 333 22222 999 4 4 4 1 222222222222222222 00 4 333333 4 222 66 66 6 444444 1 5 8888 55 888888888 8 66 55 55 0 777 8888 88 4 66 00 8 777 888 33 888 5 555555 77 5 8 0 55555555 5 6 33 88 3 0 0 0 0 33 111 0 4 8888888 0 00000000000 4 2 777 2 8 8 6 6 111 0 7 77 888 3 0 2 0 22 0 33 33 33 0 33 888888888 444444444444444444444444444444444444444444444 7777 5 6 2222 22222 2 222 0 8 777 8 88 8 0 8 66666 4 3 5 1 2 0 8 11 1 8 88888 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111 0 0 33 2 9 33 222 6666 22 11 4444444444444 8 0 5 8 777 00 99999999999999999999999 9 0 6 2 1 0000000000000000000000000000000000000000000000000000000000000 11111 0 6 6
lowQualScore : ... .. .. . .. .. . .. . .. .. . . .... ........................................ . . .. ... ..... ... . . . . .................. .. . ...... . ... .. .. . ...... . . .... .. ......... . .. .. .. . ... .... .. . .. .. . ... ... .. ... . ...... .. . . . ........ . . .. .. . . . . . .. ... . . ....... . ........... . . ... . . . . . ... . . .. ... . . . . .. . .. .. .. . .. ......... ............................................. .... . . .... ..... . ... . . ... . .. . . . ..... . . . . . . . .. . . ..... ................................................................................................................................... . . .. . . .. ... .... .. .. ............. . . . . ... .. ....................... . . . . . ............................................................. ..... . . .
lowQualScore : 888 77 11 4 11 99 0 88 1 00 11 0 0 8888 8888888888888888888888888888888888888888 4 1 11 111 33333 666 4 4 4 1 111111111111111111 66 4 999999 4 222 11 11 9 333333 8 6 6666 44 444444444 9 11 55 66 0 000 5555 55 0 11 66 2 888 444 99 888 0 777777 99 7 4 1 33333333 7 7 88 88 2 0 0 0 0 22 555 0 5 2222222 0 00000000000 0 5 555 5 0 0 0 0 000 0 0 55 000 0 0 2 0 22 0 88 88 88 0 22 888888888 222222222222222222222222222222222222222222222 0000 0 0 7777 22222 5 222 0 0 444 0 22 0 0 0 44444 8 2 4 4 2 8 0 00 4 0 55555 00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 8 0 22 5 2 88 555 4444 00 00 0000000000000 0 0 0 0 000 55 00000000000000000000000 0 0 0 8 0 7777777777777777777777777777777777777777777777777777777777777 55555 0 0 0
consensus : TTACCT---ATCC-TCTGCGTGCCTA--A-GGGCACATAAGGCCTCCACA--GACTGTTTCCACTTTGCTCTGTCGGCT--GCAGCAGCCCTT-G-CTCC---CCCC-------------C-------AC----GTT--C-------TC-CATCCTCCGATG--TTNC-GCTCTTTCTC----TACT-GTT-C-GT-CTCCAGGTGGTTTTTG--GGTC-GCC----CTTT--C-T---T--TCT-T---C--CTTCTGGTGCC--CACG-T----CATTGCCACATT-A--CAGTCA-CTN----G---CT-GC--AT--CTTG-TCTC---AG----GGTG-TGTC-CA--AT--AAACTTCCATCTT---CTTCT-CCTGACTTCTTCACTCAG--TGGT-CTCATT-----TCTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTGTTC------TTGCCAT-CTTATTC-TTA--GGATG-CGTCTTAAGCATTTGTTC-TGGAAGGTG-TT-GATCATC-TT-ATCAC-TCCTCTA-TTCATCTTCCAGGTC---TC-GCA-TT-A------A--TANTGTAGT---ANCGGTA-CCACT-AGTGTCTTG-T-ATAGT-CTGATTTTGGTGTTAGTCGTCTGAT-G-TNGT-TGGT-G-CTCC-ATAT--CTG--TTT--CAG-TCTGAC-AAAAGAT-TTCTTGCTTCTGCTAC-------------TCT-------------T--------------GTA-T-ACCTCCCCCTTCCTT--T-GATA-T-A-GTTGCACCAAG-GTATACAAACT-TTTCAACATCTT-CCAG-T-TCT-TC-ATCAT-CAATTTT-GATCTTTTC--C--GCTTGGTTTGNATTTATTCTCACGATC-TT--TGTTTT-GCTCTTGTA-T--GATCTTT---------------CGN-TTCTNC--ACT----CTTGTTG---TCGC-CT----TC-TGCTTCTTCACTG--GGCTT-GTT-GGT-TTN---CT-T-TGCATT-CGTCGTN-TGTTGATGGCATA---AACG-CA-ATGTCGTCA--GCGAAGTC-N-AGGTCATCCAGACC-TTGT-GT--AG------TAAA-TTCCATCTG-ATGCCATTCTCTCCATCTCCT-ATTGCT-TTTTCTC-GTCGTCCAATCCAT----------AN-CAA--T---AGGAAGA-GGAAGCCTGACATGCTA-------------C-ACCC-------CGG-------CCGG--TCTTGAA----CG------TTCCATANACCCAACCTACTTGTCTTCT
Reference ( gi|3 ) : TTACCT---ATCT-TCTGCGTGCCTA--A-GGGCACATAAGGCCTCCACA--GACTGTCTCCACTCTGTTCTGTCGGCT--GCAGCAGCCCTT-G-CTTC---CCCC-------------C-------AC----GTT--C-------TC-CATCCTCCGATG--TTCT-GCTCTTTCTC----TATC-GTT-C-GT-CTCCAGGTGGTTCTTGCAGATC-ACC----CTTT--C-T---T--TCT-T---C--CTTCTGGTGCC--CATG-T----CATTGCTATATT-G--CAATCA-TTC----G---CT-GC--AT--CTTG-TGTC---AG----GGTA-TGTC-CA--AT--AAACTTCCATCTT---CTTCT-CTTGACTTCTTCATTCAG--GGGT-CTCATG-----TCTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTGTCC------TTGCCAT-CTTATTC-TCA--GGATC-CGTCTTAAGCATTTGTTC-TGGAAGGTG-TT-GATCATC-TT-ATCATGTCCTCTA-TTCATCTTCCAAGTC---TC-ACA-TT-A------A--TATTGTAGT---ACCGGTA-CCACT-AGCGTTTTG-T-ATAGT-CTGATTTTGGTGT--GTCGTCTGAT-G-TTGT-TAGT-G-TTCC-ATAT--CTG--TTT--CAG-TCTGAC-AAAAGATGCTCAAGCTTTTGCTAC-------------TCT-------------T--------------GTA-T-GCCGCCCCCTTTCTT--T-GATA-T-A-GTTGCACCAAG-GCATACAAACT-TTTCAACATCTT-CCAG-T-TCT-TA-ATCAT-CAATTGT-GATCTTTTC--C--GCTTGATTTGCATTTATTATCATGATC-TT--TGTTTT-GCTCTTGT--T--GATCTCT---------------TGC-TTCTTC--ACTG-GGCTTGTTGGT-TTGCNCTGATATCTTGCTTCTTCACTG--GGCTT-GTT-GGT-TTG---CT-T-TGCATG-TGTTGTCTTGTTGATGACATA---AACG-CA-ATGTCATCA--GCGAAGTC-G-AGGTCATCCAG--C-TTG--GT--AG------T------CCACCTG-ATGCCATTCTCTCCACCTACT-ATTGC--TTTTCTC-GTCGTCCAATCCAT----------AG-CAA-CT---AGGAATA-GGGACCCTGACATGTTA-------------C-ATCC-------CGG-------CCGG--TCTTG------C-------TTCCA-AA--CCAA-TTACTTGTTTTTT
gi|6 : TTACCT---ATCT-TCTGCGTGCCTG--A-GGGCAC-TAAGGCCTCCACA--GACTGTCTCCACACTGCTCTGTCGGCT--ACAGCACCTCTT-G-CCCC---CCCC-------------CCCCACCCACCCCAATT--C-------TC-CATCCTTCGATG--TTCC-GCTCTTTCTC----TACC-GTT-C-GT-CACCAGGTGGTTTTTG---ATC-GCCATTTCTTT--C-T---T--TCT-TTTTC--CTTCTGGTGCC--CACG-T----CATTGCTATATT-A--CAATCA-CTC----C---CT-GC--AT--CT-G-CCTC---AG----GGTG-TGTT-CA--GT--AAATTTCCATCT----CTTCT-CCTGACTTCTTCACTCAG--TGGT-CTCATT-----TCTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTGT-C------TCGTCGTCCTTATTC-TCA--GGATG-CGTCTTAAGCATTTGTTC-TGGAAGGTG-TT-GATCATT-TT--TCAT---CTCTA-TTCATCTTCCAGGTC---TC-GCA-T
gi|12 : ctgTTACCT---ATCC-TCTGCGTGTCTA--A-GGGCAGATAAGGCCTCCACA--GACTGTGTCCACTTTGCTCTGCCAGCT--GCAGCAGCCCTT-GCCCCC---CCCC-------------C-------CC----CCC--C-------CC-CATCCTCCGATG--TTAC-GCTCTTTCTCTAGATACT-GTT-C-GT-CTCCAGGTGGTTTTTGc
gi|15 : gTTACCT---ATTC-TTTGCGTGCCTA--A-GGGCACATAAGGCATCCACA--GACTGCTTCCACTTTGCTCTTTCGGCT--GTAGCAGCCgt
gi|17 : TTACCT---ATCC-TCTGTGTGCCTT--A-GGGCACATAAGGCCTCCACA--GACTGTTTCCt
gi|4 : gTACCT---ATCC-TCTGTGTGTCTA--A-GGACACGTAGGGCCTCCACA--GACTGTCTCCACTTAGTTCTGTCGGCT--GCAGCAGCCCTT-G-CTT----CCCC-------------C-------AC----GTT--C-------TT-CGTCCTCCGATG--GTCC-GCTCCTTCTT----CACT-TTT-T-GT-CTCCAGG-------------CC-GCC----CCTT--C-T---T--TCT-TTTGC--CTTTTGGTGTC--CATG-TTGACCAGTGCTACATT-A--CAATCA-CTCCTGGG---CT-GCATAT--CTTG-TCTC---AG----GATG-TGTC-C
gi|11 : TACCTTAAATCTCTCTGCA--CCAG--A-AGTTGCATAAGGCCTCCACGCTGACTG--CCCATTCTTTCCTATC--CT--GT-GCTGC---T-G--TTC---TGGC-------------C-------AT----GTT--CCAACTTGTC-CATCCT-TGTTGGTTTCT--TTCTTTCAC----TGTT-GTT-C-TT-CTCCAAGTTGTT-TTG--GGCC-TGC----CTCTAGC-T---T--TTT-TC--C--CTTCTGGnccatgttgaccagtgctacattacaatcacttcggggctgcatatcttgtcccaggatgtgcccattattaaactttcatcttctcctgacttcactcagtggtctcatgtctacactttggagcctctcttctgtagtaatgtgttcttgccataccactaatgtcttgtataacctgattttggtgtgtcgtctgacgctgtaaagtgctccatatacctgtttcagtctgacaaaaatttactactctttattttaaaaatatgcaagtgtaaaagttgcacatacagttgcaccaaggtatacgaacttttcaacatatttcagttcatcatcatcaaacttgatcttttcctcttgatttgcatttattctcatggtcttcttgtttttgctcttgttgatctttagtccaactcttcatacttcttcactgtaagctttgttgattttcttctgcataatgttgtagtttgatggcctattcaacgcacatgtcatcagcaaagtcgaggtcatccagcttgtagtaaagttcacctgatgccattctgtccacctcctaatcgctttctccatccaatccatagccaatttaggaagaggaagcctgacatgttacacccctgcttcaccccggtcttgatt
gi|1 : CCT---ATCC-TCTGTGTGCCTATTACGGGCACATAAG-CCTCCACA--GACTGTTTCCACTTT-CTCTGTCGTCT--GCAGCAGCCCTTTG-CTTTTTTCCCC-------------A-------AC----ATTTTC-------TC-CAGCCTC-GATG--TTAC-GCTCTTTCT-----TACCTGTT-C-TT-CTTCAGGTTGTTTT----GGTCTGCC----CTTTT-C-T---TCTTCT-T---C--CTTCTGGTGCC--CACGAC----CATTGCCACATTTA--CAGTCA-CTG----G---CTTGC--AT--CTT--TGTCGGCAG----GGTG-TGTTTCA--AT--AA-TTTCCATCTT---TTTCTTCCTGACTTCTTCAT-CAGCTGGTT-TTC-TGCATTTTCTACACT--TTGG-AGC-TCTCTTCTGTAGTAGTGTGTTC------ATGC-AT-CTTATTC-TTA--GGATG-CGTCTTA-GCATTTGTTCCTGGAAGGTG-TTTGATCATC-TTTATCAC-TCCTCTA-TTCATCTTCCA-GTC---TCCGCA-TTTA------AGTTCCTATAGTGTAAGCGGTA-CCACT-AGTGTCTTG-TTATAGT-CTG-TTTTGGTGTTAGTCGTCTGAT-AATGGT-TGGT-GCTTCC-ATAT--CTG--TTTTTCAGGTCTGACCAAAAGAT-TTCTTGCTTCTGCTAC-------------TCT-------------TACCTTTCATGTCATGTA-TTACCTCCCCCTTCCTTATT-GATA-TTA-GTTGCAC--AG-TTATACAAACT-TTTCAACATCTTTCCAG-AATCT-TC-ATCAT-CAATTTTTGATTTTTTT--CTTGCTTGGTTTTGATTTATTCTTACGATC-TT--TATTTT-GCTCTTGTATT--GATCTTT---------------CAA-TCCT----ACT----CTT-------TCGTGCT----------TTCTTCACTG--G-CTT-GTTTGGTGTTGACCTT-T-TGCATT-CTTCGT--TGTTGTTGGCATC---AACGACA-AT-TC-TCA--GTGAAGTC-TTAGGTCATCCAGACT-TTG--GT--AG------TAAAATTCCATCTGTATGCCATT-TCTCCATCTCCT-ATTGCTTTTTTCTT-ATCGTCCAATCCAT----------TT-GAA--T---AGGAAGA-GAAAGCCTGACATGCTA-------------TAATCCTTTGCTTCAC-------CCGG--TCTTGAAGATTCGAAATCATTCCA-AAACCCAA-CTACTTGTCTTCag
gi|9 : ttCCA---ATCC-TCTTCATACCTG--T-TGGCATATAAGGCC----------CTAGTTCCACTTTTCCCTGTC--CTTGGCGACCACCCTG-G-TTGT---ACCC-------------C-------A-----GCT--CT------TC-CATC--CCAGT------T-GTTCTTTTTC----TGTT-GTT-CTGT-GT-CATGTTGTTTTTGC----C-TTC----CTAT--C-T---T--TCT-TTTCC--CATCTGGTCTC--CAGG-T----CA--GTTCAACT-GCACAAT-G-CTT----G---AT-GC--TT--TTCATTCTC---AG----CACG-TGAC-CA--ATCCAAA--TCCATCTT---CTT
gi|5 : cac-TCTGCGTGGCTA--A-GGGCACATAAGGCTTTCACA--GACTGCTTCCACTTTGCTAT-TCGGCT--GCAGCAGCCCTT-G-CTCC---CCCCACCCCCCACCCCCC-------AC----GTT--C-------TC-CATCCTCCGATG--TTAC-GCTCTTTCTC----TACT-GTT-C-GT-CTCCAGGTGGTTTTT---GGTC-GCC----CTTT--C-TTTCT--TCT-T---C--CTTCTGGTGCC--CACG-T----CATTGCCACTTT-A--CAGTCA-TTG----G---CT-GG--AT--CTTG-TCTC---GG----GGTG-TGTC-CA--AT--AAACTTCCATCTT---CTTCT-CCTGACTTCTTCACTCAG--TGGT-TTCATT-----TCTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTCTTT------TTGCCAT-CTTATTC-TTA--GAATG-CGTCTTAAGCATTTGTTC-TGGAAAGTG-TT-GATCGTC-TT-ATC---TCCTCTA-TTCATATTCCAGGTC---TC-GCA-TC-C------A--TATAGTAGT---ACCGGTA-CTACT-AGTGTCTTG-T-ATAGT-CCGATTTTGGTGT--GTCGTCTGAT-G-TTGT-TGGT-G-CTCC-ATAT--CTA--TTT--CAG-TCTGAT-AAAATTTGCTCTTGCTTTTGCTACTCTTCATTTCATGTCT-------------T--------------GTA-T-ACCTCCCCCTTCCTT--T-GATA-T-T-GTTGCACCAAG-GTATACAAACT-TTTTAACATCTT-CCAG-T-TCT-TC-ATAAT-CAATTGT-GATCTTTTC--T--GCTTGGTTTGTATTTATTCTTATGATC-TT--TGTTTT-GCTCTTGt
gi|2 : tcTCTGTCGTCT--GCAGCAGCCCTT-G-CTTTTT-CCCC-------------A-------AC----ATTTTC-------TC-CCACCTCGGATG--TTATCGCTCTTTCT-----TACT-GTT-C-TTTCTTCAGGTGGTT-TTG--GGTC-GCCG---CTTT--C-T---TCTTCT-TG--C--CTTCTGGTGCC--CA-G-A----CATTGCCACATT-A--CAGTCA-CT-----G---CTTGC--AT--CTT--TGTC---GGCACGGGTG-T-TT-CA--AT--AAA-TTCCATCTTTTTCTTCT-CCTGACTTCTTCACTCAG--TGGTTCTCATT-----TCTACACT--TTGG-AGC-TCTCTTCTGTAGT-GTGTGTTCA-----TTGCCAT-CTTATTCGTTATGGAATCGCGTCTTAAGCATTTGTTC-TGGAAGGTGTTT-GATCATCTTT-ATCAC-TCCTCTATTTCATCTTCCAGGTCCTGCC-GCATTT-AGTTCCTA--TAGTGTA-T---AGCGGTATCCACTAAGTGTCTTGTT-ATAGTGCTCGTTTTGGTGTTAGTCGTCTGATAA-TGGT-TGGTGG-CTCCGATAT--CTGTTTTT--CAG-TCTGAC--AAAGAT-TTCTTGCTTCTGCTAC-------------TCTTACCTTTCATGTCT--------------GTATT-ACCTCCCCCTTCCTT--TGGATATT-ACGTTGCACCAAGTGTATACAAACTGTTTCAACATCTT-CCAGAA-TCT-TC-ATCATGCAATTTT-GATTTTTTCT-T--GCTTGGTTTTGATTTATCTTAACGATCTTT--TATTTT-GCTCTTGTA-TTGGATCTTTAATCGCTACTCTTTGTGT-TTCTTC--ACTGAAGCTTGTTGGTGTTGC-------TTTTGCATCTT--------GTGT-GTT-G---TTG---------GCA--------TC------AAGACA-------CA-CA--TGTC-TCAATGTGAAGTCTG-AGGTCATCCAGACT-TTG--GT--AGTAAAATT------CCATCTG-ATGCCATT-TCTCCATCTCCT-ATTGCT-TTTTCTTAGTCGTCCAATCCATTTGTAAAACAAA-CAA--T---AGGAAGACGGAAGCCTGACATGCTATAATCCTTTGCTTC-ACCC-------CGG-------CTTGAAGATTGAAT---CA------TTCCATAC--CCAACTTACTTGTCTT
gi|8 : tcC---CCCC-------------C-------CC----GTT--C-------TCTCACCCTCCGATG--TAC--GCTCTTTCTC----TACT-GTTTC-GT-ATCCAG-TGGTTTTTG---GTC-GCC----CTTT--CCT---T--TCTCT---C--CTTCTGGTGCC--CACG-T----CATTGCCACATT-----AGTCA-TTG----G---TT-GG--AT--CTTG-TCTC---AG----GGTAATGTC-CA--AT--GAACTTCCACCTT---CTTCT-CCTGACTTCTTCACTCAG--TGGC-CTCATT-----TCTACTCT--TTGG-AGCATCTCTTCTGTAGTAGTATGTTC------TTGTTAT-CTTATTC-c
gi|13 : ccTTT--C-C---A--TCT-T---CTTCTCCTGACTTCTTCANA------CATTGCCACATT-A--CAGTCA-CTG----G---TT-GC--AT--CTTG-TCGC---AG----GGTG-TGTT-CA--AT--AAATTTCCATCTT---TTTCT-CCTGACTTCTTCACTCAG--TGGT-CTCATc
gi|4 : tcttgtcgcaggatgtgttcaaaaaaC--CATG-TTGACCAGTGCTACATT-A--CAATCACTTC----GGGGCT-GC--ATATCTTG-TCCC---AG----GATG-TGCC-CATTATT-AAACTTTCATCTT---CTCCT----GACTTC---ACTCAG--TGGT-CTCATG-----TCTACACT--TTGG-AGCCTCTCTTCTGTAGTAATGTGTTC------TTGCCAT-
gi|13 : tacctatcctctgtgtgtctaaggacacgtagggcctccacagactgtctccacttagttctgtcggctgcagcagcccttgcttcccccacgttcttcgtcctccgatggtccgctccttcttcactttttgtctccaggccgccccttctttcttttgccttttggtgtccatgttgaccagtgctacattacaatcactcctgggctgcatatcttgtctcaggatgtgtccnT--CTTG-TCGC---AG----GATG-TGTT-CA--AA--AAATTTCCATCTT---CTTCT-CCTGACTTCTTCANACA---TTGC-CACAT--------TACAGTCACTGGTTGCATCTTGTC-GCAG-GGTGTGTTCAATAAATTTCCAT-CTTTTTC-TCaccactaatgtcttgtataacctgattttggtgtgtcgtctgacgctgtaaagtgctccatatacctgtttcagtctgacaaaaatttactactctttattttaaaaatatgcaagtgtaaaagttgcacatacagttgcaccaaggtatacgaacttttcaacatatttcagttcatcatcatcaaacttgatcttttcctcttgatttgcatttattctcatggtcttcttgtttttgctcttgttgatctttagtccaactcttcatacttcttcactgtaagctttgttgattttcttctgcataatgttgtagtttgatggcctattcaacgcacatgtcatcagcaaagtcgaggtcatccagcttgtagtaaagttcacctgatgccattctgtccacctcctaatcgctttctccatccaatccatagccaatttaggaagaggaagcctgacatgttacacccctgcttcaccccggtcttgatt
gi|5 : GTAGT---ACCGGTA-CTACT-Actgacttcttcactcagtggtctcat
