lowQualScore                  :                             1111111111111    33333333333333333333333333333333333333333333                  99999999999999999999999999999999999999999999999999           1   222222               44444444444   11    1111                          
lowQualScore                  :                             8888888888888    99999999999999999999999999999999999999999999      999  66  66 22222222222222222222222222222222222222222222222222           0   444444     2 3    3  99999999999   11    0000        9     2           
lowQualScore                  :                             .............    ............................................      ...  ..  .. ..................................................           .   ......     . .    .  ...........   ..    ....        .     .           
lowQualScore                  :                             3333333333333    88888888888888888888888888888888888888888888      888  11  11 88888888888888888888888888888888888888888888888888           0   777777     4 6    9  44444444444   11    6666        2     2           
consensus                     :        TATTTTATTGCCATCTTATTT-------------ACAG----------------C--AA---AT---T--------------CTCACAAC-AT--TA--GT--T--CCTG---C-------TCTCCNC--TAAAC---TATGACGANTAATTGAGAAAACACGAC-A----TGGCATATAACACAT-TATAAAAAGGATAATCTTG----ATACAAAATGAAAAGAAAATACCCAC
Reference ( gi|8 )            :        TATTTTATTGCCATCTTATTT-------------ACAG----------------C--AA---AT---T--------------CTCACAGC-AT--TA--GT--T--CCTG---T-------TCTCCAC--TAAAC---TAGGACTATTTATTGAGAAAACACGAC-