gi|4 : tctctgcgtggctaagggcacataaggctttcacagactgcttccactttgctattcggctgcagcagcccttgctccccccaccccccaccccccacgttctccatcctccgatgttacgctctttctctactgttcgtctccaggtggtttttggtcgccctttctttcttcttccttctggtgcccacgtcattgccactttacagtcattggctggatcttgtctcggggtgtgtccaataaacttccatcttcttctcctgacttcttcactcagtggtttcatttctacactttggagcatctcttctgtagtagtgtctttttgccatcttattcttagaatgcgtcttaagcatttgttctggaaagtgttgatcgtcttatctcctctattcatattccaggtctcgcatccataTA-CCACT-AATGTCTTG-T-ATAAC-CTGATTTTGGTGT--GTCGTCTGAC-G-CTGTAAAGT-G-CTCC-ATATACCTG--TTT--CAG-TCTGAC-AAAAA-----------TTTACTAC-------------TCT-------------T---------------TA-T-tagtgtcttgtatagtccgattttggtgtgtcgtctgatgttgttggtgctccatatctatttcagtctgataaaatttgctcttgcttttgctactcttcatttcatgtcttgtatacctcccccttcctttgatattgttgcaccaaggtatacaaactttttaacatcttccagttcttcataatcaattgtgatcttttctgcttggtttgtatttattcttatgatctttgttttgctcttg
gi|4 : tacctatcctctgtgtgtctaaggacacgtagggcctccacagactgtctccacttagttctgtcggctgcagcagcccttgcttcccccacgttcttcgtcctccgatggtccgctccttcttcactttttgtctccaggccgccccttctttcttttgccttttggtgtccatgttgaccagtgctacattacaatcactcctgggctgcatatcttgtctcaggatgtgtccnccatgttgaccagtgctacattacaatcacttcggggctgcatatcttgtcccaggatgtgcccattattaaactttcatcttctcctgacttcactcagtggtctcatgtctacactttggagcctctcttctgtagtaatgtgttcttgccaATA-C-A-GTTGCACCAAG-GTATACGAACT-TTTCAACATATT-TCAG-T-TCA-TC-ATCAT-CAAACTT-GATCTTTTC--C--TCTTGATTTGCATTTATTCTCATGGTC-TTCTTGTTTTTGCTCTTGT--T--GATCTTT---------------AG-----TCC--A------------------ACTCT----TCATACTTCTTCACTGTAAGCTTTGTT-GAT-TTT---CT-TCTGCATAATGTTGTAGT-TTGATGGCCTATTCAACG-CACATGTCATCA--GCAAAGTC-G-AGGTCATCCAG--C-TTGTAGTAAAG------T------TCACCTG-ATGCCATTCTGTCCACCTCCTAATCGC---TTTCTC---CATCCAATCCAT----------AGCCAATTT---AGGAAGA-GGAAGCCTGACATGTTA-------------C-ACCC-------CTGCTTCACCCCGG--TCTTG------A-------TTtttaaaaatatgcaagtgtaaaagttgcacatacagttgcaccaaggtatacgaacttttcaacatatttcagttcatcatcatcaaacttgatcttttcctcttgatttgcatttattctcatggtcttcttgtttttgctcttgttgatctttagtccaactcttcatacttcttcactgtaagctttgttgattttcttctgcataatgttgtagtttgatggcctattcaacgcacatgtcatcagcaaagtcgaggtcatccagcttgtagtaaagttcacctgatgccattctgtccacctcctaatcgctttctccatccaatccatagccaatttaggaagaggaagcctgacatgttacacccctgcttcaccccggtcttgatt
gi|7 : tacctatcctctgtgtgtctaaggacacgtagggcctccacagactgtctccacttagttctgtcggctgcagcagcccttgcttcccccacgttcttcgtcctccgatggtccgctccttcttcactttttgtctccaggccgccccttctttcttttgccttttggtgtccatgttgaccagtgctacattacaatcactcctgggctgcatatcttgtctcaggatgtgtccnccatgttgaccagtgctacattacaatcacttcggggctgcatatcttgtcccaggatgtgcccattattaaactttcatcttctcctgacttcactcagtggtctcatgtctacactttggagcctctcttctgtagtaatgtgttcttgccataccactaatgtcttgtataacctgattttggtgtgtcgtctgacgctgtaaagtgctccatatacctgtttcagtctgacaaaaatttactactctttattttaaaaatatgcaagtgtaaaagttgcacAACATCTT-CTAT-T-TCTATATGTCAT-TCATCTT-TATCTTTTCATC--ACTT--CTTGCGTTCATCCTCAAAA---------TTTT-GCATTT-T--T--AGTCCAG---------------TGCTTTCTGCAAACT-----TTGTTG
gi|7 : catTT-GTT-AGA-TTT---CTCT-TGAATT-TGTTGTTTTGTATATGAGATA---AGGG-CA-ATGTTGTCT--GCGTAGTC-T-GGGTCGTCCAT--CATTGTTGT--AAACT---T------CTATCTA-ATTCCGTTCTCTCCATTCCCT-ACTGT--TTTCCTC-ATTATCCAGTCCA--------------CAA-GTAGAAGGAATA-GGAATCCtgttgttagatttctcttgaatttgttgttttgtatatgagataagggcaatgttgtctgcgtagtctgggtcgtccatcattgttgtaaacttctatctaattccgttctctccattccctactgttttcctcattatccagtccacaagtagaaggaataggaatcc
gi|18 : cataacatcttctatttctatatgtcattcatctttatcttttcatcacttcttgcgttcatcctcaaaattttgcatttttagtccagtgctttctgcaaactttgttgtgTCCAG--C-TTG--GT--AG------TAAAGTTCCACCTG-ATGCCATTCTGTCCACCTCCT-AT
4 sequences could not be aligned to this particular reference sequence:
Unaligned ( gi|10 ): CATCTTCCATAGATTTGGCCTTCATCGCTATGTTTTCGTTGCATTTTTACATTCATCCGTAATACTTCACATTTGTTGATATTTACTTCCAATCCTGTGAATCCTTTGTGCGTTTAGTTTATATTCTATGTGTAATTGCCGTCTCGTGGAGGAAATAAGAGCGAGATCTGCGAAGTCGAAACCGTCTA
Unaligned ( gi|14 ): CACTCATCCCATTCACCATCCCTCATGCCTGTTGGTATAAGCCTAGTACCACTTTTCCCTGTACTTGGCGGACCACCCTGGTTTAGCCAGATTTTCCATCCTGTTGTTCTCTTAAT
Unaligned ( gi|16 ): TAATCCTTAAATCTCTCCGCCCCAGAAGCCGCATAAGGCCTCCATGCTGTTTGCCCATTCTTTCTCAT
Unaligned ( gi|19 ): ACATCATTAAACTTTCTTTGCAGTTCTNCTTGCTGACCATGTCAGTTTT
Alignments
lowQualScore : 11111111111111111111111111111111111111 111111111111111111111111111111111111111111111111111111111111111111111
lowQualScore : 222222 3333333333333333333333333333 11111 1111 1111 11 111111 222 222222 111111111 111111 11 1 11 11 111 777777777 1 1 22 1 11 22 11 111111 9999999999999999999999999999999 11 11111111 5555555555555 444444444444 1 22222 111 33333 66666666666666666666666666666666666666 2222 1 1111 2222 2222 222222 1 1 11 111 4444444 1 1 1111 555555555555555555 111111111111111111111111111111111111111111111111111111111111111111111 22
lowQualScore : 777 4 55 4 55 11 66 1 777 55 55 4 4 222222 4444444444444444444444444444 4 4 4 88 00000 4 4 4 4 4 8888 4 3333 33 111111 4 999 55 55 3 111111 4 888888888 4 55 55 7 3 88 3 3 3 55 99 6 777 4 4 4 9999 3 5 66 5 6 999999 5 5 8 11 0 8 6 66 11 8 444 8 888888888 1 5 1 8 8 6 8 3 55 6 1 8 8 8 8 11 22 8 8 55 666666 22 1 8888888888888888888888888888888 99 0 77777777 8888888888888 111111111111 8 8 6 3 99 6 6 00000 1 2 99 222 00000 11111111111111111111111111111111111111 8888 0000 8 8 6 5555 8 8 8 6666 2 0000 1 000000 8 6 6 11 777 0000000 3 3 6 6 6 88 1111 000000000000000000 8 000000000000000000000000000000000000000000000000000000000000000000000 44
lowQualScore : ... . .. . .. .. .. . ... .. .. . . ...... ............................ . . . .. ..... . . . . . .... . .... .. ...... . ... .. .. . ...... . ......... . .. .. . . .. . . . .. .. . ... . . . .... . . .. . . ...... . . . .. . . . .. .. . ... . ......... . . . . . . . . .. . . . . . . .. .. . . .. ...... .. . ............................... .. . ........ ............. ............ . . . . .. . . ..... . . .. ... ..... ...................................... .... .... . . . .... . . . .... . .... . ...... . . . .. ... ....... . . . . . .. .... .................. . ..................................................................... ..
lowQualScore : 888 0 55 0 55 66 11 1 000 55 55 4 4 666666 1111111111111111111111111111 0 0 0 99 11111 0 0 0 0 1 7777 4 9999 55 666666 0 000 55 55 4 000000 0 000000000 0 55 00 3 6 44 6 6 6 55 55 4 000 4 4 4 4444 1 0 99 0 2 444444 0 7 0 00 8 0 0 88 22 0 000 0 222222222 0 0 0 0 0 0 0 8 88 0 0 0 0 0 0 00 00 0 0 66 888888 00 4 0000000000000000000000000000000 88 6 22222222 2222222222222 000000000000 0 0 7 3 22 7 7 33333 0 2 22 888 22222 66666666666666666666666666666666666666 4444 4444 0 0 0 0000 0 0 0 2222 8 6666 4 888888 0 0 4 00 000 7777777 3 3 7 7 7 88 6666 444444444444444444 0 111111111111111111111111111111111111111111111111111111111111111111111 00
consensus : TTACCT---ATC-CTCTGCGTGCCTA--A-GGGCACATAAGGCCTCCACA--GACTGTTTCCA--CTTTGCT---CTGTCGGCT--GCAG--CAGCCCTT-G-CT-----CCCCCC-------------C-------AC----GTTC-TC-CATCCTCCGAT-GTTA-CGCTCTTTCTC----TAC-TG-TTC-GT-CTCCAGGTGGTTTTTG--GGTC-GCC----CTTT--CT---T--TCT-T---C--CTTCTGGTGCC--CACG-T----CATTGCCACATT-ACAGTCACT----G----GCT-GC--AT--CTT-G-TCT-CA-GGGT-GTGTC-CA--AT--AAACTTCCATCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTGTTC------TTGCCAT-CTTATTC-TTA-GGA--TGCGTCTTAAGCATTTGTTC-TGGAAGGTGTTTGATCATCTTTATCAC-TCCTCTATT-CATCTTCCAGGTCT---C-GCATTT-AGTTCCTATANTGTAGTANCGGTA-CCACTA-GTGTCTTGTTATAGT-CTGATTTTGGTGTTAGTCGTCTGATGATTGT-TGGTG-CT-CC-ATAT--CTGTTTTTCAG-TCTGAC-AAAAGAT-T---TCTTGCTTCTGCTAC-------------TCTTACCTTTCATGTC--GTATTACCTCCCCCTTCCTT--T---G-ATATT----------A-GTTGCAC------------CAAG-GTATACAAACT-TTTCAACATCTT-CCAGT-TCTTCAT--CAT-CAATTTT-GATCTTTTC--C--GCTTGGTTTGCATTTATTCTCACGATCT--TT-G-TTTTGCTCTTGTA-T--GATCTTTNGATTCTCCACT---CTT--TG--TCGC--T----TC-TGC-TT-CTTCACTG--G-GC-TTG-TTGGTGTT---NCT-T-T-GCAT--TCGTTGT-NT-GTTGATGGCAT--A---AACG-CACATGTCGTCA--GCGAAGTC-T-AGGTCATCCAG-CCTTG-GTAGT-AAA-TTCCACCTG-ATGCCATTCTCTCCACCTCCT-ATTGC-TTTTTCTC-GTCGTCCAATCCAT----------A-NCAA--TAGGAAGA-GGAAGCCTGACATGCTA-------------CA--------CCCCGG-------CCGG--TCTTGAA----------CATTCCA---ACCCAA-TTACTTGTCTTCT
Reference ( family-2912 ) : TTACCT---ATC-CTCTGCGTGCCTA--A-GGGCACATAAGGCCTCCACA--GACTGTTTCCA--CTTTGCT---CTGTCGGCT--GCAG--CAGCCCTT-G-CT-----CCCCCC-------------C-------AC----GTTC-TC-CATCCTCCGAT-GTTN-CGCTCTTTCTC----TAC-TG-TTC-GT-CTCCAGGTGGTTTTTG--GGTC-GCC----CTTT--CT---T--TCT-T---C--CTTCTGGTGCC--CACG-T----CATTGCCACATT-ACAGTCACT----N----GCT-GC--AT--CTT-G-TCT-CA-GGGT-GTGTC-CA--AT--AAACTTCCATCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTGTTC------TTGCCAT-CTTATTC-TTA-GGA--TGCGTCTTAAGCATTTGTTC-TGGAAGGTGTT-GATCATCTT-ATCAC-TCCTCTATT-CATCTTCCAGGTCT---C-GCATT--A------ATANTGTAGTANCGGTA-CCACTA-GTGTCTTGT-ATAGT-CTGATTTTGGTGTTAGTCGTCTGATG-TNGT-TGGTG-CT-CC-ATAT--CTGTTT--CAG-TCTGAC-AAAAGAT-T---TCTTGCTTCTGCTAC-------------TCTT--------------GTAT-ACCTCCCCCTTCCTT--T---G-ATAT-----------A-GTTGCAC------------CAAG-GTATACAAACT-TTTCAACATCTT-CCAGT-TCTTCAT--CAT-CAATTTT-GATCTTTTC--C--GCTTGGTTTGNATTTATTCTCACGATCT--TT-G-TTTTGCTCTTGTA-T--GATCTTTCGNTTCTNCACT---CTTGTTG--TCGC-CT----TC-TGC-TT-CTTCACTG--G-GC-TTG-TTGGT-TT---NCT-T-T-GCAT--TCGTCGT-NT-GTTGATGGCAT--A---AACG-CA-ATGTCGTCA--GCGAAGTC-N-AGGTCATCCAGACCTTGTGTAGT-AAA-TTCCATCTG-ATGCCATTCTCTCCATCTCCT-ATTGC-TTTTTCTC-GTCGTCCAATCCAT----------A-NCAA--TAGGAAGA-GGAAGCCTGACATGCTA-------------CA--------CCCCGG-------CCGG--TCTTGAA----------CGTTCCATANACCCAACCTACTTGTCTTCT
gi|1 : CCT---ATC-CTCTGTGTGCCTATTACGGGCACATAAG-CCTCCACA--GACTGTTTCCA--CTTT-CT---CTGTCGTCT--GCAG--CAGCCCTTTG-CTTTTTTCCCCAA-------------C-------AT----TTTC-TC-CAGCCTC-GAT-GTTA-CGCTCTTTCT-----TACCTG-TTC-TT-CTTCAGGTTGTTTT----GGTCTGCC----CTTTT-CT---TCTTCT-T---C--CTTCTGGTGCC--CACGAC----CATTGCCACATTTACAGTCACT----G----GCTTGC--AT--CTTTG-TCGGCA-GGGT-GTGTTTCA--AT--AA-TTTCCATCTT---TTTCTTCCTGACTTCTTCA-TCAGCTGGT-TTTCTGCATTTTCTACACT--TTGG-AGC-TCTCTTCTGTAGTAGTGTGTTC------ATGC-AT-CTTATTC-TTA-GGA--TGCGTCTTA-GCATTTGTTCCTGGAAGGTGTTTGATCATCTTTATCAC-TCCTCTATT-CATCTTCCAG-TCT---CCGCATTTAAGTTCCTATAGTGTA--AGCGGTA-CCACTA-GTGTCTTGTTATAGT-CTG-TTTTGGTGTTAGTCGTCTGATAATGGT-TGGTG-CTTCC-ATAT--CTGTTTTTCAGGTCTGACCAAAAGAT-T---TCTTGCTTCTGCTAC-------------TCTTACCTTTCATGTCATGTATTACCTCCCCCTTCCTTATT---G-ATATT----------A-GTTGCAC--------------AG-TTATACAAACT-TTTCAACATCTTTCCAGAATCTTCAT--CAT-CAATTTTTGATTTTTTT--CTTGCTTGGTTTTGATTTATTCTTACGATCT--TT-A-TTTTGCTCTTGTATT--GATCTTTCAATCCT--ACT---CTT------TCG-----------TGCTTT-CTTCACT---G-GC-TTGTTTGGTGTTGACCTT-T-T-GCAT--TCTTCGT--T-GTTGTTGGCAT--C---AACGACA-AT-TC-TCA--GTGAAGTCTT-AGGTCATCCAGACTTTG-GTAGTAAAA-TTCCATCTGTATGCCATT-TCTCCATCTCCT-ATTGCTTTTTTCTT-ATCGTCCAATCCAT----------T-TGAA--TAGGAAGA-GAAAGCCTGACATGCTA-------------TAATCCTTTGCTTCAC-------CCGG--TCTTGAAGATTCGAAATCATTCCA-AAACCCAA-CTACTTGTCTTCT
gi|11 : ttTACCTTAAATCTCTCTGCA--CCAG--A-AGTTGCATAAGGCCTCCACGCTGACTG--CCCATTCTTTCCTATCCTGT--GCT--GCTGTTCTGGCCAT-G-TT---------CC-------------A-------AC-----TTG-TC-CATCCT-TGTTGGTTT-CTTTCTTTCAC----TGT-TG-TTC-TT-CTCCAAGTTG-TTTTG--GGCC-TGC----CTCTAGCT---T--TTT-TC--C--CTTCTGG
gi|12 : TTACCT---ATC-CTCTGCGTGTCTA--A-GGGCAGATAAGGCCTCCACA--GACTGTGTCCA--CTTTGCT---CTGCCAGCT--GCAG--CAGCCCTT-GCCC-----CCCCCC-------------C-------CC----CCCC-CC-CATCCTCCGAT-GTTA-CGCTCTTTCTCTAGATAC-TG-TTC-GT-CTCCAGGTGGTTTTTG--Gag
gi|13 : gT--CTT-G-TCG-CA-GGAT-GTGTT-CA--AA--AAATTTCCATCTT---CTTCT-CCTGACTTCTTCANACA--TTGC-CA----CAT----TACAGTCACTGGTTGCATCTTGTC-GCAG-GGTGTGTTCAATAAATTTCCAT-CTTTTTC-Tt
gi|13 : TTT--CC---A--TCT-T---CTTCTCCTGACTTCTTCANA------CATTGCCACATT-ACAGTCACT----G----GTT-GC--AT--CTT-G-TCG-CA-GGGT-GTGTT-CA--AT--AAATTTCCATCTT---TTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATcctgacttcttcactcagtggtctcat
gi|15 : tcttgtcgcaggatgtgttcaaaaaaTTACCT---ATT-CTTTGCGTGCCTA--A-GGGCACATAAGGCATCCACA--GACTGCTTCCA--CTTTGCT---CTTTCGGCT--GTAG--CAGCC
gi|17 : TTACCT---ATC-CTCTGTGTGCCTT--A-GGGCACATAAGGCCTCCACA--GACTGTTTCCt
gi|18 : gTCCAG--CTTG-GTAGT-AAAGTTCCACCTG-ATGCCATTCTGTCCACCTCCT-AT
gi|2 : CT---CTGTCGTCT--GCAG--CAGCCCTT-G-CTTTTT-CCCCAA-------------C-------AT----TTTC-TC-CCACCTCGGAT-GTTATCGCTCTTTCT-----TAC-TG-TTC-TTTCTTCAGGTGGTTTT-G--GGTC-GCCG---CTTT--CT---TCTTCT-TG--C--CTTCTGGTGCC--CA-G-A----CATTGCCACATT-ACAGTCACT----G----CTT-GC--AT--CTTTG-TCGGCACGGGT-GT-TT-CA--AT--AAA-TTCCATCTTTTTCTTCT-CCTGACTTCTTCACTCAG-TGGTTCT----CATTT-CTACACT--TTGG-AGC-TCTCTTCTGTAGT-GTGTGTTCA-----TTGCCAT-CTTATTCGTTATGGAATCGCGTCTTAAGCATTTGTTC-TGGAAGGTGTTTGATCATCTTTATCAC-TCCTCTATTTCATCTTCCAGGTCCTGCC-GCATTT-AGTTCCTATAGTGTA-TAGCGGTATCCACTAAGTGTCTTGTTATAGTGCTCGTTTTGGTGTTAGTCGTCTGATAATGGT-TGGTGGCT-CCGATAT--CTGTTTTTCAG-TCTGAC-AAA-GAT-T---TCTTGCTTCTGCTAC-------------TCTTACCTTTCATGTCT-GTATTACCTCCCCCTTCCTT--T---GGATATT----------ACGTTGCAC------------CAAGTGTATACAAACTGTTTCAACATCTT-CCAGAATCTTCAT--CATGCAATTTT-GATTTTTTC--TT-GCTTGGTTTTGATTTATCTTAACGATCT--TTTA-TTTTGCTCTTGTA-TTGGATCTTT--AATCGCTACT---CTT--TG--T--------------GT-TT-CTTCACTG--AAGC-TTG-TTGGTGTT---GCT-T-TTGCAT--C--TTGT-GT-GTTGTTGGCATCAA---GACA-CACATGTC-TCAATGTGAAGTC-TGAGGTCATCCAGACTTTG-GTAGTAAAA-TTCCATCTG-ATGCCATT-TCTCCATCTCCT-ATTGC-TTTTTCTTAGTCGTCCAATCCATTTGTAAAACAA-ACAA--TAGGAAGACGGAAGCCTGACATGCTATAATCCTTTGCTTCA--------CCCCGG-------CTTGAAGATTGAAT---------CATTCCAT--ACCCAACTTACTTGTCTTC
gi|3 : tTTACCT---ATC-TTCTGCGTGCCTA--A-GGGCACATAAGGCCTCCACA--GACTGTCTCCA--CTCTGTT---CTGTCGGCT--GCAG--CAGCCCTT-G-CT-----TCCCCC-------------C-------AC----GTTC-TC-CATCCTCCGAT-GTTC-TGCTCTTTCTC----TAT-CG-TTC-GT-CTCCAGGTGGTTCTTGCAGATC-ACC----CTTT--CT---T--TCT-T---C--CTTCTGGTGCC--CATG-T----CATTGCTATATT-GCAATCATT----C----GCT-GC--AT--CTT-G-TGT-CA-GGGT-ATGTC-CA--AT--AAACTTCCATCTT---CTTCT-CTTGACTTCTTCATTCAG-GGGT-CT----CATGT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTGTCC------TTGCCAT-CTTATTC-TCA-GGA--TCCGTCTTAAGCATTTGTTC-TGGAAGGTGTT-GATCATCTT-ATCATGTCCTCTATT-CATCTTCCAAGTCT---C-ACATT--A------ATATTGTAGTACCGGTA-CCACTA-GCGTTTTGT-ATAGT-CTGATTTTGGTGT--GTCGTCTGATG-TTGT-TAGTG-TT-CC-ATAT--CTGTTT--CAG-TCTGAC-AAAAGATGC---TCAAGCTTTTGCTAC-------------TCTT--------------GTAT-GCCGCCCCCTTTCTT--T---G-ATAT-----------A-GTTGCAC------------CAAG-GCATACAAACT-TTTCAACATCTT-CCAGT-TCTTAAT--CAT-CAATTGT-GATCTTTTC--C--GCTTGATTTGCATTTATTATCATGATCT--TT-G-TTTTGCTCTTGT--T--GATCTCTTGCTTCTTCACTGGGCTTGTTGGTTTGCNCTGATATCTTGC-TT-CTTCACTG--G-GC-TTG-TTGGT-TT---GCT-T-T-GCAT--GTGTTGTCTT-GTTGATGACAT--A---AACG-CA-ATGTCATCA--GCGAAGTC-G-AGGTCATCCAG--CTTG-GTAG-------TCCACCTG-ATGCCATTCTCTCCACCTACT-ATTGC--TTTTCTC-GTCGTCCAATCCAT----------A-GCAAC-TAGGAATA-GGGACCCTGACATGTTA-------------CA--------TCCCGG-------CCGG--TCTTG------------C-TTCCA---AACCAA-TTACTTGTTTTTT
gi|4 : TACCT---ATC-CTCTGTGTGTCTA--A-GGACACGTAGGGCCTCCACA--GACTGTCTCCA--CTTAGTT---CTGTCGGCT--GCAG--CAGCCCTT-G-CT------TCCCC-------------C-------AC----GTTC-TT-CGTCCTCCGAT-GGTC-CGCTCCTTCTT----CAC-TT-TTT-GT-CTCCA-------------GGCC-GCC----CCTT--CT---T--TCT-TTTGC--CTTTTGGTGTC--CATG-TTGACCAGTGCTACATT-ACAATCACTCCTGG----GCT-GCATAT--CTT-G-TCT-CA-GGAT-GTGTC-C
gi|4 : C--CATG-TTGACCAGTGCTACATT-ACAATCACT----TCGGGGCT-GC--ATATCTT-G-TCC-CA-GGAT-GTGCC-CATTATT-AAACTTTCATCTT---CT----CCTGACTTC---ACTCAG-TGGT-CT----CATGT-CTACACT--TTGG-AGCCTCTCTTCTGTAGTAATGTGTTC------TTGCCAT-nccatgttgaccagtgctacattacaatcacttcggggctgcatatcttgtcccaggatgtgcccattattaaactttcatcttctcctgacttcactcagtggtctcatgtctacactttggagcctctcttctgtagtaatgtgttcttgccataccactaatgtcttgtataacctgattttggtgtgtcgtctgacgctgtaaagtgctccatatacctgtttcagtctgacaaaaatttactactctttattttaaaaatatgcaagtgtaaaagttgcacatacagttgcaccaaggtatacgaacttttcaacatatttcagttcatcatcatcaaacttgatcttttcctcttgatttgcatttattctcatggtcttcttgtttttgctcttgttgatctttagtccaactcttcatacttcttcactgtaagctttgttgattttcttctgcataatgttgtagtttgatggcctattcaacgcacatgtcatcagcaaagtcgaggtcatccagcttgtagtaaagttcacctgatgccattctgtccacctcctaatcgctttctccatccaatccatagccaatttaggaagaggaagcctgacatgttacacccctgcttcaccccggtcttgatt
gi|4 : tacctatcctctgtgtgtctaaggacacgtagggcctccacagactgtctccacttagttctgtcggctgcagcagcccttgcttcccccacgttcttcgtcctccgatggtccgctccttcttcactttttgtctccaggccgccccttctttcttttgccttttggtgtccatgttgaccagtgctacattacaatcactcctgggctgcatatcttgtctcaggatgtgtccnTA-CCACTA-ATGTCTTGT-ATAAC-CTGATTTTGGTGT--GTCGTCTGACG-CTGTAAAGTG-CT-CC-ATATACCTGTTT--CAG-TCTGAC-AAAA-AT-T------------TACTAC-------------TCTT---------------TAT--------------TT--TAAAA-ATATGCAAGTGTAAAA-GTTGCACATACAGTTGCACCAAG-GTATACGAACT-TTTCAACATATT-TCAGT-TCATCAT--CAT-CAAACTT-GATCTTTTC--C--TCTTGATTTGCATTTATTCTCATGGTCTTCTT-GTTTTTGCTCTTGT--T--GATCTTTAG--TCCA-ACT---CT-------TCA-----------TAC-TT-CTTCACTGTAA-GCTTTG-TTGAT-TT---TCT-TCT-GCATAAT-GTTGT-AG-TTTGATGGCCT--ATTCAACG-CACATGTCATCA--GCAAAGTC-G-AGGTCATCCAG--CT--TGTAGT-AAA-GTTCACCTG-ATGCCATTCTGTCCACCTCCTAATCGC-TTTCTC-----CATCCAATCCAT----------AGCCAATTTAGGAAGA-GGAAGCCTGACATGTTA-------------CA--------CCCCTGCTTCACCCCGG--TCTTGAaccactaatgtcttgtataacctgattttggtgtgtcgtctgacgctgtaaagtgctccatatacctgtttcagtctgacaaaaatttactactctttattttaaaaatatgcaagtgtaaaagttgcacatacagttgcaccaaggtatacgaacttttcaacatatttcagttcatcatcatcaaacttgatcttttcctcttgatttgcatttattctcatggtcttcttgtttttgctcttgttgatctttagtccaactcttcatacttcttcactgtaagctttgttgattttcttctgcataatgttgtagtttgatggcctattcaacgcacatgtcatcagcaaagtcgaggtcatccagcttgtagtaaagttcacctgatgccattctgtccacctcctaatcgctttctccatccaatccatagccaatttaggaagaggaagcctgacatgttacacccctgcttcaccccggtcttgatt
gi|5 : tacctatcctctgtgtgtctaaggacacgtagggcctccacagactgtctccacttagttctgtcggctgcagcagcccttgcttcccccacgttcttcgtcctccgatggtccgctccttcttcactttttgtctccaggccgccccttctttcttttgccttttggtgtccatgttgaccagtgctacattacaatcactcctgggctgcatatcttgtctcaggatgtgtccnccatgttgaccagtgctacattacaatcacttcggggctgcatatcttgtcccaggatgtgcccattattaaactttcatcttctcctgacttcactcagtggtctcatgtctacactttggagcctctcttctgtagtaatgtgttcttgcca-CTCTGCGTGGCTA--A-GGGCACATAAGGCTTTCACA--GACTGCTTCCA--CTTTGCT---AT-TCGGCT--GCAG--CAGCCCTT-G-CT-----CCCCCCACCCCCCACCCCCC-------AC----GTTC-TC-CATCCTCCGAT-GTTA-CGCTCTTTCTC----TAC-TG-TTC-GT-CTCCAGGTGGTTTTT---GGTC-GCC----CTTT--CTTTCT--TCT-T---C--CTTCTGGTGCC--CACG-T----CATTGCCACTTT-ACAGTCATT----G----GCT-GG--AT--CTT-G-TCT-CG-GGGT-GTGTC-CA--AT--AAACTTCCATCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGT-TT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTCTTT------TTGCCAT-CTTATTC-TTA-GAA--TGCGTCTTAAGCATTTGTTC-TGGAAAGTGTT-GATCGTCTT-AT--C-TCCTCTATT-CATATTCCAGGTCT---C-GCATC--C------ATATAGTAGTACCGGTA-CTACTA-GTGTCTTGT-ATAGT-CCGATTTTGGTGT--GTCGTCTGATG-TTGT-TGGTG-CT-CC-ATAT--CTATTT--CAG-TCTGAT-AAA--AT-TTGCTCTTGCTTTTGCTACTCTTCATTTCATGTCTT--------------GTAT-ACCTCCCCCTTCCTT--T---G-ATAT-----------T-GTTGCAC------------CAAG-GTATACAAACT-TTTTAACATCTT-CCAGT-TCTTCAT--AAT-CAATTGT-GATCTTTTC--T--GCTTGGTTTGTATTTATTCTTATGATCT--TT-G-TTTTGCTCTTGtt
gi|6 : tTTACCT---ATC-TTCTGCGTGCCTG--A-GGGCAC-TAAGGCCTCCACA--GACTGTCTCCA--CACTGCT---CTGTCGGCT--ACAG--CACCTCTT-G-CC-----CCCCCC-------------CCCCACCCACCCCAATTC-TC-CATCCTTCGAT-GTTC-CGCTCTTTCTC----TAC-CG-TTC-GT-CACCAGGTGGTTTTTG--A-TC-GCCATTTCTTT--CT---T--TCT-TTTTC--CTTCTGGTGCC--CACG-T----CATTGCTATATT-ACAATCACT----C----CCT-GC--AT--CT--G-CCT-CA-GGGT-GTGTT-CA--GT--AAATTTCCATCT----CTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTG-TC------TCGTCGTCCTTATTC-TCA-GGA--TGCGTCTTAAGCATTTGTTC-TGGAAGGTGTT-GATCATTTT--TCA---TCTCTATT-CATCTTCCAGGTCT---C-GCAT
gi|7 : ctgAACATCTT-CTATT-TCTATATGTCAT-TCATCTT-TATCTTTTCATC--ACTT--CTTGCGTTCATCCTCAAAAT----------TTTGC------------ATTTTTAG----TCCA-----------G--T-GC-TT----TC-TGC-AAACTTTGTTG--T-G--TTG-TTAGA-TT---TCTCT-T-GAAT--TTGTTGT-TTTGTATATGAGAT--A---AGGG-CA-ATGTTGTCT--GCGTAGTC-T-GGGTCGTCCA--TCAT-TGTTGT-AAACTTCTATCTA-ATTCCGTTCTCTCCATTCCCT-ACTG--TTTTCCTC-ATTATCCAGTCCACA---------A-GTAG--AAGGAATA-GGAATCCc
gi|8 : cat-----CCCCCC-------------C-------CC----GTTC-TCTCACCCTCCGAT-GT-A-CGCTCTTTCTC----TAC-TGTTTC-GT-ATCCA-GTGGTTTTT---GGTC-GCC----CTTTC-CT---T--TCTCT---C--CTTCTGGTGCC--CACG-T----CATTGCCACATT---AGTCATT----G----GTT-GG--AT--CTT-G-TCT-CA-GGGTAATGTC-CA--AT--GAACTTCCACCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGC-CT----CATTT-CTACTCT--TTGG-AGCATCTCTTCTGTAGTAGTATGTTC------TTGTTAT-CTTATTC-
gi|9 : cCCA---ATC-CTCTTCATACCTG--T-TGGCATATAAGGCC----------CTAGTTCCA--CTTTTCC---CTGTC--CTTGGCGA--CCACCCTG-G-TT-----GTACCC-------------C-------A-----GCTCTTC-CATC--CCA---GTT---GTTCTTTTTC----TGT-TG-TTCTGT-GT-CATGTTGTTTTT----GCC-TTC----CTAT--CT---T--TCT-TTTCC--CATCTGGTCTC--CAGG-T----CAGTTCAACTGC-ACAAT-GCT----T----GAT-GC--TT--TTC-ATTCT-CA-GCAC-GTGAC-CA--ATCCAAA--TCCATCTT---CTTc
4 sequences could not be aligned to this reference sequence:
Unaligned ( gi|10 ): CATCTTCCATAGATTTGGCCTTCATCGCTATGTTTTCGTTGCATTTTTACATTCATCCGTAATACTTCACATTTGTTGATATTTACTTCCAATCCTGTGAATCCTTTGTGCGTTTAGTTTATATTCTATGTGTAATTGCCGTCTCGTGGAGGAAATAAGAGCGAGATCTGCGAAGTCGAAACCGTCTA
Unaligned ( gi|14 ): CACTCATCCCATTCACCATCCCTCATGCCTGTTGGTATAAGCCTAGTACCACTTTTCCCTGTACTTGGCGGACCACCCTGGTTTAGCCAGATTTTCCATCCTGTTGTTCTCTTAAT
Unaligned ( gi|16 ): TAATCCTTAAATCTCTCCGCCCCAGAAGCCGCATAAGGCCTCCATGCTGTTTGCCCATTCTTTCTCAT
Unaligned ( gi|19 ): ACATCATTAAACTTTCTTTGCAGTTCTNCTTGCTGACCATGTCAGTTTT
Alignments
lowQualScore : 11111111111111111111111111111111111111 11111111111111111111111111111111111111111111111111111111111
lowQualScore : 222222 3333333333333333333333333333 11111 1111 1111 11 111111 222 222222 1111 111111 11 2 1111111 1111 11111 33333333 1 3333333333 11 22 2 11 11 111111 1 33 1 11 1 1 22222 1111 33333 44444444444444444444444444444444444444 222 111111 2222 2222 222222 1 1 11 111 222 1 1 1111 555555555555555555 00000000000000000000000000000000000000000000000000000000000 2222 1
lowQualScore : 777 4 55 4 55 11 66 1 777 55 55 4 4 222222 4444444444444444444444444444 4 4 4 99 00000 4 4 4 4 4 8888 4 3333 33 111111 4 999 55 55 3 111111 4 7777 4 55 55 7 3 88 3 3 3 55 99 6 777 4 4 4 9999 3 5 66 5 6 999999 5 5 8 11 0 8 0 7 0000000 99 99 6 4444 5 11111 22 33333333 1 0 1 5555555555 8 8 11 8 3 55 0 0 8 8 8 8 11 11 0 8 8 0 55 666666 22 1 5 2 77 5 33 0 3 88 8 8 6 3 99 6 6 00000 1 2 0000 6 00000 1 66666666666666666666666666666666666666 8888 000 8 8 99 999999 8 6666 0000 1 000000 0 6 11 666 222 3 3 6 6 6 88 1111 000000000000000000 8 00000000000000000000000000000000000000000000000000000000000 7 2222 3
lowQualScore : ... . .. . .. .. .. . ... .. .. . . ...... ............................ . . . .. ..... . . . . . .... . .... .. ...... . ... .. .. . ...... . .... . .. .. . . .. . . . .. .. . ... . . . .... . . .. . . ...... . . . .. . . . . ....... .. .. . .... . ..... .. ........ . . . .......... . . .. . . .. . . . . . . .. .. . . . . .. ...... .. . . . .. . .. . . .. . . . . .. . . ..... . . .... . ..... . ...................................... .... ... . . .. ...... . .... .... . ...... . . .. ... ... . . . . . .. .... .................. . ........................................................... . .... .
lowQualScore : 888 0 55 0 55 66 11 1 000 55 55 4 4 666666 1111111111111111111111111111 0 0 0 77 11111 0 0 0 0 1 7777 4 9999 55 666666 0 000 55 55 4 000000 0 0000 0 55 00 3 6 44 6 6 6 55 55 4 000 4 4 4 4444 1 0 99 0 2 444444 0 7 0 00 8 0 4 3 5555555 22 22 7 2222 2 88888 55 22222222 0 0 0 0000000000 0 0 44 0 8 88 4 6 0 0 0 0 00 22 8 0 0 8 88 888888 00 4 5 5 55 5 88 0 2 88 0 0 7 3 22 7 7 33333 0 2 8888 7 22222 0 22222222222222222222222222222222222222 4444 444 0 0 00 444444 0 2222 6666 4 888888 0 4 00 666 222 3 3 7 7 7 88 6666 444444444444444444 0 44444444444444444444444444444444444444444444444444444444444 3 7777 3
consensus : TTACCT---ATC-CTCTGCGTGCCTA--A-GGGCACATAAGGCCTCCACA--GACTGTTTCCA--CTTTGCT---CTGTCGGCT--GCAG--CAGCCCTT-G-CT-----CCCCCC-------------C-------AC----GTTC-TC-CATCCTCCGAT-GTTA-CGCTCTTTCTC----TAC-TG-TTC-GT-CTCCAGGTGGTTTTTG--GGTC-GCC----CTTT--CT---T--TCT-T---C--CTTCTGGTGCC--CACG-T----CATTGCCACATT-ACAGTCACT----GGCT-GC--AT--CTT-G-TCT-CA-GGGT-GTGTC-CA--AT--AAACTTCCATCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTGTTC------TTGCCAT-CTTATTC-TTA-GGA--TGCGTCTTAAGCATTTGTT-CTGGAAGGTGTTTGATCATCTTTATCAC-TCCT--CT--A-TTCA----TCTTCCAGGTC---T-CGCATTT---AGTTCCTATANTGTAGTANCG----------GTA-CCACT-AGTGTCTTGTTATAGT-CTGATTTTGGTGTTAGTCGTCTGATGATTGTTG-GT-GC-TCC-ATAT--CTGTTTTTCA-GTCTGA-CAAAAGAT-T---TCTTGCTTCTGCTACTCTTACCTTTCATGTCTTGTATTACCTCCCCCTTCCT--TT-GATATTA-GTTGCACCAAG-GTATACAAACT-TTTCAACATC-TTCCAG-TTCTTCAT--CAT-CAA-TTTTGATCTTTTC--C--GCTTGGTTTGCATTTATTCTCACGATC-T--TTG-TTTTGCTCTTGTA-T--GATCTTTAG-TTCTCC-ACT---CT--TCG--T-GC-------T-C-TGC-TT-CTTCACTG--GGC-TTG-TTGGTGTT---NC-T-TTGCAT--TCGTTGT-NT-GTTGATGGCAT--A---AACGCACATGTCGTCA--GCGAAGTC-T-AGGTCATCCAG-CTTTGGTAGT-AAA-TTCCACCTG-ATGCCATTCTCTCCACCTCCT-ATTGC-TTTTTCTC-GTCGTCCAATCCAT----------A-NCAA--TAGGAAGA-GGAAGCCTGACATGCTA-------------CA--------CCCCGG-------CCGG--TCTTGAA----------CATTCC--A-ACCCAA-TTACTTGTCTTCT
Reference ( family-2912 ) : TTACCT---ATC-CTCTGCGTGCCTA--A-GGGCACATAAGGCCTCCACA--GACTGTTTCCA--CTTTGCT---CTGTCGGCT--GCAG--CAGCCCTT-G-CT-----CCCCCC-------------C-------AC----GTTC-TC-CATCCTCCGAT-GTTA-CGCTCTTTCTC----TAC-TG-TTC-GT-CTCCAGGTGGTTTTTG--GGTC-GCC----CTTT--CT---T--TCT-T---C--CTTCTGGTGCC--CACG-T----CATTGCCACATT-ACAGTCACT----GGCT-GC--AT--CTT-G-TCT-CA-GGGT-GTGTC-CA--AT--AAACTTCCATCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTGTTC------TTGCCAT-CTTATTC-TTA-GGA--TGCGTCTTAAGCATTTGTT-CTGGAAGGTGTTTGATCATCTTTATCAC-TCCT--CT--A-TTCA----TCTTCCAGGTC---T-CGCATTT---AGTTCCTATANTGTAGTANCG----------GTA-CCACT-AGTGTCTTGTTATAGT-CTGATTTTGGTGTTAGTCGTCTGATGATTGTTG-GT-GC-TCC-ATAT--CTGTTTTTCA-GTCTGA-CAAAAGAT-T---TCTTGCTTCTGCTACTCTTACCTTTCATGTC--GTATTACCTCCCCCTTCCT--TT-GATATTA-GTTGCACCAAG-GTATACAAACT-TTTCAACATC-TTCCAG-TTCTTCAT--CAT-CAA-TTTTGATCTTTTC--C--GCTTGGTTTGCATTTATTCTCACGATC-T--TTG-TTTTGCTCTTGTA-T--GATCTTTNGATTCTCC-ACT---CT--TTG--TCGCT------T-C-TGC-TT-CTTCACTG--GGC-TTG-TTGGTGTT---NC-T-TTGCAT--TCGTTGT-NT-GTTGATGGCAT--A---AACGCACATGTCGTCA--GCGAAGTC-T-AGGTCATCCAG-CCTTGGTAGT-AAA-TTCCACCTG-ATGCCATTCTCTCCACCTCCT-ATTGC-TTTTTCTC-GTCGTCCAATCCAT----------A-NCAA--TAGGAAGA-GGAAGCCTGACATGCTA-------------CA--------CCCCGG-------CCGG--TCTTGAA----------CATTCC--A-ACCCAA-TTACTTGTCTTCT
gi|1 : CCT---ATC-CTCTGTGTGCCTATTACGGGCACATAAG-CCTCCACA--GACTGTTTCCA--CTTT-CT---CTGTCGTCT--GCAG--CAGCCCTTTG-CTTTTTTCCCCAA-------------C-------AT----TTTC-TC-CAGCCTC-GAT-GTTA-CGCTCTTTCT-----TACCTG-TTC-TT-CTTCAGGTTGTTTT----GGTCTGCC----CTTTT-CT---TCTTCT-T---C--CTTCTGGTGCC--CACGAC----CATTGCCACATTTACAGTCACT----GGCTTGC--AT--CTTTG-TCGGCA-GGGT-GTGTTTCA--AT--AA-TTTCCATCTT---TTTCTTCCTGACTTCTTCA-TCAGCTGGT-TTTCTGCATTTTCTACACT--TTGG-AGC-TCTCTTCTGTAGTAGTGTGTTC------ATGC-AT-CTTATTC-TTA-GGA--TGCGTCTT-AGCATTTGTTCCTGGAAGGTGTTTGATCATCTTTATCAC-TCCT--CT--A-TTCA----TCTTCCA-GTC---TCCGCATTTA--AGTTCCTATAGTGTA--AGCG----------GTA-CCACT-AGTGTCTTGTTATAGT-CTG-TTTTGGTGTTAGTCGTCTGATAATGGTTG-GT-GCTTCC-ATAT--CTGTTTTTCAGGTCTGACCAAAAGAT-T---TCTTGCTTCTGCTACTCTTACCTTTCATGTCATGTATTACCTCCCCCTTCCTTATT-GATATTA-GTTGCAC--AG-TTATACAAACT-TTTCAACATCTTTCCAGAATCTTCAT--CAT-CAATTTTTGATTTTTTT--CTTGCTTGGTTTTGATTTATTCTTACGATC-T--TTA-TTTTGCTCTTGTATT--GATCTTTCAATCCT---ACT---CT--T----TCG------------TGCTTT-CTTCACT---GGC-TTGTTTGGTGTTGACCT-T-TTGCAT--TCTTCGT--T-GTTGTTGGCAT--C---AACG-ACAATTC-TCA--GTGAAGTCTT-AGGTCATCCAGACTTTGGTAGTAAAA-TTCCATCTGTATGCCATT-TCTCCATCTCCT-ATTGCTTTTTTCTT-ATCGTCCAATCCAT----------T-TGAA--TAGGAAGA-GAAAGCCTGACATGCTA-------------TAATCCTTTGCTTCAC-------CCGG--TCTTGAAGATTCGAAATCATTCCAAA-ACCCAA-CTACTTGTCTTCT
gi|11 : ttTACCTTAAATCTCTCTGCA--CCAG--A-AGTTGCATAAGGCCTCCACGCTGACTG--CCCATTCTTTCCTATCCTGT--GCT--GCTGTTCTGGCCAT-G-TT---------CC-------------A-------AC-----TTG-TC-CATCCT-TGTTGGTTT-CTTTCTTTCAC----TGT-TG-TTC-TT-CTCCAAGTTG-TTTTG--GGCC-TGC----CTCTAGCT---T--TTT-TC--C--CTTCTGG
gi|12 : TTACCT---ATC-CTCTGCGTGTCTA--A-GGGCAGATAAGGCCTCCACA--GACTGTGTCCA--CTTTGCT---CTGCCAGCT--GCAG--CAGCCCTT-GCCC-----CCCCCC-------------C-------CC----CCCC-CC-CATCCTCCGAT-GTTA-CGCTCTTTCTCTAGATAC-TG-TTC-GT-CTCCAGGTGGTTTTTG--Gag
gi|13 : gT--CTT-G-TCG-CA-GGAT-GTGTT-CA--AA--AAATTTCCATCTT---CTTCT-CCTGACTTCTTCANACA--TTGC-CA----CAT----TACAGTCACTGGTTGCATCTTGTC-GCAG-GGTGTGTTCAATAAATTTCCAT-CTTTTTC-Tt
gi|13 : TTT--CC---A--TCT-T---CTTCTCCTGACTTCTTCANA------CATTGCCACATT-ACAGTCACT----GGTT-GC--AT--CTT-G-TCG-CA-GGGT-GTGTT-CA--AT--AAATTTCCATCTT---TTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATcctgacttcttcactcagtggtctcat
gi|15 : tcttgtcgcaggatgtgttcaaaaaaTTACCT---ATT-CTTTGCGTGCCTA--A-GGGCACATAAGGCATCCACA--GACTGCTTCCA--CTTTGCT---CTTTCGGCT--GTAG--CAGCC
gi|17 : TTACCT---ATC-CTCTGTGTGCCTT--A-GGGCACATAAGGCCTCCACA--GACTGTTTCCt
gi|18 : gTCCAG-C-TTGGTAGT-AAAGTTCCACCTG-ATGCCATTCTGTCCACCTCCT-AT
gi|2 : CT---CTGTCGTCT--GCAG--CAGCCCTT-G-CTTTTT-CCCCAA-------------C-------AT----TTTC-TC-CCACCTCGGAT-GTTATCGCTCTTTCT-----TAC-TG-TTC-TTTCTTCAGGTGGTTTT-G--GGTC-GCCG---CTTT--CT---TCTTCT-TG--C--CTTCTGGTGCC--CA-G-A----CATTGCCACATT-ACAGTCACT----GCTT-GC--AT--CTTTG-TCGGCACGGGT-GT-TT-CA--AT--AAA-TTCCATCTTTTTCTTCT-CCTGACTTCTTCACTCAG-TGGTTCT----CATTT-CTACACT--TTGG-AGC-TCTCTTCTGTAGT-GTGTGTTCA-----TTGCCAT-CTTATTCGTTATGGAATCGCGTCTTAAGCATTTGTT-CTGGAAGGTGTTTGATCATCTTTATCAC-TCCT--CT--ATTTCA----TCTTCCAGGTCCTGC-CGCATTT---AGTTCCTATAGTGTA-TAGCG----------GTATCCACTAAGTGTCTTGTTATAGTGCTCGTTTTGGTGTTAGTCGTCTGATAATGGTTG-GTGGC-TCCGATAT--CTGTTTTTCA-GTCTGA-C-AAAGAT-T---TCTTGCTTCTGCTACTCTTACCTTTCATGTCT-GTATTACCTCCCCCTTCCT--TTGGATATTACGTTGCACCAAGTGTATACAAACTGTTTCAACATC-TTCCAGAATCTTCAT--CATGCAA-TTTTGATTTTTTCT-T--GCTTGGTTTTGATTTATCTTAACGATCTT--TTA-TTTTGCTCTTGTA-TTGGATCTTTAA--TCGCT-ACT---CT--TTG-----------------TGT-TT-CTTCACTGA-AGC-TTG-TTGGTGTT---GCTT-TTGCAT--C--TTGT-GT-GTTGTTGGCATCAA---GACACACATGTC-TCAATGTGAAGTC-TGAGGTCATCCAGACTTTGGTAGTAAAA-TTCCATCTG-ATGCCATT-TCTCCATCTCCT-ATTGC-TTTTTCTTAGTCGTCCAATCCATTTGTAAAACAA-ACAA--TAGGAAGACGGAAGCCTGACATGCTATAATCCTTTGCTTCA--------CCCCGG-------CTTGAAGATTGAAT---------CATTCC--ATACCCAACTTACTTGTCTTC
gi|3 : tTTACCT---ATC-TTCTGCGTGCCTA--A-GGGCACATAAGGCCTCCACA--GACTGTCTCCA--CTCTGTT---CTGTCGGCT--GCAG--CAGCCCTT-G-CT-----TCCCCC-------------C-------AC----GTTC-TC-CATCCTCCGAT-GTTC-TGCTCTTTCTC----TAT-CG-TTC-GT-CTCCAGGTGGTTCTTGCAGATC-ACC----CTTT--CT---T--TCT-T---C--CTTCTGGTGCC--CATG-T----CATTGCTATATT-GCAATCATT----CGCT-GC--AT--CTT-G-TGT-CA-GGGT-ATGTC-CA--AT--AAACTTCCATCTT---CTTCT-CTTGACTTCTTCATTCAG-GGGT-CT----CATGT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTGTCC------TTGCCAT-CTTATTC-TCA-GGA--TCCGTCTTAAGCATTTGTT-CTGGAAGGTG-TTGATCATC-TTATCATGTCCT--CT--A-TTCA----TCTTCCAAGTC---T-CACA-TT---A------ATATTGTAGTACCG----------GTA-CCACT-AGCGTTTTG-TATAGT-CTGATTTTGGTGT--GTCGTCTGATG-TTGTTA-GT-GT-TCC-ATAT--CTG--TTTCA-GTCTGA-CAAAAGATGC---TCAAGCTTTTGCTACTCTT--------------GTA-TGCCGCCCCCTTTCT--TT-GATA-TA-GTTGCACCAAG-GCATACAAACT-TTTCAACATC-TTCCAG-TTCTTAAT--CAT-CAA-TTGTGATCTTTTC--C--GCTTGATTTGCATTTATTATCATGATC-T--TTG-TTTTGCTCTTGT--T--GATCTCTTGCTTCTTC-ACTGGGCTTGTTGGTTTGCNCTGATAT-CTTGC-TT-CTTCACTG--GGC-TTG-TTGGT-TT---GC-T-TTGCAT--GTGTTGTCTT-GTTGATGACAT--A---AACGCA-ATGTCATCA--GCGAAGTC-G-AGGTCATCCAG--CTTGGTAG-------TCCACCTG-ATGCCATTCTCTCCACCTACT-ATTGC--TTTTCTC-GTCGTCCAATCCAT----------A-GCAAC-TAGGAATA-GGGACCCTGACATGTTA-------------CA--------TCCCGG-------CCGG--TCTTG------------C-TTCC--A-AACCAA-TTACTTGTTTTTT
gi|4 : TACCT---ATC-CTCTGTGTGTCTA--A-GGACACGTAGGGCCTCCACA--GACTGTCTCCA--CTTAGTT---CTGTCGGCT--GCAG--CAGCCCTT-G-CT------TCCCC-------------C-------AC----GTTC-TT-CGTCCTCCGAT-GGTC-CGCTCCTTCTT----CAC-TT-TTT-GT-CTCCA-------------GGCC-GCC----CCTT--CT---T--TCT-TTTGC--CTTTTGGTGTC--CATG-TTGACCAGTGCTACATT-ACAATCACTCCTGGGCT-GCATAT--CTT-G-TCT-CA-GGAT-GTGTC-C
gi|4 : C--CATG-TTGACCAGTGCTACATT-ACAATCACTTCGGGGCT-GC--ATATCTT-G-TCC-CA-GGAT-GTGCC-CATTATT-AAACTTTCATCTT---CT----CCTGACTTC---ACTCAG-TGGT-CT----CATGT-CTACACT--TTGG-AGCCTCTCTTCTGTAGTAATGTGTTC------TTGCCAT-nccatgttgaccagtgctacattacaatcacttcggggctgcatatcttgtcccaggatgtgcccattattaaactttcatcttctcctgacttcactcagtggtctcatgtctacactttggagcctctcttctgtagtaatgtgttcttgccataccactaatgtcttgtataacctgattttggtgtgtcgtctgacgctgtaaagtgctccatatacctgtttcagtctgacaaaaatttactactctttattttaaaaatatgcaagtgtaaaagttgcacatacagttgcaccaaggtatacgaacttttcaacatatttcagttcatcatcatcaaacttgatcttttcctcttgatttgcatttattctcatggtcttcttgtttttgctcttgttgatctttagtccaactcttcatacttcttcactgtaagctttgttgattttcttctgcataatgttgtagtttgatggcctattcaacgcacatgtcatcagcaaagtcgaggtcatccagcttgtagtaaagttcacctgatgccattctgtccacctcctaatcgctttctccatccaatccatagccaatttaggaagaggaagcctgacatgttacacccctgcttcaccccggtcttgatt
gi|4 : tacctatcctctgtgtgtctaaggacacgtagggcctccacagactgtctccacttagttctgtcggctgcagcagcccttgcttcccccacgttcttcgtcctccgatggtccgctccttcttcactttttgtctccaggccgccccttctttcttttgccttttggtgtccatgttgaccagtgctacattacaatcactcctgggctgcatatcttgtctcaggatgtgtccnTCATCTT-----C-TCCTGACTTCA-CTCAGTGGTCT--CATGTC---T--ACACTTTGGAGCCTCTCTTCTGTAGTAATGTGTTCTTGCCATA-CCACT-AATGTCTTGT-ATAAC-CTGATTTTGGTGT--GTCGTCTGACG-CTGTAAAGT-GC-TCC-ATATACCTGTTT--CA-GTCTGA-CAAAA-AT-T------------TACTACTCTTaccactaatgtcttgtataacctgattttggtgtgtcgtctgacgctgtaaagtgctccatatacctgtttcagtctgacaaaaatttactactctttattttaaaaatatgcaagtgtaaaagttgcacatacagttgcaccaaggtatacgaacttttcaacatatttcagttcatcatcatcaaacttgatcttttcctcttgatttgcatttattctcatggtcttcttgtttttgctcttgttgatctttagtccaactcttcatacttcttcactgtaagctttgttgattttcttctgcataatgttgtagtttgatggcctattcaacgcacatgtcatcagcaaagtcgaggtcatccagcttgtagtaaagttcacctgatgccattctgtccacctcctaatcgctttctccatccaatccatagccaatttaggaagaggaagcctgacatgttacacccctgcttcaccccggtcttgatt
gi|4 : tacctatcctctgtgtgtctaaggacacgtagggcctccacagactgtctccacttagttctgtcggctgcagcagcccttgcttcccccacgttcttcgtcctccgatggtccgctccttcttcactttttgtctccaggccgccccttctttcttttgccttttggtgtccatgttgaccagtgctacattacaatcactcctgggctgcatatcttgtctcaggatgtgtccnccatgttgaccagtgctacattacaatcacttcggggctgcatatcttgtcccaggatgtgcccattattaaacttA-GTTGCACCAAG-GTATACGAACT-TTTCAACATA-TTTCAG-TTCATCAT--CAT-CAA-ACTTGATCTTTTC--C--TCTTGATTTGCATTTATTCTCATGGTC-TTCTTGTTTTTGCTCTTGT--T--GATCTTTAG----TCCAACT---CT--TCA-----------------TAC-TT-CTTCACTGTAAGCTTTG-TTGATTTT---CT-T-CTGCATAAT-GTTGT-AG-TTTGATGGCCT--ATTCAACGCACATGTCATCA--GCAAAGTC-G-AGGTCATCCAG-CTT--GTAGT-AAA-GTTCACCTG-ATGCCATTCTGTCCACCTCCTAATCGC-TTTCTC-----CATCCAATCCAT----------AGCCAATTTAGGAAGA-GGAAGCCTGACATGTTA-------------CA--------CCCCTGCTTCACCCCGG--TCTTGAtattttaaaaatatgcaagtgtaaaagttgcacatacagttgcaccaaggtatacgaacttttcaacatatttcagttcatcatcatcaaacttgatcttttcctcttgatttgcatttattctcatggtcttcttgtttttgctcttgttgatctttagtccaactcttcatacttcttcactgtaagctttgttgattttcttctgcataatgttgtagtttgatggcctattcaacgcacatgtcatcagcaaagtcgaggtcatccagcttgtagtaaagttcacctgatgccattctgtccacctcctaatcgctttctccatccaatccatagccaatttaggaagaggaagcctgacatgttacacccctgcttcaccccggtcttgatt
gi|5 : tacctatcctctgtgtgtctaaggacacgtagggcctccacagactgtctccacttagttctgtcggctgcagcagcccttgcttcccccacgttcttcgtcctccgatggtccgctccttcttcactttttgtctccaggccgccccttctttcttttgccttttggtgtccatgttgaccagtgctacattacaatcactcctgggctgcatatcttgtctcaggatgtgtccnccatgttgaccagtgctacattacaatcacttcggggctgcatatcttgtcccaggatgtgcccattattaaactttcatcttctcctgacttcactcagtggtctcatgtctacactttggagcctctcttctgtagtaatgtgttcttgccataccactaatgtcttgtataacctgattttggtgtgtcgtctgacgctgtaaagtgctccatatacctgtttcagtctgacaaaaatttactactctttattttaaaaatatgcaagtgtaaaagttgcacatac-CTCTGCGTGGCTA--A-GGGCACATAAGGCTTTCACA--GACTGCTTCCA--CTTTGCT---AT-TCGGCT--GCAG--CAGCCCTT-G-CT-----CCCCCCACCCCCCACCCCCC-------AC----GTTC-TC-CATCCTCCGAT-GTTA-CGCTCTTTCTC----TAC-TG-TTC-GT-CTCCAGGTGGTTTTT---GGTC-GCC----CTTT--CTTTCT--TCT-T---C--CTTCTGGTGCC--CACG-T----CATTGCCACTTT-ACAGTCATT----GGCT-GG--AT--CTT-G-TCT-CG-GGGT-GTGTC-CA--AT--AAACTTCCATCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGT-TT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTCTTT------TTGCCAT-CTTATTC-TTA-GAA--TGCGTCTTAAGCATTTGTT-CTGGAAAGTG-TTGATCGTC-TTAT--C-TCCT--CT--A-TTCA----TATTCCAGGTC---T-CGCAT----------CCATATAGTAGTACCG----------GTA-CTACT-AGTGTCTTG-TATAGT-CCGATTTTGGTGT--GTCGTCTGATG-TTGTTG-GT-GC-TCC-ATAT--CTA--TTTCA-GTCTGA-TAAA--AT-TTGCTCTTGCTTTTGCTACTCTT-CATTTCATGTCTTGTA-TACCTCCCCCTTCCT--TT-GATATT--GTTGCACCAAG-GTATACAAACT-TTTTAACATC-TTCCAG-TTCTTCAT--AAT-CAA-TTGTGATCTTTTC--T--GCTTGGTTTGTATTTATTCTTATGATC-T--TTG-TTTTGCTCTTGtt
gi|6 : tTTACCT---ATC-TTCTGCGTGCCTG--A-GGGCAC-TAAGGCCTCCACA--GACTGTCTCCA--CACTGCT---CTGTCGGCT--ACAG--CACCTCTT-G-CC-----CCCCCC-------------CCCCACCCACCCCAATTC-TC-CATCCTTCGAT-GTTC-CGCTCTTTCTC----TAC-CG-TTC-GT-CACCAGGTGGTTTTTG--A-TC-GCCATTTCTTT--CT---T--TCT-TTTTC--CTTCTGGTGCC--CACG-T----CATTGCTATATT-ACAATCACT----CCCT-GC--AT--CT--G-CCT-CA-GGGT-GTGTT-CA--GT--AAATTTCCATCT----CTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTG-TC------TCGTCGTCCTTATTC-TCA-GGA--TGCGTCTTAAGCATTTGTT-CTGGAAGGTG-TTGATCATTTT--TCA---TCT--CT--A-TTCA----TCTTCCAGGTC---T-CGCAT
gi|7 : ctgAACATC-TTCTAT-TTCTATATGTCAT-TCA-TCTTTATCTTTTCATC--ACTT--CTTGCGTTCATCCTCAAAAT----------TTTGC------------ATTTTTAG----TCC-A-----------G--T-GCT------TTC-TGC-AAACTTTGTTG--TG--TTG-TTAG-ATT---TC-TCTTGAAT--TTGTTGT-TTTGTATATGAGAT--A---AGGGCA-ATGTTGTCT--GCGTAGTC-T-GGGTCGTCCAT-CATTGTT-GT-AAACTTCTATCTA-ATTCCGTTCTCTCCATTCCCT-ACTG--TTTTCCTC-ATTATCCAGTCCACA---------A-GTAG--AAGGAATA-GGAATCCc
gi|8 : cat-----CCCCCC-------------C-------CC----GTTC-TCTCACCCTCCGAT-GT-A-CGCTCTTTCTC----TAC-TGTTTC-GT-ATCCA-GTGGTTTTT---GGTC-GCC----CTTTC-CT---T--TCTCT---C--CTTCTGGTGCC--CACG-T----CATTGCCACATT---AGTCATT----GGTT-GG--AT--CTT-G-TCT-CA-GGGTAATGTC-CA--AT--GAACTTCCACCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGC-CT----CATTT-CTACTCT--TTGG-AGCATCTCTTCTGTAGTAGTATGTTC------TTGTTAT-CTTATTC-
gi|9 : cCCA---ATC-CTCTTCATACCTG--T-TGGCATATAAGGCC----------CTAGTTCCA--CTTTTCC---CTGTC--CTTGGCGA--CCACCCTG-G-TT-----GTACCC-------------C-------A-----GCTCTTC-CATC--CCA---GTT---GTTCTTTTTC----TGT-TG-TTCTGT-GT-CATGTTGTTTTT----GCC-TTC----CTAT--CT---T--TCT-TTTCC--CATCTGGTCTC--CAGG-T----CAGTTCAACTGC-ACAAT-GCT----TGAT-GC--TT--TTC-ATTCT-CA-GCAC-GTGAC-CA--ATCCAAA--TCCATCTT---CTTc
4 sequences could not be aligned to this reference sequence:
Unaligned ( gi|10 ): CATCTTCCATAGATTTGGCCTTCATCGCTATGTTTTCGTTGCATTTTTACATTCATCCGTAATACTTCACATTTGTTGATATTTACTTCCAATCCTGTGAATCCTTTGTGCGTTTAGTTTATATTCTATGTGTAATTGCCGTCTCGTGGAGGAAATAAGAGCGAGATCTGCGAAGTCGAAACCGTCTA
Unaligned ( gi|14 ): CACTCATCCCATTCACCATCCCTCATGCCTGTTGGTATAAGCCTAGTACCACTTTTCCCTGTACTTGGCGGACCACCCTGGTTTAGCCAGATTTTCCATCCTGTTGTTCTCTTAAT
Unaligned ( gi|16 ): TAATCCTTAAATCTCTCCGCCCCAGAAGCCGCATAAGGCCTCCATGCTGTTTGCCCATTCTTTCTCAT
Unaligned ( gi|19 ): ACATCATTAAACTTTCTTTGCAGTTCTNCTTGCTGACCATGTCAGTTTT
Alignments
lowQualScore : 11111111111111111111111111111111111111111111 11111111111111111111111111111111111111111111111111111111111
lowQualScore : 222222 3333333333333333333333333333 11111 1111 1111 11 111111 222 222222 1111 111111 11 2 1111111 1111 11111 33333333 1 3333333333 11 22 2 11 11 111111 1 11 1 1 22222 1111 33333 00000000000000000000000000000000000000000000 222 111111 2222 2222 222222 1 1 11 111 1 1 1 1111 555555555555555555 00000000000000000000000000000000000000000000000000000000000 2222 1
lowQualScore : 777 4 55 4 55 11 66 1 777 55 55 4 4 222222 4444444444444444444444444444 4 4 4 99 00000 4 4 4 4 4 8888 4 3333 33 111111 4 999 55 55 3 111111 4 7777 4 55 55 7 3 88 3 3 3 55 99 6 777 4 4 4 9999 3 5 66 5 6 999999 5 5 8 11 0 8 0 7 0000000 99 99 6 4444 5 11111 22 33333333 1 0 1 5555555555 8 8 11 8 3 55 0 0 8 8 8 8 11 11 0 8 8 0 55 666666 22 1 0 9 2 9 5 33 0 3 88 8 8 6 3 99 6 6 00000 1 2 0000 6 00000 8 44444444444444444444444444444444444444444444 8 000 8 8 99 999999 8 6666 0000 1 000000 0 6 11 666 3 3 7 3 3 6 6 6 88 1111 000000000000000000 8 00000000000000000000000000000000000000000000000000000000000 7 2222 3
lowQualScore : ... . .. . .. .. .. . ... .. .. . . ...... ............................ . . . .. ..... . . . . . .... . .... .. ...... . ... .. .. . ...... . .... . .. .. . . .. . . . .. .. . ... . . . .... . . .. . . ...... . . . .. . . . . ....... .. .. . .... . ..... .. ........ . . . .......... . . .. . . .. . . . . . . .. .. . . . . .. ...... .. . . . . . . .. . . .. . . . . .. . . ..... . . .... . ..... . ............................................ . ... . . .. ...... . .... .... . ...... . . .. ... . . . . . . . . .. .... .................. . ........................................................... . .... .
lowQualScore : 888 0 55 0 55 66 11 1 000 55 55 4 4 666666 1111111111111111111111111111 0 0 0 77 11111 0 0 0 0 1 7777 4 9999 55 666666 0 000 55 55 4 000000 0 0000 0 55 00 3 6 44 6 6 6 55 55 4 000 4 4 4 4444 1 0 99 0 2 444444 0 7 0 00 8 0 4 3 5555555 22 22 7 2222 2 88888 55 22222222 0 0 0 0000000000 0 0 44 0 8 88 4 6 0 0 0 0 00 22 8 0 0 8 88 888888 00 4 8 2 5 8 5 88 0 2 88 0 0 7 3 22 7 7 33333 0 2 8888 7 22222 0 88888888888888888888888888888888888888888888 0 444 0 0 00 444444 0 2222 6666 4 888888 0 4 00 666 3 5 3 3 3 7 7 7 88 6666 444444444444444444 0 44444444444444444444444444444444444444444444444444444444444 3 7777 3
consensus : TTACCT---ATC-CTCTGCGTGCCTA--A-GGGCACATAAGGCCTCCACA--GACTGTTTCCA--CTTTGCT---CTGTCGGCT--GCAG--CAGCCCTT-G-CT-----CCCCCC-------------C-------AC----GTTC-TC-CATCCTCCGAT-GTTA-CGCTCTTTCTC----TAC-TG-TTC-GT-CTCCAGGTGGTTTTTG--GGTC-GCC----CTTT--CT---T--TCT-T---C--CTTCTGGTGCC--CACG-T----CATTGCCACATT-ACAGTCACT----GGCT-GC--AT--CTT-G-TCT-CA-GGGT-GTGTC-CA--AT--AAACTTCCATCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTGTTC------TTGCCAT-CTTATTC-TTA-GGA--TGCGTCTTAAGCATTTGTT-CTGGAAGGTGTTTGATCATCTTTATCAC-TCCT--CT--A-TTCA----TCTTCCAGGTC---T-CGCATTT---AGTTCCTATANTGTAGTANCG----------GTA-CCACT-AGTGTCTTGTTATAGT-CTGATTTTGGTGTTAGTCGTCTGATGATTGTTG-GT-GC-TCC-ATAT--CTGTTTTTCA-GTCTGA-CAAAAGAT-T---TCTTGCTTCTGCTACTCTTACCTTTCATGTCTTGTATTACCTCCCCCTTCCT--TT-GATATTA-GTTGCACCAAG-GTATACAAACT-TTTCAACATC-TTCCAG-TTCTTCAT--CAT-CAA-TTTTGATCTTTTC--C--GCTTGGTTTGCATTTATTCTCACGATC-T--TTG-TTTTGCTCTTGTA-T--GATCT-TT-AGTTCTCC-ACT---C-T--TCG---TGCT--CTG--------CTT-CTTCACTG--GGC-TTG-TTGGTGTT---NC-T-TTGCAT--TCGTTGT-NT-GTTGATGGCAT--A---AACGCACATGTCGTCA--GCGAAGTC-T-AGGTCATCCAG-CTTTGGTAGT-AAA-TTCCACCTG-ATGCCATTCTCTCCACCTCCT-ATTGC-TTTTTCTC-GTCGTCCAATCCAT----------A-NCAA--TAGGAAGA-GGAAGCCTGACATGCTA-------------CA--------CCCCGG-------CCGG--TCTTGAA----------CATTCC--A-ACCCAA-TTACTTGTCTTCT
Reference ( family-2912 ) : TTACCT---ATC-CTCTGCGTGCCTA--A-GGGCACATAAGGCCTCCACA--GACTGTTTCCA--CTTTGCT---CTGTCGGCT--GCAG--CAGCCCTT-G-CT-----CCCCCC-------------C-------AC----GTTC-TC-CATCCTCCGAT-GTTA-CGCTCTTTCTC----TAC-TG-TTC-GT-CTCCAGGTGGTTTTTG--GGTC-GCC----CTTT--CT---T--TCT-T---C--CTTCTGGTGCC--CACG-T----CATTGCCACATT-ACAGTCACT----GGCT-GC--AT--CTT-G-TCT-CA-GGGT-GTGTC-CA--AT--AAACTTCCATCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTGTTC------TTGCCAT-CTTATTC-TTA-GGA--TGCGTCTTAAGCATTTGTT-CTGGAAGGTGTTTGATCATCTTTATCAC-TCCT--CT--A-TTCA----TCTTCCAGGTC---T-CGCATTT---AGTTCCTATANTGTAGTANCG----------GTA-CCACT-AGTGTCTTGTTATAGT-CTGATTTTGGTGTTAGTCGTCTGATGATTGTTG-GT-GC-TCC-ATAT--CTGTTTTTCA-GTCTGA-CAAAAGAT-T---TCTTGCTTCTGCTACTCTTACCTTTCATGTCTTGTATTACCTCCCCCTTCCT--TT-GATATTA-GTTGCACCAAG-GTATACAAACT-TTTCAACATC-TTCCAG-TTCTTCAT--CAT-CAA-TTTTGATCTTTTC--C--GCTTGGTTTGCATTTATTCTCACGATC-T--TTG-TTTTGCTCTTGTA-T--GATCT-TT-AGTTCTCC-ACT---C-T--TCG---TGCT--CTG--------CTT-CTTCACTG--GGC-TTG-TTGGTGTT---NC-T-TTGCAT--TCGTTGT-NT-GTTGATGGCAT--A---AACGCACATGTCGTCA--GCGAAGTC-T-AGGTCATCCAG-CTTTGGTAGT-AAA-TTCCACCTG-ATGCCATTCTCTCCACCTCCT-ATTGC-TTTTTCTC-GTCGTCCAATCCAT----------A-NCAA--TAGGAAGA-GGAAGCCTGACATGCTA-------------CA--------CCCCGG-------CCGG--TCTTGAA----------CATTCC--A-ACCCAA-TTACTTGTCTTCT
gi|1 : CCT---ATC-CTCTGTGTGCCTATTACGGGCACATAAG-CCTCCACA--GACTGTTTCCA--CTTT-CT---CTGTCGTCT--GCAG--CAGCCCTTTG-CTTTTTTCCCCAA-------------C-------AT----TTTC-TC-CAGCCTC-GAT-GTTA-CGCTCTTTCT-----TACCTG-TTC-TT-CTTCAGGTTGTTTT----GGTCTGCC----CTTTT-CT---TCTTCT-T---C--CTTCTGGTGCC--CACGAC----CATTGCCACATTTACAGTCACT----GGCTTGC--AT--CTTTG-TCGGCA-GGGT-GTGTTTCA--AT--AA-TTTCCATCTT---TTTCTTCCTGACTTCTTCA-TCAGCTGGT-TTTCTGCATTTTCTACACT--TTGG-AGC-TCTCTTCTGTAGTAGTGTGTTC------ATGC-AT-CTTATTC-TTA-GGA--TGCGTCTT-AGCATTTGTTCCTGGAAGGTGTTTGATCATCTTTATCAC-TCCT--CT--A-TTCA----TCTTCCA-GTC---TCCGCATTTA--AGTTCCTATAGTGTA--AGCG----------GTA-CCACT-AGTGTCTTGTTATAGT-CTG-TTTTGGTGTTAGTCGTCTGATAATGGTTG-GT-GCTTCC-ATAT--CTGTTTTTCAGGTCTGACCAAAAGAT-T---TCTTGCTTCTGCTACTCTTACCTTTCATGTCATGTATTACCTCCCCCTTCCTTATT-GATATTA-GTTGCAC--AG-TTATACAAACT-TTTCAACATCTTTCCAGAATCTTCAT--CAT-CAATTTTTGATTTTTTT--CTTGCTTGGTTTTGATTTATTCTTACGATC-T--TTA-TTTTGCTCTTGTATT--GATCT-TTCAATCCT---ACT---CTT--TCG---TGCT--------------TT-CTTCACT---GGC-TTGTTTGGTGTTGACCT-T-TTGCAT--TCTTCGT--T-GTTGTTGGCAT--C---AACG-ACAATTC-TCA--GTGAAGTCTT-AGGTCATCCAGACTTTGGTAGTAAAA-TTCCATCTGTATGCCATT-TCTCCATCTCCT-ATTGCTTTTTTCTT-ATCGTCCAATCCAT----------T-TGAA--TAGGAAGA-GAAAGCCTGACATGCTA-------------TAATCCTTTGCTTCAC-------CCGG--TCTTGAAGATTCGAAATCATTCCAAA-ACCCAA-CTACTTGTCTTCT
gi|11 : ttTACCTTAAATCTCTCTGCA--CCAG--A-AGTTGCATAAGGCCTCCACGCTGACTG--CCCATTCTTTCCTATCCTGT--GCT--GCTGTTCTGGCCAT-G-TT---------CC-------------A-------AC-----TTG-TC-CATCCT-TGTTGGTTT-CTTTCTTTCAC----TGT-TG-TTC-TT-CTCCAAGTTG-TTTTG--GGCC-TGC----CTCTAGCT---T--TTT-TC--C--CTTCTGG
gi|12 : TTACCT---ATC-CTCTGCGTGTCTA--A-GGGCAGATAAGGCCTCCACA--GACTGTGTCCA--CTTTGCT---CTGCCAGCT--GCAG--CAGCCCTT-GCCC-----CCCCCC-------------C-------CC----CCCC-CC-CATCCTCCGAT-GTTA-CGCTCTTTCTCTAGATAC-TG-TTC-GT-CTCCAGGTGGTTTTTG--Gag
gi|13 : gT--CTT-G-TCG-CA-GGAT-GTGTT-CA--AA--AAATTTCCATCTT---CTTCT-CCTGACTTCTTCANACA--TTGC-CA----CAT----TACAGTCACTGGTTGCATCTTGTC-GCAG-GGTGTGTTCAATAAATTTCCAT-CTTTTTC-Tt
gi|13 : TTT--CC---A--TCT-T---CTTCTCCTGACTTCTTCANA------CATTGCCACATT-ACAGTCACT----GGTT-GC--AT--CTT-G-TCG-CA-GGGT-GTGTT-CA--AT--AAATTTCCATCTT---TTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATcctgacttcttcactcagtggtctcat
gi|15 : tcttgtcgcaggatgtgttcaaaaaaTTACCT---ATT-CTTTGCGTGCCTA--A-GGGCACATAAGGCATCCACA--GACTGCTTCCA--CTTTGCT---CTTTCGGCT--GTAG--CAGCC
gi|17 : TTACCT---ATC-CTCTGTGTGCCTT--A-GGGCACATAAGGCCTCCACA--GACTGTTTCCt
gi|18 : gTCCAG-CTT-GGTAGT-AAAGTTCCACCTG-ATGCCATTCTGTCCACCTCCT-AT
gi|2 : CT---CTGTCGTCT--GCAG--CAGCCCTT-G-CTTTTT-CCCCAA-------------C-------AT----TTTC-TC-CCACCTCGGAT-GTTATCGCTCTTTCT-----TAC-TG-TTC-TTTCTTCAGGTGGTTTT-G--GGTC-GCCG---CTTT--CT---TCTTCT-TG--C--CTTCTGGTGCC--CA-G-A----CATTGCCACATT-ACAGTCACT----GCTT-GC--AT--CTTTG-TCGGCACGGGT-GT-TT-CA--AT--AAA-TTCCATCTTTTTCTTCT-CCTGACTTCTTCACTCAG-TGGTTCT----CATTT-CTACACT--TTGG-AGC-TCTCTTCTGTAGT-GTGTGTTCA-----TTGCCAT-CTTATTCGTTATGGAATCGCGTCTTAAGCATTTGTT-CTGGAAGGTGTTTGATCATCTTTATCAC-TCCT--CT--ATTTCA----TCTTCCAGGTCCTGC-CGCATTT---AGTTCCTATAGTGTA-TAGCG----------GTATCCACTAAGTGTCTTGTTATAGTGCTCGTTTTGGTGTTAGTCGTCTGATAATGGTTG-GTGGC-TCCGATAT--CTGTTTTTCA-GTCTGA-C-AAAGAT-T---TCTTGCTTCTGCTACTCTTACCTTTCATGTC-TGTATTACCTCCCCCTTCCT--TTGGATATTACGTTGCACCAAGTGTATACAAACTGTTTCAACATC-TTCCAGAATCTTCAT--CATGCAA-TTTTGATTTTTTCT-T--GCTTGGTTTTGATTTATCTTAACGATCTT--TTA-TTTTGCTCTTGTA-TTGGATCT-TT-AA-TCGCT-ACT---C-T--TTG----------TG--------TTT-CTTCACTGA-AGC-TTG-TTGGTGTT---GCTT-TTGCAT--C--TTGT-GT-GTTGTTGGCATCAA---GACACACATGTC-TCAATGTGAAGTC-TGAGGTCATCCAGACTTTGGTAGTAAAA-TTCCATCTG-ATGCCATT-TCTCCATCTCCT-ATTGC-TTTTTCTTAGTCGTCCAATCCATTTGTAAAACAA-ACAA--TAGGAAGACGGAAGCCTGACATGCTATAATCCTTTGCTTCA--------CCCCGG-------CTTGAAGATTGAAT---------CATTCC--ATACCCAACTTACTTGTCTTC
gi|3 : tTTACCT---ATC-TTCTGCGTGCCTA--A-GGGCACATAAGGCCTCCACA--GACTGTCTCCA--CTCTGTT---CTGTCGGCT--GCAG--CAGCCCTT-G-CT-----TCCCCC-------------C-------AC----GTTC-TC-CATCCTCCGAT-GTTC-TGCTCTTTCTC----TAT-CG-TTC-GT-CTCCAGGTGGTTCTTGCAGATC-ACC----CTTT--CT---T--TCT-T---C--CTTCTGGTGCC--CATG-T----CATTGCTATATT-GCAATCATT----CGCT-GC--AT--CTT-G-TGT-CA-GGGT-ATGTC-CA--AT--AAACTTCCATCTT---CTTCT-CTTGACTTCTTCATTCAG-GGGT-CT----CATGT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTGTCC------TTGCCAT-CTTATTC-TCA-GGA--TCCGTCTTAAGCATTTGTT-CTGGAAGGTG-TTGATCATC-TTATCATGTCCT--CT--A-TTCA----TCTTCCAAGTC---T-CACA-TT---A------ATATTGTAGTACCG----------GTA-CCACT-AGCGTTTTG-TATAGT-CTGATTTTGGTGT--GTCGTCTGATG-TTGTTA-GT-GT-TCC-ATAT--CTG--TTTCA-GTCTGA-CAAAAGATGC---TCAAGCTTTTGCTAC--------------TCTTGTA-TGCCGCCCCCTTTCT--TT-GATA-TA-GTTGCACCAAG-GCATACAAACT-TTTCAACATC-TTCCAG-TTCTTAAT--CAT-CAA-TTGTGATCTTTTC--C--GCTTGATTTGCATTTATTATCATGATC-T--TTG-TTTTGCTCTTGT--T--GATCTCTT-GCTTCTTC-ACTGGGC-TTGTTGGTTTGCN--CTGATATCTTGCTT-CTTCACTG--GGC-TTG-TTGGT-TT---GC-T-TTGCAT--GTGTTGTCTT-GTTGATGACAT--A---AACGCA-ATGTCATCA--GCGAAGTC-G-AGGTCATCCAG-C-TTGGTAG-------TCCACCTG-ATGCCATTCTCTCCACCTACT-ATTGC--TTTTCTC-GTCGTCCAATCCAT----------A-GCAAC-TAGGAATA-GGGACCCTGACATGTTA-------------CA--------TCCCGG-------CCGG--TCTTG------------C-TTCC--A-AACCAA-TTACTTGTTTTTT
gi|4 : TACCT---ATC-CTCTGTGTGTCTA--A-GGACACGTAGGGCCTCCACA--GACTGTCTCCA--CTTAGTT---CTGTCGGCT--GCAG--CAGCCCTT-G-CT------TCCCC-------------C-------AC----GTTC-TT-CGTCCTCCGAT-GGTC-CGCTCCTTCTT----CAC-TT-TTT-GT-CTCCA-------------GGCC-GCC----CCTT--CT---T--TCT-TTTGC--CTTTTGGTGTC--CATG-TTGACCAGTGCTACATT-ACAATCACTCCTGGGCT-GCATAT--CTT-G-TCT-CA-GGAT-GTGTC-C
gi|4 : C--CATG-TTGACCAGTGCTACATT-ACAATCACTTCGGGGCT-GC--ATATCTT-G-TCC-CA-GGAT-GTGCC-CATTATT-AAACTTTCATCTT---CT----CCTGACTTC---ACTCAG-TGGT-CT----CATGT-CTACACT--TTGG-AGCCTCTCTTCTGTAGTAATGTGTTC------TTGCCAT-nccatgttgaccagtgctacattacaatcacttcggggctgcatatcttgtcccaggatgtgcccattattaaactttcatcttctcctgacttcactcagtggtctcatgtctacactttggagcctctcttctgtagtaatgtgttcttgccataccactaatgtcttgtataacctgattttggtgtgtcgtctgacgctgtaaagtgctccatatacctgtttcagtctgacaaaaatttactactctttattttaaaaatatgcaagtgtaaaagttgcacatacagttgcaccaaggtatacgaacttttcaacatatttcagttcatcatcatcaaacttgatcttttcctcttgatttgcatttattctcatggtcttcttgtttttgctcttgttgatctttagtccaactcttcatacttcttcactgtaagctttgttgattttcttctgcataatgttgtagtttgatggcctattcaacgcacatgtcatcagcaaagtcgaggtcatccagcttgtagtaaagttcacctgatgccattctgtccacctcctaatcgctttctccatccaatccatagccaatttaggaagaggaagcctgacatgttacacccctgcttcaccccggtcttgatt
gi|4 : tacctatcctctgtgtgtctaaggacacgtagggcctccacagactgtctccacttagttctgtcggctgcagcagcccttgcttcccccacgttcttcgtcctccgatggtccgctccttcttcactttttgtctccaggccgccccttctttcttttgccttttggtgtccatgttgaccagtgctacattacaatcactcctgggctgcatatcttgtctcaggatgtgtccnTCATCTT-----C-TCCTGACTTCA-CTCAGTGGTCT--CATGTC---T--ACACTTTGGAGCCTCTCTTCTGTAGTAATGTGTTCTTGCCATA-CCACT-AATGTCTTGT-ATAAC-CTGATTTTGGTGT--GTCGTCTGACG-CTGTAAAGT-GC-TCC-ATATACCTGTTT--CA-GTCTGA-CAAAA-AT-T------------TACTACTCTTaccactaatgtcttgtataacctgattttggtgtgtcgtctgacgctgtaaagtgctccatatacctgtttcagtctgacaaaaatttactactctttattttaaaaatatgcaagtgtaaaagttgcacatacagttgcaccaaggtatacgaacttttcaacatatttcagttcatcatcatcaaacttgatcttttcctcttgatttgcatttattctcatggtcttcttgtttttgctcttgttgatctttagtccaactcttcatacttcttcactgtaagctttgttgattttcttctgcataatgttgtagtttgatggcctattcaacgcacatgtcatcagcaaagtcgaggtcatccagcttgtagtaaagttcacctgatgccattctgtccacctcctaatcgctttctccatccaatccatagccaatttaggaagaggaagcctgacatgttacacccctgcttcaccccggtcttgatt
gi|4 : tacctatcctctgtgtgtctaaggacacgtagggcctccacagactgtctccacttagttctgtcggctgcagcagcccttgcttcccccacgttcttcgtcctccgatggtccgctccttcttcactttttgtctccaggccgccccttctttcttttgccttttggtgtccatgttgaccagtgctacattacaatcactcctgggctgcatatcttgtctcaggatgtgtccnccatgttgaccagtgctacattacaatcacttcggggctgcatatcttgtcccaggatgtgcccattattaaacttA-GTTGCACCAAG-GTATACGAACT-TTTCAACATA-TTTCAG-TTCATCAT--CAT-CAA-ACTTGATCTTTTC--C--TCTTGATTTGCATTTATTCTCATGGTC-TTCTTGTTTTTGCTCTTGT--T--GATCT-TT-AG---TCCAACT---C-T--TCA----------TA--------CTT-CTTCACTGTAAGCTTTG-TTGATTTT---CT-T-CTGCATAAT-GTTGT-AG-TTTGATGGCCT--ATTCAACGCACATGTCATCA--GCAAAGTC-G-AGGTCATCCAG-CTT--GTAGT-AAA-GTTCACCTG-ATGCCATTCTGTCCACCTCCTAATCGC-TTTCTC-----CATCCAATCCAT----------AGCCAATTTAGGAAGA-GGAAGCCTGACATGTTA-------------CA--------CCCCTGCTTCACCCCGG--TCTTGAtattttaaaaatatgcaagtgtaaaagttgcacatacagttgcaccaaggtatacgaacttttcaacatatttcagttcatcatcatcaaacttgatcttttcctcttgatttgcatttattctcatggtcttcttgtttttgctcttgttgatctttagtccaactcttcatacttcttcactgtaagctttgttgattttcttctgcataatgttgtagtttgatggcctattcaacgcacatgtcatcagcaaagtcgaggtcatccagcttgtagtaaagttcacctgatgccattctgtccacctcctaatcgctttctccatccaatccatagccaatttaggaagaggaagcctgacatgttacacccctgcttcaccccggtcttgatt
gi|5 : tacctatcctctgtgtgtctaaggacacgtagggcctccacagactgtctccacttagttctgtcggctgcagcagcccttgcttcccccacgttcttcgtcctccgatggtccgctccttcttcactttttgtctccaggccgccccttctttcttttgccttttggtgtccatgttgaccagtgctacattacaatcactcctgggctgcatatcttgtctcaggatgtgtccnccatgttgaccagtgctacattacaatcacttcggggctgcatatcttgtcccaggatgtgcccattattaaactttcatcttctcctgacttcactcagtggtctcatgtctacactttggagcctctcttctgtagtaatgtgttcttgccataccactaatgtcttgtataacctgattttggtgtgtcgtctgacgctgtaaagtgctccatatacctgtttcagtctgacaaaaatttactactctttattttaaaaatatgcaagtgtaaaagttgcacatac-CTCTGCGTGGCTA--A-GGGCACATAAGGCTTTCACA--GACTGCTTCCA--CTTTGCT---AT-TCGGCT--GCAG--CAGCCCTT-G-CT-----CCCCCCACCCCCCACCCCCC-------AC----GTTC-TC-CATCCTCCGAT-GTTA-CGCTCTTTCTC----TAC-TG-TTC-GT-CTCCAGGTGGTTTTT---GGTC-GCC----CTTT--CTTTCT--TCT-T---C--CTTCTGGTGCC--CACG-T----CATTGCCACTTT-ACAGTCATT----GGCT-GG--AT--CTT-G-TCT-CG-GGGT-GTGTC-CA--AT--AAACTTCCATCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGT-TT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTCTTT------TTGCCAT-CTTATTC-TTA-GAA--TGCGTCTTAAGCATTTGTT-CTGGAAAGTG-TTGATCGTC-TTAT--C-TCCT--CT--A-TTCA----TATTCCAGGTC---T-CGCAT----------CCATATAGTAGTACCG----------GTA-CTACT-AGTGTCTTG-TATAGT-CCGATTTTGGTGT--GTCGTCTGATG-TTGTTG-GT-GC-TCC-ATAT--CTA--TTTCA-GTCTGA-TAAA--AT-TTGCTCTTGCTTTTGCTACTCTT-CATTTCATGTCTTGTA-TACCTCCCCCTTCCT--TT-GATATT--GTTGCACCAAG-GTATACAAACT-TTTTAACATC-TTCCAG-TTCTTCAT--AAT-CAA-TTGTGATCTTTTC--T--GCTTGGTTTGTATTTATTCTTATGATC-T--TTG-TTTTGCTCTTGtt
gi|6 : tTTACCT---ATC-TTCTGCGTGCCTG--A-GGGCAC-TAAGGCCTCCACA--GACTGTCTCCA--CACTGCT---CTGTCGGCT--ACAG--CACCTCTT-G-CC-----CCCCCC-------------CCCCACCCACCCCAATTC-TC-CATCCTTCGAT-GTTC-CGCTCTTTCTC----TAC-CG-TTC-GT-CACCAGGTGGTTTTTG--A-TC-GCCATTTCTTT--CT---T--TCT-TTTTC--CTTCTGGTGCC--CACG-T----CATTGCTATATT-ACAATCACT----CCCT-GC--AT--CT--G-CCT-CA-GGGT-GTGTT-CA--GT--AAATTTCCATCT----CTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTG-TC------TCGTCGTCCTTATTC-TCA-GGA--TGCGTCTTAAGCATTTGTT-CTGGAAGGTG-TTGATCATTTT--TCA---TCT--CT--A-TTCA----TCTTCCAGGTC---T-CGCAT
gi|7 : ctgAACATC-TTCTAT-TTCTATATGTCAT-TCA-TCTTTATCTTTTCATC--ACTT--CTTGCGTTCATCCTCAAAAT----------TTTGC------------ATTT-TT-AGT---CC-A------------G---TGCTTTCTG--------CAAACTTTGTTG--TG--TTG-TTAG-ATT---TC-TCTTGAAT--TTGTTGT-TTTGTATATGAGAT--A---AGGGCA-ATGTTGTCT--GCGTAGTC-T-GGGTCGTCCAT-CATTGTT-GT-AAACTTCTATCTA-ATTCCGTTCTCTCCATTCCCT-ACTG--TTTTCCTC-ATTATCCAGTCCACA---------A-GTAG--AAGGAATA-GGAATCCc
gi|8 : cat-----CCCCCC-------------C-------CC----GTTC-TCTCACCCTCCGAT-GT-A-CGCTCTTTCTC----TAC-TGTTTC-GT-ATCCA-GTGGTTTTT---GGTC-GCC----CTTTC-CT---T--TCTCT---C--CTTCTGGTGCC--CACG-T----CATTGCCACATT---AGTCATT----GGTT-GG--AT--CTT-G-TCT-CA-GGGTAATGTC-CA--AT--GAACTTCCACCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGC-CT----CATTT-CTACTCT--TTGG-AGCATCTCTTCTGTAGTAGTATGTTC------TTGTTAT-CTTATTC-
gi|9 : cCCA---ATC-CTCTTCATACCTG--T-TGGCATATAAGGCC----------CTAGTTCCA--CTTTTCC---CTGTC--CTTGGCGA--CCACCCTG-G-TT-----GTACCC-------------C-------A-----GCTCTTC-CATC--CCA---GTT---GTTCTTTTTC----TGT-TG-TTCTGT-GT-CATGTTGTTTTT----GCC-TTC----CTAT--CT---T--TCT-TTTCC--CATCTGGTCTC--CAGG-T----CAGTTCAACTGC-ACAAT-GCT----TGAT-GC--TT--TTC-ATTCT-CA-GCAC-GTGAC-CA--ATCCAAA--TCCATCTT---CTTc
4 sequences could not be aligned to this reference sequence:
Unaligned ( gi|10 ): CATCTTCCATAGATTTGGCCTTCATCGCTATGTTTTCGTTGCATTTTTACATTCATCCGTAATACTTCACATTTGTTGATATTTACTTCCAATCCTGTGAATCCTTTGTGCGTTTAGTTTATATTCTATGTGTAATTGCCGTCTCGTGGAGGAAATAAGAGCGAGATCTGCGAAGTCGAAACCGTCTA
Unaligned ( gi|14 ): CACTCATCCCATTCACCATCCCTCATGCCTGTTGGTATAAGCCTAGTACCACTTTTCCCTGTACTTGGCGGACCACCCTGGTTTAGCCAGATTTTCCATCCTGTTGTTCTCTTAAT
Unaligned ( gi|16 ): TAATCCTTAAATCTCTCCGCCCCAGAAGCCGCATAAGGCCTCCATGCTGTTTGCCCATTCTTTCTCAT
Unaligned ( gi|19 ): ACATCATTAAACTTTCTTTGCAGTTCTNCTTGCTGACCATGTCAGTTTT
Alignments
lowQualScore : 11111111111111111111111111111111111111111111 11111111111111111111111111111111111111111111111111111111111
lowQualScore : 222222 3333333333333333333333333333 11111 1111 1111 11 111111 222 222222 1111 111111 11 2 1111111 1111 11111 33333333 1 3333333333 11 22 2 11 11 111111 1 11 1 1 22222 1111 33333 00000000000000000000000000000000000000000000 222 111111 2222 2222 222222 1 1 11 111 1 1 1 1111 555555555555555555 00000000000000000000000000000000000000000000000000000000000 2222 1
lowQualScore : 777 4 55 4 55 11 66 1 777 55 55 4 4 222222 4444444444444444444444444444 4 4 4 99 00000 4 4 4 4 4 8888 4 3333 33 111111 4 999 55 55 3 111111 4 7777 4 55 55 7 3 88 3 3 3 55 99 6 777 4 4 4 9999 3 5 66 5 6 999999 5 5 8 11 0 8 0 7 0000000 99 99 6 4444 5 11111 22 33333333 1 0 1 5555555555 8 8 11 8 3 55 0 0 8 8 8 8 11 11 0 8 8 0 55 666666 22 1 0 9 2 9 5 33 0 3 88 8 8 6 3 99 6 6 00000 1 2 0000 6 00000 8 44444444444444444444444444444444444444444444 8 000 8 8 99 999999 8 6666 0000 1 000000 0 6 11 666 3 3 7 3 3 6 6 6 88 1111 000000000000000000 8 00000000000000000000000000000000000000000000000000000000000 7 2222 3
lowQualScore : ... . .. . .. .. .. . ... .. .. . . ...... ............................ . . . .. ..... . . . . . .... . .... .. ...... . ... .. .. . ...... . .... . .. .. . . .. . . . .. .. . ... . . . .... . . .. . . ...... . . . .. . . . . ....... .. .. . .... . ..... .. ........ . . . .......... . . .. . . .. . . . . . . .. .. . . . . .. ...... .. . . . . . . .. . . .. . . . . .. . . ..... . . .... . ..... . ............................................ . ... . . .. ...... . .... .... . ...... . . .. ... . . . . . . . . .. .... .................. . ........................................................... . .... .
lowQualScore : 888 0 55 0 55 66 11 1 000 55 55 4 4 666666 1111111111111111111111111111 0 0 0 77 11111 0 0 0 0 1 7777 4 9999 55 666666 0 000 55 55 4 000000 0 0000 0 55 00 3 6 44 6 6 6 55 55 4 000 4 4 4 4444 1 0 99 0 2 444444 0 7 0 00 8 0 4 3 5555555 22 22 7 2222 2 88888 55 22222222 0 0 0 0000000000 0 0 44 0 8 88 4 6 0 0 0 0 00 22 8 0 0 8 88 888888 00 4 8 2 5 8 5 88 0 2 88 0 0 7 3 22 7 7 33333 0 2 8888 7 22222 0 88888888888888888888888888888888888888888888 0 444 0 0 00 444444 0 2222 6666 4 888888 0 4 00 666 3 5 3 3 3 7 7 7 88 6666 444444444444444444 0 44444444444444444444444444444444444444444444444444444444444 3 7777 3
consensus : TTACCT---ATC-CTCTGCGTGCCTA--A-GGGCACATAAGGCCTCCACA--GACTGTTTCCA--CTTTGCT---CTGTCGGCT--GCAG--CAGCCCTT-G-CT-----CCCCCC-------------C-------AC----GTTC-TC-CATCCTCCGAT-GTTA-CGCTCTTTCTC----TAC-TG-TTC-GT-CTCCAGGTGGTTTTTG--GGTC-GCC----CTTT--CT---T--TCT-T---C--CTTCTGGTGCC--CACG-T----CATTGCCACATT-ACAGTCACT----GGCT-GC--AT--CTT-G-TCT-CA-GGGT-GTGTC-CA--AT--AAACTTCCATCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTGTTC------TTGCCAT-CTTATTC-TTA-GGA--TGCGTCTTAAGCATTTGTT-CTGGAAGGTGTTTGATCATCTTTATCAC-TCCT--CT--A-TTCA----TCTTCCAGGTC---T-CGCATTT---AGTTCCTATANTGTAGTANCG----------GTA-CCACT-AGTGTCTTGTTATAGT-CTGATTTTGGTGTTAGTCGTCTGATGATTGTTG-GT-GC-TCC-ATAT--CTGTTTTTCA-GTCTGA-CAAAAGAT-T---TCTTGCTTCTGCTACTCTTACCTTTCATGTCTTGTATTACCTCCCCCTTCCT--TT-GATATTA-GTTGCACCAAG-GTATACAAACT-TTTCAACATC-TTCCAG-TTCTTCAT--CAT-CAA-TTTTGATCTTTTC--C--GCTTGGTTTGCATTTATTCTCACGATC-T--TTG-TTTTGCTCTTGTA-T--GATCT-TT-AGTTCTCC-ACT---C-T--TCG---TGCT--CTG--------CTT-CTTCACTG--GGC-TTG-TTGGTGTT---NC-T-TTGCAT--TCGTTGT-NT-GTTGATGGCAT--A---AACGCACATGTCGTCA--GCGAAGTC-T-AGGTCATCCAG-CTTTGGTAGT-AAA-TTCCACCTG-ATGCCATTCTCTCCACCTCCT-ATTGC-TTTTTCTC-GTCGTCCAATCCAT----------A-NCAA--TAGGAAGA-GGAAGCCTGACATGCTA-------------CA--------CCCCGG-------CCGG--TCTTGAA----------CATTCC--A-ACCCAA-TTACTTGTCTTCT
Reference ( family-2912 ) : TTACCT---ATC-CTCTGCGTGCCTA--A-GGGCACATAAGGCCTCCACA--GACTGTTTCCA--CTTTGCT---CTGTCGGCT--GCAG--CAGCCCTT-G-CT-----CCCCCC-------------C-------AC----GTTC-TC-CATCCTCCGAT-GTTA-CGCTCTTTCTC----TAC-TG-TTC-GT-CTCCAGGTGGTTTTTG--GGTC-GCC----CTTT--CT---T--TCT-T---C--CTTCTGGTGCC--CACG-T----CATTGCCACATT-ACAGTCACT----GGCT-GC--AT--CTT-G-TCT-CA-GGGT-GTGTC-CA--AT--AAACTTCCATCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTGTTC------TTGCCAT-CTTATTC-TTA-GGA--TGCGTCTTAAGCATTTGTT-CTGGAAGGTGTTTGATCATCTTTATCAC-TCCT--CT--A-TTCA----TCTTCCAGGTC---T-CGCATTT---AGTTCCTATANTGTAGTANCG----------GTA-CCACT-AGTGTCTTGTTATAGT-CTGATTTTGGTGTTAGTCGTCTGATGATTGTTG-GT-GC-TCC-ATAT--CTGTTTTTCA-GTCTGA-CAAAAGAT-T---TCTTGCTTCTGCTACTCTTACCTTTCATGTCTTGTATTACCTCCCCCTTCCT--TT-GATATTA-GTTGCACCAAG-GTATACAAACT-TTTCAACATC-TTCCAG-TTCTTCAT--CAT-CAA-TTTTGATCTTTTC--C--GCTTGGTTTGCATTTATTCTCACGATC-T--TTG-TTTTGCTCTTGTA-T--GATCT-TT-AGTTCTCC-ACT---C-T--TCG---TGCT--CTG--------CTT-CTTCACTG--GGC-TTG-TTGGTGTT---NC-T-TTGCAT--TCGTTGT-NT-GTTGATGGCAT--A---AACGCACATGTCGTCA--GCGAAGTC-T-AGGTCATCCAG-CTTTGGTAGT-AAA-TTCCACCTG-ATGCCATTCTCTCCACCTCCT-ATTGC-TTTTTCTC-GTCGTCCAATCCAT----------A-NCAA--TAGGAAGA-GGAAGCCTGACATGCTA-------------CA--------CCCCGG-------CCGG--TCTTGAA----------CATTCC--A-ACCCAA-TTACTTGTCTTCT
gi|1 : CCT---ATC-CTCTGTGTGCCTATTACGGGCACATAAG-CCTCCACA--GACTGTTTCCA--CTTT-CT---CTGTCGTCT--GCAG--CAGCCCTTTG-CTTTTTTCCCCAA-------------C-------AT----TTTC-TC-CAGCCTC-GAT-GTTA-CGCTCTTTCT-----TACCTG-TTC-TT-CTTCAGGTTGTTTT----GGTCTGCC----CTTTT-CT---TCTTCT-T---C--CTTCTGGTGCC--CACGAC----CATTGCCACATTTACAGTCACT----GGCTTGC--AT--CTTTG-TCGGCA-GGGT-GTGTTTCA--AT--AA-TTTCCATCTT---TTTCTTCCTGACTTCTTCA-TCAGCTGGT-TTTCTGCATTTTCTACACT--TTGG-AGC-TCTCTTCTGTAGTAGTGTGTTC------ATGC-AT-CTTATTC-TTA-GGA--TGCGTCTT-AGCATTTGTTCCTGGAAGGTGTTTGATCATCTTTATCAC-TCCT--CT--A-TTCA----TCTTCCA-GTC---TCCGCATTTA--AGTTCCTATAGTGTA--AGCG----------GTA-CCACT-AGTGTCTTGTTATAGT-CTG-TTTTGGTGTTAGTCGTCTGATAATGGTTG-GT-GCTTCC-ATAT--CTGTTTTTCAGGTCTGACCAAAAGAT-T---TCTTGCTTCTGCTACTCTTACCTTTCATGTCATGTATTACCTCCCCCTTCCTTATT-GATATTA-GTTGCAC--AG-TTATACAAACT-TTTCAACATCTTTCCAGAATCTTCAT--CAT-CAATTTTTGATTTTTTT--CTTGCTTGGTTTTGATTTATTCTTACGATC-T--TTA-TTTTGCTCTTGTATT--GATCT-TTCAATCCT---ACT---CTT--TCG---TGCT--------------TT-CTTCACT---GGC-TTGTTTGGTGTTGACCT-T-TTGCAT--TCTTCGT--T-GTTGTTGGCAT--C---AACG-ACAATTC-TCA--GTGAAGTCTT-AGGTCATCCAGACTTTGGTAGTAAAA-TTCCATCTGTATGCCATT-TCTCCATCTCCT-ATTGCTTTTTTCTT-ATCGTCCAATCCAT----------T-TGAA--TAGGAAGA-GAAAGCCTGACATGCTA-------------TAATCCTTTGCTTCAC-------CCGG--TCTTGAAGATTCGAAATCATTCCAAA-ACCCAA-CTACTTGTCTTCT
gi|11 : ttTACCTTAAATCTCTCTGCA--CCAG--A-AGTTGCATAAGGCCTCCACGCTGACTG--CCCATTCTTTCCTATCCTGT--GCT--GCTGTTCTGGCCAT-G-TT---------CC-------------A-------AC-----TTG-TC-CATCCT-TGTTGGTTT-CTTTCTTTCAC----TGT-TG-TTC-TT-CTCCAAGTTG-TTTTG--GGCC-TGC----CTCTAGCT---T--TTT-TC--C--CTTCTGG
gi|12 : TTACCT---ATC-CTCTGCGTGTCTA--A-GGGCAGATAAGGCCTCCACA--GACTGTGTCCA--CTTTGCT---CTGCCAGCT--GCAG--CAGCCCTT-GCCC-----CCCCCC-------------C-------CC----CCCC-CC-CATCCTCCGAT-GTTA-CGCTCTTTCTCTAGATAC-TG-TTC-GT-CTCCAGGTGGTTTTTG--Gag
gi|13 : gT--CTT-G-TCG-CA-GGAT-GTGTT-CA--AA--AAATTTCCATCTT---CTTCT-CCTGACTTCTTCANACA--TTGC-CA----CAT----TACAGTCACTGGTTGCATCTTGTC-GCAG-GGTGTGTTCAATAAATTTCCAT-CTTTTTC-Tt
gi|13 : TTT--CC---A--TCT-T---CTTCTCCTGACTTCTTCANA------CATTGCCACATT-ACAGTCACT----GGTT-GC--AT--CTT-G-TCG-CA-GGGT-GTGTT-CA--AT--AAATTTCCATCTT---TTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATcctgacttcttcactcagtggtctcat
gi|15 : tcttgtcgcaggatgtgttcaaaaaaTTACCT---ATT-CTTTGCGTGCCTA--A-GGGCACATAAGGCATCCACA--GACTGCTTCCA--CTTTGCT---CTTTCGGCT--GTAG--CAGCC
gi|17 : TTACCT---ATC-CTCTGTGTGCCTT--A-GGGCACATAAGGCCTCCACA--GACTGTTTCCt
gi|18 : gTCCAG-CTT-GGTAGT-AAAGTTCCACCTG-ATGCCATTCTGTCCACCTCCT-AT
gi|2 : CT---CTGTCGTCT--GCAG--CAGCCCTT-G-CTTTTT-CCCCAA-------------C-------AT----TTTC-TC-CCACCTCGGAT-GTTATCGCTCTTTCT-----TAC-TG-TTC-TTTCTTCAGGTGGTTTT-G--GGTC-GCCG---CTTT--CT---TCTTCT-TG--C--CTTCTGGTGCC--CA-G-A----CATTGCCACATT-ACAGTCACT----GCTT-GC--AT--CTTTG-TCGGCACGGGT-GT-TT-CA--AT--AAA-TTCCATCTTTTTCTTCT-CCTGACTTCTTCACTCAG-TGGTTCT----CATTT-CTACACT--TTGG-AGC-TCTCTTCTGTAGT-GTGTGTTCA-----TTGCCAT-CTTATTCGTTATGGAATCGCGTCTTAAGCATTTGTT-CTGGAAGGTGTTTGATCATCTTTATCAC-TCCT--CT--ATTTCA----TCTTCCAGGTCCTGC-CGCATTT---AGTTCCTATAGTGTA-TAGCG----------GTATCCACTAAGTGTCTTGTTATAGTGCTCGTTTTGGTGTTAGTCGTCTGATAATGGTTG-GTGGC-TCCGATAT--CTGTTTTTCA-GTCTGA-C-AAAGAT-T---TCTTGCTTCTGCTACTCTTACCTTTCATGTC-TGTATTACCTCCCCCTTCCT--TTGGATATTACGTTGCACCAAGTGTATACAAACTGTTTCAACATC-TTCCAGAATCTTCAT--CATGCAA-TTTTGATTTTTTCT-T--GCTTGGTTTTGATTTATCTTAACGATCTT--TTA-TTTTGCTCTTGTA-TTGGATCT-TT-AA-TCGCT-ACT---C-T--TTG----------TG--------TTT-CTTCACTGA-AGC-TTG-TTGGTGTT---GCTT-TTGCAT--C--TTGT-GT-GTTGTTGGCATCAA---GACACACATGTC-TCAATGTGAAGTC-TGAGGTCATCCAGACTTTGGTAGTAAAA-TTCCATCTG-ATGCCATT-TCTCCATCTCCT-ATTGC-TTTTTCTTAGTCGTCCAATCCATTTGTAAAACAA-ACAA--TAGGAAGACGGAAGCCTGACATGCTATAATCCTTTGCTTCA--------CCCCGG-------CTTGAAGATTGAAT---------CATTCC--ATACCCAACTTACTTGTCTTC
gi|3 : tTTACCT---ATC-TTCTGCGTGCCTA--A-GGGCACATAAGGCCTCCACA--GACTGTCTCCA--CTCTGTT---CTGTCGGCT--GCAG--CAGCCCTT-G-CT-----TCCCCC-------------C-------AC----GTTC-TC-CATCCTCCGAT-GTTC-TGCTCTTTCTC----TAT-CG-TTC-GT-CTCCAGGTGGTTCTTGCAGATC-ACC----CTTT--CT---T--TCT-T---C--CTTCTGGTGCC--CATG-T----CATTGCTATATT-GCAATCATT----CGCT-GC--AT--CTT-G-TGT-CA-GGGT-ATGTC-CA--AT--AAACTTCCATCTT---CTTCT-CTTGACTTCTTCATTCAG-GGGT-CT----CATGT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTGTCC------TTGCCAT-CTTATTC-TCA-GGA--TCCGTCTTAAGCATTTGTT-CTGGAAGGTG-TTGATCATC-TTATCATGTCCT--CT--A-TTCA----TCTTCCAAGTC---T-CACA-TT---A------ATATTGTAGTACCG----------GTA-CCACT-AGCGTTTTG-TATAGT-CTGATTTTGGTGT--GTCGTCTGATG-TTGTTA-GT-GT-TCC-ATAT--CTG--TTTCA-GTCTGA-CAAAAGATGC---TCAAGCTTTTGCTAC--------------TCTTGTA-TGCCGCCCCCTTTCT--TT-GATA-TA-GTTGCACCAAG-GCATACAAACT-TTTCAACATC-TTCCAG-TTCTTAAT--CAT-CAA-TTGTGATCTTTTC--C--GCTTGATTTGCATTTATTATCATGATC-T--TTG-TTTTGCTCTTGT--T--GATCTCTT-GCTTCTTC-ACTGGGC-TTGTTGGTTTGCN--CTGATATCTTGCTT-CTTCACTG--GGC-TTG-TTGGT-TT---GC-T-TTGCAT--GTGTTGTCTT-GTTGATGACAT--A---AACGCA-ATGTCATCA--GCGAAGTC-G-AGGTCATCCAG-C-TTGGTAG-------TCCACCTG-ATGCCATTCTCTCCACCTACT-ATTGC--TTTTCTC-GTCGTCCAATCCAT----------A-GCAAC-TAGGAATA-GGGACCCTGACATGTTA-------------CA--------TCCCGG-------CCGG--TCTTG------------C-TTCC--A-AACCAA-TTACTTGTTTTTT
gi|4 : TACCT---ATC-CTCTGTGTGTCTA--A-GGACACGTAGGGCCTCCACA--GACTGTCTCCA--CTTAGTT---CTGTCGGCT--GCAG--CAGCCCTT-G-CT------TCCCC-------------C-------AC----GTTC-TT-CGTCCTCCGAT-GGTC-CGCTCCTTCTT----CAC-TT-TTT-GT-CTCCA-------------GGCC-GCC----CCTT--CT---T--TCT-TTTGC--CTTTTGGTGTC--CATG-TTGACCAGTGCTACATT-ACAATCACTCCTGGGCT-GCATAT--CTT-G-TCT-CA-GGAT-GTGTC-C
gi|4 : C--CATG-TTGACCAGTGCTACATT-ACAATCACTTCGGGGCT-GC--ATATCTT-G-TCC-CA-GGAT-GTGCC-CATTATT-AAACTTTCATCTT---CT----CCTGACTTC---ACTCAG-TGGT-CT----CATGT-CTACACT--TTGG-AGCCTCTCTTCTGTAGTAATGTGTTC------TTGCCAT-nccatgttgaccagtgctacattacaatcacttcggggctgcatatcttgtcccaggatgtgcccattattaaactttcatcttctcctgacttcactcagtggtctcatgtctacactttggagcctctcttctgtagtaatgtgttcttgccataccactaatgtcttgtataacctgattttggtgtgtcgtctgacgctgtaaagtgctccatatacctgtttcagtctgacaaaaatttactactctttattttaaaaatatgcaagtgtaaaagttgcacatacagttgcaccaaggtatacgaacttttcaacatatttcagttcatcatcatcaaacttgatcttttcctcttgatttgcatttattctcatggtcttcttgtttttgctcttgttgatctttagtccaactcttcatacttcttcactgtaagctttgttgattttcttctgcataatgttgtagtttgatggcctattcaacgcacatgtcatcagcaaagtcgaggtcatccagcttgtagtaaagttcacctgatgccattctgtccacctcctaatcgctttctccatccaatccatagccaatttaggaagaggaagcctgacatgttacacccctgcttcaccccggtcttgatt
gi|4 : tacctatcctctgtgtgtctaaggacacgtagggcctccacagactgtctccacttagttctgtcggctgcagcagcccttgcttcccccacgttcttcgtcctccgatggtccgctccttcttcactttttgtctccaggccgccccttctttcttttgccttttggtgtccatgttgaccagtgctacattacaatcactcctgggctgcatatcttgtctcaggatgtgtccnTCATCTT-----C-TCCTGACTTCA-CTCAGTGGTCT--CATGTC---T--ACACTTTGGAGCCTCTCTTCTGTAGTAATGTGTTCTTGCCATA-CCACT-AATGTCTTGT-ATAAC-CTGATTTTGGTGT--GTCGTCTGACG-CTGTAAAGT-GC-TCC-ATATACCTGTTT--CA-GTCTGA-CAAAA-AT-T------------TACTACTCTTaccactaatgtcttgtataacctgattttggtgtgtcgtctgacgctgtaaagtgctccatatacctgtttcagtctgacaaaaatttactactctttattttaaaaatatgcaagtgtaaaagttgcacatacagttgcaccaaggtatacgaacttttcaacatatttcagttcatcatcatcaaacttgatcttttcctcttgatttgcatttattctcatggtcttcttgtttttgctcttgttgatctttagtccaactcttcatacttcttcactgtaagctttgttgattttcttctgcataatgttgtagtttgatggcctattcaacgcacatgtcatcagcaaagtcgaggtcatccagcttgtagtaaagttcacctgatgccattctgtccacctcctaatcgctttctccatccaatccatagccaatttaggaagaggaagcctgacatgttacacccctgcttcaccccggtcttgatt
gi|4 : tacctatcctctgtgtgtctaaggacacgtagggcctccacagactgtctccacttagttctgtcggctgcagcagcccttgcttcccccacgttcttcgtcctccgatggtccgctccttcttcactttttgtctccaggccgccccttctttcttttgccttttggtgtccatgttgaccagtgctacattacaatcactcctgggctgcatatcttgtctcaggatgtgtccnccatgttgaccagtgctacattacaatcacttcggggctgcatatcttgtcccaggatgtgcccattattaaacttA-GTTGCACCAAG-GTATACGAACT-TTTCAACATA-TTTCAG-TTCATCAT--CAT-CAA-ACTTGATCTTTTC--C--TCTTGATTTGCATTTATTCTCATGGTC-TTCTTGTTTTTGCTCTTGT--T--GATCT-TT-AG---TCCAACT---C-T--TCA----------TA--------CTT-CTTCACTGTAAGCTTTG-TTGATTTT---CT-T-CTGCATAAT-GTTGT-AG-TTTGATGGCCT--ATTCAACGCACATGTCATCA--GCAAAGTC-G-AGGTCATCCAG-CTT--GTAGT-AAA-GTTCACCTG-ATGCCATTCTGTCCACCTCCTAATCGC-TTTCTC-----CATCCAATCCAT----------AGCCAATTTAGGAAGA-GGAAGCCTGACATGTTA-------------CA--------CCCCTGCTTCACCCCGG--TCTTGAtattttaaaaatatgcaagtgtaaaagttgcacatacagttgcaccaaggtatacgaacttttcaacatatttcagttcatcatcatcaaacttgatcttttcctcttgatttgcatttattctcatggtcttcttgtttttgctcttgttgatctttagtccaactcttcatacttcttcactgtaagctttgttgattttcttctgcataatgttgtagtttgatggcctattcaacgcacatgtcatcagcaaagtcgaggtcatccagcttgtagtaaagttcacctgatgccattctgtccacctcctaatcgctttctccatccaatccatagccaatttaggaagaggaagcctgacatgttacacccctgcttcaccccggtcttgatt
gi|5 : tacctatcctctgtgtgtctaaggacacgtagggcctccacagactgtctccacttagttctgtcggctgcagcagcccttgcttcccccacgttcttcgtcctccgatggtccgctccttcttcactttttgtctccaggccgccccttctttcttttgccttttggtgtccatgttgaccagtgctacattacaatcactcctgggctgcatatcttgtctcaggatgtgtccnccatgttgaccagtgctacattacaatcacttcggggctgcatatcttgtcccaggatgtgcccattattaaactttcatcttctcctgacttcactcagtggtctcatgtctacactttggagcctctcttctgtagtaatgtgttcttgccataccactaatgtcttgtataacctgattttggtgtgtcgtctgacgctgtaaagtgctccatatacctgtttcagtctgacaaaaatttactactctttattttaaaaatatgcaagtgtaaaagttgcacatac-CTCTGCGTGGCTA--A-GGGCACATAAGGCTTTCACA--GACTGCTTCCA--CTTTGCT---AT-TCGGCT--GCAG--CAGCCCTT-G-CT-----CCCCCCACCCCCCACCCCCC-------AC----GTTC-TC-CATCCTCCGAT-GTTA-CGCTCTTTCTC----TAC-TG-TTC-GT-CTCCAGGTGGTTTTT---GGTC-GCC----CTTT--CTTTCT--TCT-T---C--CTTCTGGTGCC--CACG-T----CATTGCCACTTT-ACAGTCATT----GGCT-GG--AT--CTT-G-TCT-CG-GGGT-GTGTC-CA--AT--AAACTTCCATCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGT-TT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTCTTT------TTGCCAT-CTTATTC-TTA-GAA--TGCGTCTTAAGCATTTGTT-CTGGAAAGTG-TTGATCGTC-TTAT--C-TCCT--CT--A-TTCA----TATTCCAGGTC---T-CGCAT----------CCATATAGTAGTACCG----------GTA-CTACT-AGTGTCTTG-TATAGT-CCGATTTTGGTGT--GTCGTCTGATG-TTGTTG-GT-GC-TCC-ATAT--CTA--TTTCA-GTCTGA-TAAA--AT-TTGCTCTTGCTTTTGCTACTCTT-CATTTCATGTCTTGTA-TACCTCCCCCTTCCT--TT-GATATT--GTTGCACCAAG-GTATACAAACT-TTTTAACATC-TTCCAG-TTCTTCAT--AAT-CAA-TTGTGATCTTTTC--T--GCTTGGTTTGTATTTATTCTTATGATC-T--TTG-TTTTGCTCTTGtt
gi|6 : tTTACCT---ATC-TTCTGCGTGCCTG--A-GGGCAC-TAAGGCCTCCACA--GACTGTCTCCA--CACTGCT---CTGTCGGCT--ACAG--CACCTCTT-G-CC-----CCCCCC-------------CCCCACCCACCCCAATTC-TC-CATCCTTCGAT-GTTC-CGCTCTTTCTC----TAC-CG-TTC-GT-CACCAGGTGGTTTTTG--A-TC-GCCATTTCTTT--CT---T--TCT-TTTTC--CTTCTGGTGCC--CACG-T----CATTGCTATATT-ACAATCACT----CCCT-GC--AT--CT--G-CCT-CA-GGGT-GTGTT-CA--GT--AAATTTCCATCT----CTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTG-TC------TCGTCGTCCTTATTC-TCA-GGA--TGCGTCTTAAGCATTTGTT-CTGGAAGGTG-TTGATCATTTT--TCA---TCT--CT--A-TTCA----TCTTCCAGGTC---T-CGCAT
gi|7 : ctgAACATC-TTCTAT-TTCTATATGTCAT-TCA-TCTTTATCTTTTCATC--ACTT--CTTGCGTTCATCCTCAAAAT----------TTTGC------------ATTT-TT-AGT---CC-A------------G---TGCTTTCTG--------CAAACTTTGTTG--TG--TTG-TTAG-ATT---TC-TCTTGAAT--TTGTTGT-TTTGTATATGAGAT--A---AGGGCA-ATGTTGTCT--GCGTAGTC-T-GGGTCGTCCAT-CATTGTT-GT-AAACTTCTATCTA-ATTCCGTTCTCTCCATTCCCT-ACTG--TTTTCCTC-ATTATCCAGTCCACA---------A-GTAG--AAGGAATA-GGAATCCc
gi|8 : cat-----CCCCCC-------------C-------CC----GTTC-TCTCACCCTCCGAT-GT-A-CGCTCTTTCTC----TAC-TGTTTC-GT-ATCCA-GTGGTTTTT---GGTC-GCC----CTTTC-CT---T--TCTCT---C--CTTCTGGTGCC--CACG-T----CATTGCCACATT---AGTCATT----GGTT-GG--AT--CTT-G-TCT-CA-GGGTAATGTC-CA--AT--GAACTTCCACCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGC-CT----CATTT-CTACTCT--TTGG-AGCATCTCTTCTGTAGTAGTATGTTC------TTGTTAT-CTTATTC-
gi|9 : cCCA---ATC-CTCTTCATACCTG--T-TGGCATATAAGGCC----------CTAGTTCCA--CTTTTCC---CTGTC--CTTGGCGA--CCACCCTG-G-TT-----GTACCC-------------C-------A-----GCTCTTC-CATC--CCA---GTT---GTTCTTTTTC----TGT-TG-TTCTGT-GT-CATGTTGTTTTT----GCC-TTC----CTAT--CT---T--TCT-TTTCC--CATCTGGTCTC--CAGG-T----CAGTTCAACTGC-ACAAT-GCT----TGAT-GC--TT--TTC-ATTCT-CA-GCAC-GTGAC-CA--ATCCAAA--TCCATCTT---CTTc
blockSeqs : TAA T . . CT TG TT C ATC TG TT . C TTTTC ACCCCCCACCCCCCACG T T G AT CTAGA . T T T A TGCA . ATTT AG TTCT C TTG TT TT N TTGAC . CCTG . AT AT T T GG C A . TT CC T TTT . . T . T . CA T A AATAAA C G T AT . T T TATCATG GA TC T GTGG G CTGC TT TGGAGCCT G G G TGTTCTTGCC T A TT G G TA A A G . G AC TT . . AG TTGCT TT C A C T T . G T AC T G . A GT G . ATC G C TTC T ATTG C GCTTCTTCACTGGGCTTGTTGGTTTGCNCTGATATCTTG A TAA T . TG GCT C AAT CTT T ATTC C A AT TG A T T A G . C A T TTAG TTGTAAAACAAACAA C TAATCCTTTGCTTCACCCCGGCTTGAAGATTGAAT A AT C
blockSeqs : . . . . . CT . G . . . . . C CCCCACCCACCCCAA . . . T C . . . . G TG . G C TCT . TTT . . T TTGAC . TCGG . . . . . G . . . . T T . . . . . G . . . A A . . . . . . T TATCAC . . . . A T CT AGTTC T G C . . . T . A . . . . . . . TT . . AG GCT AA T . A T . . . T A . . . . . . . TT C T TT . T . AATCGCTACTCTTTGTG . AA . . TT GC . GT TTT A CAA C A . G . T T . C . C . T TCG AGCCAATT . CATCCCGGCCGGTCTTG . A .
blockSeqs : . . . . . TT . G . . . . . T CCCC . . . A C . . . . G TG . . . T . TTC . . T A . . . . . . . G . . . . . C . . . . . G . . . C . . . . . . . T TATC . . . . T T T A C G A . . . T . A . . . . . . . . . . A TT TT T . . . . . . . A . . . . . . . C C T T . T . AGTCCAACTCTTCATA . G . . T CT . TT GT A A . G . G . T T . . . C . T TCA AGCAAC .
blockSeqs : . . . . . TC . G . . . . . C CATT . . . C T . . . . G TG . . . A . C . . T T . . . . . . . T . . . . . C . . . . . T . . . A . . . . . . . . TCA . . . . G T T . T . C . . . T . A . . . . . . . . . . . T . . . . . . . . . . C T T T . . . AGTCCAGTGCTTTCTG . T . . A TC . C AG A A . . . T . A . . . . C . . . AAGTAG .
blockSeqs : . . . . . TC . G . . . . . C CACG . . . C C . . . . G G . . . T . G . . C T . . . . . . . T . . . . . C . . . . . T . . . A . . . . C . . . . G T . . . . . T C A . . . . . . . . . .
blockSeqs : . . . . . CT . G . . . . . C CACG . . . A C . . . . G T . . . T . . . . C T . . . . . . . C . . . . . T . . . . . T . . . A . . .
blockSeqs : . . . . . TC . G . . . . . G CCCG . . . C C . . . . T T . . . T . . . . C T . . . . . . . T . . . . . C . . . . . . . . . . . .
blockSeqs : . . . . . GT . T . . . . . . AAC . . . A C . . . . . T . . . T . . . . G T . . . . . . . T . . . . . . . . . . .
blockSeqs : . . . . . . . . . CAG . . . . . . . . . . . . T . . . . . . . . . . . . . T . . . . . . .
blockSeqs : . . . T . . .
blockSeqCons : ** C***** C**** TG** ** T***** T***** T* **** T**** A******* T* ** ** C**** T**** ANTCCNACTCTTTNTG**************************** NC**** NT** G** T* AGCAA*************
originalCons : TTACCT---ATC-CTCTGCGTGCCTA--A-GGGCACATAAGGCCTCCACA--GACTGTTTCCA--CTTTGCT---CTGTCGGCT--GCAG--CAGCCCTT-G-CT-----CCCCCC-------------C-------AC----GTTC-TC-CATCCTCCGAT-GTTA-CGCTCTTTCTC----TAC-TG-TTC-GT-CTCCAGGTGGTTTTTG--GGTC-GCC----CTTT--CT---T--TCT-T---C--CTTCTGGTGCC--CACG-T----CATTGCCACATT-ACAGTCACT----GGCT-GC--AT--CTT-G-TCT-CA-GGGT-GTGTC-CA--AT--AAACTTCCATCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTGTTC------TTGCCAT-CTTATTC-TTA-GGA--TGCGTCTTAAGCATTTGTT-CTGGAAGGTGTTTGATCATCTTTATCAC-TCCT--CT--A-TTCA----TCTTCCAGGTC---T-CGCATTT---AGTTCCTATANTGTAGTANCG----------GTA-CCACT-AGTGTCTTGTTATAGT-CTGATTTTGGTGTTAGTCGTCTGATGATTGTTG-GT-GC-TCC-ATAT--CTGTTTTTCA-GTCTGA-CAAAAGAT-T---TCTTGCTTCTGCTACTCTTACCTTTCATGTCTTGTATTACCTCCCCCTTCCT--TT-GATATTA-GTTGCACCAAG-GTATACAAACT-TTTCAACATC-TTCCAG-TTCTTCAT--CAT-CAA-TTTTGATCTTTTC--C--GCTTGGTTTGCATTTATTCTCACGATC-T--TTG-TTTTGCTCTTGTA-T--GATCT-TT-AGTTCTCC-ACT---C-T--TCG---TGCT--CTG--------CTT-CTTCACTG--GGC-TTG-TTGGTGTT---NC-T-TTGCAT--TCGTTGT-NT-GTTGATGGCAT--A---AACGCACATGTCGTCA--GCGAAGTC-T-AGGTCATCCAG-CTTTGGTAGT-AAA-TTCCACCTG-ATGCCATTCTCTCCACCTCCT-ATTGC-TTTTTCTC-GTCGTCCAATCCAT----------A-NCAA--TAGGAAGA-GGAAGCCTGACATGCTA-------------CA--------CCCCGG-------CCGG--TCTTGAA----------CATTCC--A-ACCCAA-TTACTTGTCTTCT
finalCons : TTACCT---ATC-CTCTGCGTGCCTA--A-GGGCACATAAGGCCTCCACA--GACTGTTTCCA--CTTTGCT---CTGTCGGCT--GCAG--CAGCCCTT-G-CTC-----CCCCC-------------C-------AC----GTTC-TC-CATCCTCCGAT-GTTA-CGCTCTTTCTC----TAC-TG-TTC-GT-CTCCAGGTGGTTTTTG--GGTC-GCC----CTTT--CTT-----TCT-T---C--CTTCTGGTGCC--CACGT-----CATTGCCACATT-ACAGTCACT----GGCT-GC--AT--CTT-G-TCT-CA-GGGT-GTGTC-CA--AT--AAACTTCCATCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTGTTC------TTGCCAT-CTTATTC-TTA-GGA--TGCGTCTTAAGCATTTGTT-CTGGAAGGTGTTTGATCATCTTTATCAC-TCCT--CT--A-TTCA----TCTTCCAGGTCT----CGCATTTA-------CTATANTGTAGTANCG----------GTA-CCACT-AGTGTCTTGT-ATAGT-CTGATTTTGGTGT--GTCGTCTGATGATTGTTG-GT-GC-TCC-ATAT--CTG--TTTCA-GTCTGA-CAAAAGAT-T---TCTTGCTTCTGCTACTCTTACCTTTCATGTCTTGTATTACCTCCCCCTTCCT--TT-GATATTA-GTTGCACCAAG-GTATACAAACT-TTTCAACATC-TTCCAG-TTCTTCAT--CAT-CAA-TTTTGATCTTTTCC----GCTTGGTTTGCATTTATTCTCACGATC-T--TTG-TTTTGCTCTTGTT----GATCT-TTANTCCNACTCTTTNTG----------------------------CTT-CTTCACTG--GGC-TTG-TTGGTGTTNC----T-TTGCAT--TCGTTGTNT--GTTGATGGCAT--A---AACGCACATGTCGTCA--GCGAAGTCG--AGGTCATCCAG-CTTTGGTAGT-AAA-TTCCACCTG-ATGCCATTCTCTCCACCTCCT-ATTGCT-TTTTCTC-GTCGTCCAATCCATAGCAA-------------TAGGAAGA-GGAAGCCTGACATGCTA-------------CA--------CCCCGG-------CCGG--TCTTGAA----------CATTCC--A-ACCCAA-TTACTTGTCTTCT
4 sequences could not be aligned to this reference sequence:
Unaligned ( gi|10 ): CATCTTCCATAGATTTGGCCTTCATCGCTATGTTTTCGTTGCATTTTTACATTCATCCGTAATACTTCACATTTGTTGATATTTACTTCCAATCCTGTGAATCCTTTGTGCGTTTAGTTTATATTCTATGTGTAATTGCCGTCTCGTGGAGGAAATAAGAGCGAGATCTGCGAAGTCGAAACCGTCTA
Unaligned ( gi|14 ): CACTCATCCCATTCACCATCCCTCATGCCTGTTGGTATAAGCCTAGTACCACTTTTCCCTGTACTTGGCGGACCACCCTGGTTTAGCCAGATTTTCCATCCTGTTGTTCTCTTAAT
Unaligned ( gi|16 ): TAATCCTTAAATCTCTCCGCCCCAGAAGCCGCATAAGGCCTCCATGCTGTTTGCCCATTCTTTCTCAT
Unaligned ( gi|19 ): ACATCATTAAACTTTCTTTGCAGTTCTNCTTGCTGACCATGTCAGTTTT
Alignments
lowQualScore : 11111111111111111111111111111111111111111111111111111111111
lowQualScore : 222222 3333333333333333333333333333 11111 1111 1111 11 11 3333333 222222 1111 111111 11 1 2 111 11111 666666 1 1 1 22 2 11 22 1 111111 1 1 1 11 1 111 1 22222 1111 333333333333333333 3333333333333 1111 222 111111 2222 222 222222 1 1 11 1 1 1 11111 1111 444444444444444444 00000000000000000000000000000000000000000000000000000000000 2222 1
lowQualScore : 777 4 55 4 55 11 66 1 777 55 55 4 4 222222 4444444444444444444444444444 4 4 4 99 00000 4 4 4 4 4 3333 2 4 3333 33 11 4 1111111 55 3 111111 4 7777 4 55 55 7 3 88 3 3 3 55 99 6 777 4 4 4 9999 3 5 66 5 6 999999 5 5 8 11 0 8 0 0 0 777 8 3 66666 7 111111 0 5 1 8 8 6 8 3 22 0 0 8 8 8 8 11 22 8 8 0 0 666666 22 1 5 2 5 5 33 0 222 8 8 6 3 99 6 6 00000 1 2 0000 6 777777777777777777 8 1 9999999999999 1 7777 99 8888 000 8 8 99 999999 8 6666 000 1 000000 0 6 11 6 3 5 55555 6 6 6 88 1111 777777777777777777 8 00000000000000000000000000000000000000000000000000000000000 7 2222 3
lowQualScore : ... . .. . .. .. .. . ... .. .. . . ...... ............................ . . . .. ..... . . . . . .... . . .... .. .. . ....... .. . ...... . .... . .. .. . . .. . . . .. .. . ... . . . .... . . .. . . ...... . . . .. . . . . . ... . . ..... . ...... . . . . . . . . .. . . . . . . .. .. . . . . ...... .. . . . . . .. . ... . . . . .. . . ..... . . .... . .................. . . ............. . .... .. .... ... . . .. ...... . .... ... . ...... . . .. . . . ..... . . . .. .... .................. . ........................................................... . .... .
lowQualScore : 888 0 55 0 55 66 11 1 000 55 55 4 4 666666 1111111111111111111111111111 0 0 0 77 11111 0 0 0 0 1 7777 9 4 9999 55 00 0 5555555 55 4 000000 0 0000 0 55 00 3 6 44 6 6 6 55 55 4 000 4 4 4 4444 1 0 99 0 2 444444 0 7 0 00 8 0 8 6 4 000 0 2 00000 0 222222 8 0 0 0 0 0 0 8 00 4 6 0 0 0 0 00 00 0 0 8 0 888888 00 4 5 5 8 5 88 0 111 0 0 7 3 22 7 7 33333 0 2 8888 7 888888888888888888 0 0 2222222222222 0 0000 00 4444 444 0 0 00 444444 0 2222 666 4 888888 0 4 00 0 3 5 88888 7 7 7 88 6666 666666666666666666 0 44444444444444444444444444444444444444444444444444444444444 3 7777 3
consensus : TTACCT---ATC-CTCTGCGTGCCTA--A-GGGCACATAAGGCCTCCACA--GACTGTTTCCA--CTTTGCT---CTGTCGGCT--GCAG--CAGCCCTT-G-CT-----CCCCCC-------------C-------AC----GTTC-TC-CATCCTCCGAT-GTTA-CGCTCTTTCTC----TAC-TG-TTC-GT-CTCCAGGTGGTTTTTG--GGTC-GCC----CTTT--CTT--TCT-T---C---CTTCTGGTGCC--CACG-T----CATTGCCACATT-ACAGTCACT----GGCT-GC--AT--CTT-G-TCT-CA-GGGT-GTGTC-CA--AT--AAACTTCCATCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTGTTC------TTGCCAT-CTTATTC-TTA-GGA--TGCGTCTTAAGCATTTGTT-CTGGAAGGTGTTTGATCATCTTTATCAC-TCCTCTA-TTCATCTTCCAGGTC---T-CGCATTTAG-TC-CTATAGTGTAGTANCGGTA-CCACT-AGTGTCTTGTTATAGT-CTGATTTTGGTGTTAGTCGTCTGATGATTGT-TGGT-GC-TCC-ATAT--CTGTTTTTCA-GTCTGA-CAAAAGAT-TT---CTTGCTTCTGCTACTCTTACCTTTCATGTC-TGTATTACCTCCCCCTTCCT--TT-GATATTA-GTTGCACCAAG-GTATACAAACT-TTTCAACATC-TTCCAG-TTCTTCAT--CAT-CAA-TTTTGATCTTTTC--C--GCTTGGTTTGCATTTATTCTCACGATC-T--TTG-TTTTGCTCTTG--T-T--GA---------TCTTT-AGT-----------C-CTACTCT----TC-GTGC-TT-CTTCACTG--GGC-TTG-TTGGTGTT---NC-T-TTGCAT--TCGTTGTNTTGTTGATGGCAT--A---AACGCACATGTCGTCA--GCGAAGTCTGAGGTCATCCAG-CTTTGGTAGT-AAA-TTCCACCTG-ATGCCATTCTCTCCACCTCCT-ATTGC-TTTTTCTC-GTCGTCCAATCCAT----------AG-CAA--TAGGAAGA-GGAAGCCTGACATGCTA-------------CA--------CCCCGG-------CCGG--TCTTGAA----------CATTCC--A-ACCCAA-TTACTTGTCTTCT
Reference ( family-2912 ) : TTACCT---ATC-CTCTGCGTGCCTA--A-GGGCACATAAGGCCTCCACA--GACTGTTTCCA--CTTTGCT---CTGTCGGCT--GCAG--CAGCCCTT-G-CT-----CCCCCC-------------C-------AC----GTTC-TC-CATCCTCCGAT-GTTA-CGCTCTTTCTC----TAC-TG-TTC-GT-CTCCAGGTGGTTTTTG--GGTC-GCC----CTTT--CTT--TCT-T---C---CTTCTGGTGCC--CACG-T----CATTGCCACATT-ACAGTCACT----GGCT-GC--AT--CTT-G-TCT-CA-GGGT-GTGTC-CA--AT--AAACTTCCATCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTGTTC------TTGCCAT-CTTATTC-TTA-GGA--TGCGTCTTAAGCATTTGTT-CTGGAAGGTGTTTGATCATCTTTATCAC-TCCTCTA-TTCATCTTCCAGGTC---T-CGCATTTA-----CTATANTGTAGTANCGGTA-CCACT-AGTGTCTTG-TATAGT-CTGATTTTGGTGT--GTCGTCTGATGATTGT-TGGT-GC-TCC-ATAT--CTG--TTTCA-GTCTGA-CAAAAGAT-TT---CTTGCTTCTGCTACTCTTACCTTTCATGTCTTGTATTACCTCCCCCTTCCT--TT-GATATTA-GTTGCACCAAG-GTATACAAACT-TTTCAACATC-TTCCAG-TTCTTCAT--CAT-CAA-TTTTGATCTTTTC--C--GCTTGGTTTGCATTTATTCTCACGATC-T--TTG-TTTTGCTCTTG--T-T--GA---------TCTTT-ANT-----------C-CNACTCT----TT-NTGC-TT-CTTCACTG--GGC-TTG-TTGGTGTT---NC-T-TTGCAT--TCGTTGTNT-GTTGATGGCAT--A---AACGCACATGTCGTCA--GCGAAGTC-GAGGTCATCCAG-CTTTGGTAGT-AAA-TTCCACCTG-ATGCCATTCTCTCCACCTCCT-ATTGC-TTTTTCTC-GTCGTCCAATCCAT----------AG-CAA--TAGGAAGA-GGAAGCCTGACATGCTA-------------CA--------CCCCGG-------CCGG--TCTTGAA----------CATTCC--A-ACCCAA-TTACTTGTCTTCT
gi|1 : CCT---ATC-CTCTGTGTGCCTATTACGGGCACATAAG-CCTCCACA--GACTGTTTCCA--CTTT-CT---CTGTCGTCT--GCAG--CAGCCCTTTG-CTTTTTTCCCCAA-------------C-------AT----TTTC-TC-CAGCCTC-GAT-GTTA-CGCTCTTTCT-----TACCTG-TTC-TT-CTTCAGGTTGTTTT----GGTCTGCC----CTTTT-CTTCTTCT-T---C---CTTCTGGTGCC--CACGAC----CATTGCCACATTTACAGTCACT----GGCTTGC--AT--CTTTG-TCGGCA-GGGT-GTGTTTCA--AT--AA-TTTCCATCTT---TTTCTTCCTGACTTCTTCA-TCAGCTGGT-TTTCTGCATTTTCTACACT--TTGG-AGC-TCTCTTCTGTAGTAGTGTGTTC------ATGC-AT-CTTATTC-TTA-GGA--TGCGTCTT-AGCATTTGTTCCTGGAAGGTGTTTGATCATCTTTATCAC-TCCTCTA-TTCATCTTCCA-GTC---TCCGCATTTAAGTTCCTATAGTGTA--AGCGGTA-CCACT-AGTGTCTTGTTATAGT-CTG-TTTTGGTGTTAGTCGTCTGATAATGGT-TGGT-GCTTCC-ATAT--CTGTTTTTCAGGTCTGACCAAAAGAT-TT---CTTGCTTCTGCTACTCTTACCTTTCATGTCATGTATTACCTCCCCCTTCCTTATT-GATATTA-GTTGCAC--AG-TTATACAAACT-TTTCAACATCTTTCCAGAATCTTCAT--CAT-CAATTTTTGATTTTTTT--CTTGCTTGGTTTTGATTTATTCTTACGATC-T--TTA-TTTTGCTCTTGTAT-T--GA---------TCTTTCAAT-----------C-CTACTCT----TTCGTGCTTT-CTTCACT---GGC-TTGTTTGGTGTTGACCT-T-TTGCAT--TCTTCGT-T-GTTGTTGGCAT--C---AACG-ACAATTC-TCA--GTGAAGTCTTAGGTCATCCAGACTTTGGTAGTAAAA-TTCCATCTGTATGCCATT-TCTCCATCTCCT-ATTGCTTTTTTCTT-ATCGTCCAATCCAT----------TT-GAA--TAGGAAGA-GAAAGCCTGACATGCTA-------------TAATCCTTTGCTTCAC-------CCGG--TCTTGAAGATTCGAAATCATTCCAAA-ACCCAA-CTACTTGTCTTCT
gi|11 : ttTACCTTAAATCTCTCTGCA--CCAG--A-AGTTGCATAAGGCCTCCACGCTGACTG--CCCATTCTTTCCTATCCTGT--GCT--GCTGTTCTGGCCAT-G-TT---------CC-------------A-------AC-----TTG-TC-CATCCT-TGTTGGTTT-CTTTCTTTCAC----TGT-TG-TTC-TT-CTCCAAGTTG-TTTTG--GGCC-TGC----CTCTAGCTT--TTT-TC--C---CTTCTGG
gi|12 : TTACCT---ATC-CTCTGCGTGTCTA--A-GGGCAGATAAGGCCTCCACA--GACTGTGTCCA--CTTTGCT---CTGCCAGCT--GCAG--CAGCCCTT-GCCC-----CCCCCC-------------C-------CC----CCCC-CC-CATCCTCCGAT-GTTA-CGCTCTTTCTCTAGATAC-TG-TTC-GT-CTCCAGGTGGTTTTTG--Gag
gi|13 : gT--CTT-G-TCG-CA-GGAT-GTGTT-CA--AA--AAATTTCCATCTT---CTTCT-CCTGACTTCTTCANACA--TTGC-CA----CAT----TACAGTCACTGGTTGCATCTTGTC-GCAG-GGTGTGTTCAATAAATTTCCAT-CTTTTTC-Tt
gi|13 : TTT--CCA--TCT-T---CTT-CTCCTGACTTCTTCANA------CATTGCCACATT-ACAGTCACT----GGTT-GC--AT--CTT-G-TCG-CA-GGGT-GTGTT-CA--AT--AAATTTCCATCTT---TTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATcctgacttcttcactcagtggtctcat
gi|15 : tcttgtcgcaggatgtgttcaaaaaaTTACCT---ATT-CTTTGCGTGCCTA--A-GGGCACATAAGGCATCCACA--GACTGCTTCCA--CTTTGCT---CTTTCGGCT--GTAG--CAGCC
gi|17 : TTACCT---ATC-CTCTGTGTGCCTT--A-GGGCACATAAGGCCTCCACA--GACTGTTTCCt
gi|18 : gTCCAG-CTT-GGTAGT-AAAGTTCCACCTG-ATGCCATTCTGTCCACCTCCT-AT
gi|2 : CT---CTGTCGTCT--GCAG--CAGCCCTT-G-CTTTTT-CCCCAA-------------C-------AT----TTTC-TC-CCACCTCGGAT-GTTATCGCTCTTTCT-----TAC-TG-TTC-TTTCTTCAGGTGGTTTT-G--GGTC-GCCG---CTTT--CTTCTTCT-TG--C---CTTCTGGTGCC--CA-G-A----CATTGCCACATT-ACAGTCACT----GCTT-GC--AT--CTTTG-TCGGCACGGGT-GT-TT-CA--AT--AAA-TTCCATCTTTTTCTTCT-CCTGACTTCTTCACTCAG-TGGTTCT----CATTT-CTACACT--TTGG-AGC-TCTCTTCTGTAGT-GTGTGTTCA-----TTGCCAT-CTTATTCGTTATGGAATCGCGTCTTAAGCATTTGTT-CTGGAAGGTGTTTGATCATCTTTATCAC-TCCTCTATTTCATCTTCCAGGTCCTGC-CGCATTTAGTTC-CTATAGTGTA-TAGCGGTATCCACTAAGTGTCTTGTTATAGTGCTCGTTTTGGTGTTAGTCGTCTGATAATGGT-TGGTGGC-TCCGATAT--CTGTTTTTCA-GTCTGA-C-AAAGAT-TT---CTTGCTTCTGCTACTCTTACCTTTCATGTC-TGTATTACCTCCCCCTTCCT--TTGGATATTACGTTGCACCAAGTGTATACAAACTGTTTCAACATC-TTCCAGAATCTTCAT--CATGCAA-TTTTGATTTTTTCT-T--GCTTGGTTTTGATTTATCTTAACGATCTT--TTA-TTTTGCTCTTG--TATTGGA---------TCTTT-AAT-----------CGCTACTCT----TT-GTGT-TT-CTTCACTGA-AGC-TTG-TTGGTGTT---GCTT-TTGCAT--C--TTGTGT-GTTGTTGGCATCAA---GACACACATGTC-TCAATGTGAAGTCTGAGGTCATCCAGACTTTGGTAGTAAAA-TTCCATCTG-ATGCCATT-TCTCCATCTCCT-ATTGC-TTTTTCTTAGTCGTCCAATCCATTTGTAAAACAAA-CAA--TAGGAAGACGGAAGCCTGACATGCTATAATCCTTTGCTTCA--------CCCCGG-------CTTGAAGATTGAAT---------CATTCC--ATACCCAACTTACTTGTCTTC
gi|3 : tTTACCT---ATC-TTCTGCGTGCCTA--A-GGGCACATAAGGCCTCCACA--GACTGTCTCCA--CTCTGTT---CTGTCGGCT--GCAG--CAGCCCTT-G-CT-----TCCCCC-------------C-------AC----GTTC-TC-CATCCTCCGAT-GTTC-TGCTCTTTCTC----TAT-CG-TTC-GT-CTCCAGGTGGTTCTTGCAGATC-ACC----CTTT--CTT--TCT-T---C---CTTCTGGTGCC--CATG-T----CATTGCTATATT-GCAATCATT----CGCT-GC--AT--CTT-G-TGT-CA-GGGT-ATGTC-CA--AT--AAACTTCCATCTT---CTTCT-CTTGACTTCTTCATTCAG-GGGT-CT----CATGT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTGTCC------TTGCCAT-CTTATTC-TCA-GGA--TCCGTCTTAAGCATTTGTT-CTGGAAGGTGTT-GATCATCTT-ATCATGTCCTCTA-TTCATCTTCCAAGTC---T-CACATT-A-------ATATTGTAGTACCGGTA-CCACT-AGCGTTTTG-TATAGT-CTGATTTTGGTGT--GTCGTCTGATG-TTGT-TAGT-GT-TCC-ATAT--CTG--TTTCA-GTCTGA-CAAAAGATGCT---CAAGCTTTTGCTACTCTT--------------GTAT-GCCGCCCCCTTTCT--TT-GATAT-A-GTTGCACCAAG-GCATACAAACT-TTTCAACATC-TTCCAG-TTCTTAAT--CAT-CAA-TTGTGATCTTTTC--C--GCTTGATTTGCATTTATTATCATGATC-T--TTG-TTTTGCTCTTG--T-T--GATCTCTTGCTTCTTC-ACTGGGCTTGTTGGT-TTGCNCTGATATC-TTGC-TT-CTTCACTG--GGC-TTG-TTGGT-TT---GC-T-TTGCAT--GTGTTGTCTTGTTGATGACAT--A---AACGCA-ATGTCATCA--GCGAAGTC-GAGGTCATCCAG-CTT-GGTAGT-------CCACCTG-ATGCCATTCTCTCCACCTACT-ATTGC--TTTTCTC-GTCGTCCAATCCAT----------AG-CAAC-TAGGAATA-GGGACCCTGACATGTTA-------------CA--------TCCCGG-------CCGG--TCTTG------------C-TTCC--A-AACCAA-TTACTTGTTTTTT
gi|4 : TACCT---ATC-CTCTGTGTGTCTA--A-GGACACGTAGGGCCTCCACA--GACTGTCTCCA--CTTAGTT---CTGTCGGCT--GCAG--CAGCCCTT-G-CT------TCCCC-------------C-------AC----GTTC-TT-CGTCCTCCGAT-GGTC-CGCTCCTTCTT----CAC-TT-TTT-GT-CTCCA-------------GGCC-GCC----CCTT--CTT--TCT-TTTGC---CTTTTGGTGTC--CATG-TTGACCAGTGCTACATT-ACAATCACTCCTGGGCT-GCATAT--CTT-G-TCT-CA-GGAT-GTGTC-C
gi|4 : C--CATG-TTGACCAGTGCTACATT-ACAATCACTTCGGGGCT-GC--ATATCTT-G-TCC-CA-GGAT-GTGCC-CATTATT-AAACTTTCATCTT---CT----CCTGACTTC---ACTCAG-TGGT-CT----CATGT-CTACACT--TTGG-AGCCTCTCTTCTGTAGTAATGTGTTC------TTGCCAT-nccatgttgaccagtgctacattacaatcacttcggggctgcatatcttgtcccaggatgtgcccattattaaactttcatcttctcctgacttcactcagtggtctcatgtctacactttggagcctctcttctgtagtaatgtgttcttgccataccactaatgtcttgtataacctgattttggtgtgtcgtctgacgctgtaaagtgctccatatacctgtttcagtctgacaaaaatttactactctttattttaaaaatatgcaagtgtaaaagttgcacatacagttgcaccaaggtatacgaacttttcaacatatttcagttcatcatcatcaaacttgatcttttcctcttgatttgcatttattctcatggtcttcttgtttttgctcttgttgatctttagtccaactcttcatacttcttcactgtaagctttgttgattttcttctgcataatgttgtagtttgatggcctattcaacgcacatgtcatcagcaaagtcgaggtcatccagcttgtagtaaagttcacctgatgccattctgtccacctcctaatcgctttctccatccaatccatagccaatttaggaagaggaagcctgacatgttacacccctgcttcaccccggtcttgatt
gi|4 : tacctatcctctgtgtgtctaaggacacgtagggcctccacagactgtctccacttagttctgtcggctgcagcagcccttgcttcccccacgttcttcgtcctccgatggtccgctccttcttcactttttgtctccaggccgccccttctttcttttgccttttggtgtccatgttgaccagtgctacattacaatcactcctgggctgcatatcttgtctcaggatgtgtccnTA-CCACT-AATGTCTTG-TATAAC-CTGATTTTGGTGT--GTCGTCTGACG-CTGTAAAGT-GC-TCC-ATATACCTG--TTTCA-GTCTGA-CAAAA-AT-T------------TACTACTCTTaccactaatgtcttgtataacctgattttggtgtgtcgtctgacgctgtaaagtgctccatatacctgtttcagtctgacaaaaatttactactctttattttaaaaatatgcaagtgtaaaagttgcacatacagttgcaccaaggtatacgaacttttcaacatatttcagttcatcatcatcaaacttgatcttttcctcttgatttgcatttattctcatggtcttcttgtttttgctcttgttgatctttagtccaactcttcatacttcttcactgtaagctttgttgattttcttctgcataatgttgtagtttgatggcctattcaacgcacatgtcatcagcaaagtcgaggtcatccagcttgtagtaaagttcacctgatgccattctgtccacctcctaatcgctttctccatccaatccatagccaatttaggaagaggaagcctgacatgttacacccctgcttcaccccggtcttgatt
gi|4 : tacctatcctctgtgtgtctaaggacacgtagggcctccacagactgtctccacttagttctgtcggctgcagcagcccttgcttcccccacgttcttcgtcctccgatggtccgctccttcttcactttttgtctccaggccgccccttctttcttttgccttttggtgtccatgttgaccagtgctacattacaatcactcctgggctgcatatcttgtctcaggatgtgtccnccatgttgaccagtgctacattacaatcacttcggggctgcatatcttgtcccaggatgtgcccattattaaactttcatcttctcctgacttcactcagtggtctcatgtctacactttggagcctctcttctgtagtaatgtgttcttgccaA-GTTGCACCAAG-GTATACGAACT-TTTCAACATA-TTTCAG-TTCATCAT--CAT-CAA-ACTTGATCTTTTC--C--TCTTGATTTGCATTTATTCTCATGGTC-TTCTTGTTTTTGCTCTTG--T-T--GA---------TCTTT-AGT-----------C-CAACTCT----TC-ATAC-TT-CTTCACTGTAAGCTTTG-TTGATTTT---CT-T-CTGCATAAT-GTTGTAG-TTTGATGGCCT--ATTCAACGCACATGTCATCA--GCAAAGTC-GAGGTCATCCAG-CTT--GTAGT-AAA-GTTCACCTG-ATGCCATTCTGTCCACCTCCTAATCGC-TTTCTC-----CATCCAATCCAT----------AGCCAATTTAGGAAGA-GGAAGCCTGACATGTTA-------------CA--------CCCCTGCTTCACCCCGG--TCTTGAtattttaaaaatatgcaagtgtaaaagttgcacatacagttgcaccaaggtatacgaacttttcaacatatttcagttcatcatcatcaaacttgatcttttcctcttgatttgcatttattctcatggtcttcttgtttttgctcttgttgatctttagtccaactcttcatacttcttcactgtaagctttgttgattttcttctgcataatgttgtagtttgatggcctattcaacgcacatgtcatcagcaaagtcgaggtcatccagcttgtagtaaagttcacctgatgccattctgtccacctcctaatcgctttctccatccaatccatagccaatttaggaagaggaagcctgacatgttacacccctgcttcaccccggtcttgatt
gi|5 : tacctatcctctgtgtgtctaaggacacgtagggcctccacagactgtctccacttagttctgtcggctgcagcagcccttgcttcccccacgttcttcgtcctccgatggtccgctccttcttcactttttgtctccaggccgccccttctttcttttgccttttggtgtccatgttgaccagtgctacattacaatcactcctgggctgcatatcttgtctcaggatgtgtccnccatgttgaccagtgctacattacaatcacttcggggctgcatatcttgtcccaggatgtgcccattattaaactttcatcttctcctgacttcactcagtggtctcatgtctacactttggagcctctcttctgtagtaatgtgttcttgccataccactaatgtcttgtataacctgattttggtgtgtcgtctgacgctgtaaagtgctccatatacctgtttcagtctgacaaaaatttactactctttattttaaaaatatgcaagtgtaaaagttgcacatac-CTCTGCGTGGCTA--A-GGGCACATAAGGCTTTCACA--GACTGCTTCCA--CTTTGCT---AT-TCGGCT--GCAG--CAGCCCTT-G-CT-----CCCCCCACCCCCCACCCCCC-------AC----GTTC-TC-CATCCTCCGAT-GTTA-CGCTCTTTCTC----TAC-TG-TTC-GT-CTCCAGGTGGTTTTTG--G-TC-GCC----CTTT--CTT--TCT-T---CTTCCTTCTGGTGCC--CACG-T----CATTGCCACTTT-ACAGTCATT----GGCT-GG--AT--CTT-G-TCT-CG-GGGT-GTGTC-CA--AT--AAACTTCCATCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGT-TT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTCTTT------TTGCCAT-CTTATTC-TTA-GAA--TGCGTCTTAAGCATTTGTT-CTGGAAAGTGTT-GATCGTCTT-ATC---TCCTCTA-TTCATATTCCAGGTC---T-CGCATCCA------TATA--GTAGTACCGGTA-CTACT-AGTGTCTTG-TATAGT-CCGATTTTGGTGT--GTCGTCTGATG-TTGT-TGGT-GC-TCC-ATAT--CTA--TTTCA-GTCTGA-TAAAA--T-TTGCTCTTGCTTTTGCTACTCTT-CATTTCATGTCTTGTAT-ACCTCCCCCTTCCT--TT-GATATT--GTTGCACCAAG-GTATACAAACT-TTTTAACATC-TTCCAG-TTCTTCAT--AAT-CAA-TTGTGATCTTTTC--T--GCTTGGTTTGTATTTATTCTTATGATC-T--TTG-TTTTGCTCTTG--tt
gi|6 : tTTACCT---ATC-TTCTGCGTGCCTG--A-GGGCAC-TAAGGCCTCCACA--GACTGTCTCCA--CACTGCT---CTGTCGGCT--ACAG--CACCTCTT-G-CC-----CCCCCC-------------CCCCACCCACCCCAATTC-TC-CATCCTTCGAT-GTTC-CGCTCTTTCTC----TAC-CG-TTC-GT-CACCAGGTGGTTTTTG--A-TC-GCCATTTCTTT--CTT--TCT-TTTTC---CTTCTGGTGCC--CACG-T----CATTGCTATATT-ACAATCACT----CCCT-GC--AT--CT--G-CCT-CA-GGGT-GTGTT-CA--GT--AAATTTCCATCT----CTTCT-CCTGACTTCTTCACTCAG-TGGT-CT----CATTT-CTACACT--TTGG-AGCATCTCTTCTGTAGTAGTGTG-TC------TCGTCGTCCTTATTC-TCA-GGA--TGCGTCTTAAGCATTTGTT-CTGGAAGGTG-TTGATCATTTT--TCA---TCTCTA-TTCATCTTCCAGGTC---T-CGCAT
gi|7 : ctgAACATC-TTCTAT-TTCTATATGTCAT-TCA-TCTTTATCTTTTCATC--ACTT--CTTGCGTTCATCCTCAAAAT----------TTTGC-------------A---------TTTTT-AGT-----------C-CAGTGCT----TT-CTGC-AAACTTTGTTG--TG--TTG-TTAG-ATT---TC-TCTTGAAT--TTGTTGTTTTGTATATGAGAT--A---AGGGCA-ATGTTGTCT--GCGTAGTC-TGGGTCGTCCAT-CATTGTT-GT-AAACTTCTATCTA-ATTCCGTTCTCTCCATTCCCT-ACTG--TTTTCCTC-ATTATCCAGTCCACA---------AG-TAG--AAGGAATA-GGAATCCc
gi|8 : cat-----CCCCCC-------------C-------CC----GTTC-TCTCACCCTCCGAT-GT-A-CGCTCTTTCTC----TAC-TGTTTC-GT-ATCCA-GTGGTTTTT---GGTC-GCC----CTTTC-CTT--TCTCT---C---CTTCTGGTGCC--CACG-T----CATTGCCACATT---AGTCATT----GGTT-GG--AT--CTT-G-TCT-CA-GGGTAATGTC-CA--AT--GAACTTCCACCTT---CTTCT-CCTGACTTCTTCACTCAG-TGGC-CT----CATTT-CTACTCT--TTGG-AGCATCTCTTCTGTAGTAGTATGTTC------TTGTTAT-CTTATTC-
gi|9 : cCCA---ATC-CTCTTCATACCTG--T-TGGCATATAAGGCC----------CTAGTTCCA--CTTTTCC---CTGTC--CTTGGCGA--CCACCCTG-G-TT-----GTACCC-------------C-------A-----GCTCTTC-CATC--CCA---GTT---GTTCTTTTTC----TGT-TG-TTCTGT-GT-CATGTTGTTTTT----GCC-TTC----CTAT--CTT--TCT-TTTCC---CATCTGGTCTC--CAGG-T----CAGTTCAACTGC-ACAAT-GCT----TGAT-GC--TT--TTC-ATTCT-CA-GCAC-GTGAC-CA--ATCCAAA--TCCATCTT---CTTc
4 sequences could not be aligned to this reference sequence:
Unaligned ( gi|10 ): CATCTTCCATAGATTTGGCCTTCATCGCTATGTTTTCGTTGCATTTTTACATTCATCCGTAATACTTCACATTTGTTGATATTTACTTCCAATCCTGTGAATCCTTTGTGCGTTTAGTTTATATTCTATGTGTAATTGCCGTCTCGTGGAGGAAATAAGAGCGAGATCTGCGAAGTCGAAACCGTCTA
Unaligned ( gi|14 ): CACTCATCCCATTCACCATCCCTCATGCCTGTTGGTATAAGCCTAGTACCACTTTTCCCTGTACTTGGCGGACCACCCTGGTTTAGCCAGATTTTCCATCCTGTTGTTCTCTTAAT
Unaligned ( gi|16 ): TAATCCTTAAATCTCTCCGCCCCAGAAGCCGCATAAGGCCTCCATGCTGTTTGCCCATTCTTTCTCAT
Unaligned ( gi|19 ): ACATCATTAAACTTTCTTTGCAGTTCTNCTTGCTGACCATGTCAGTTTT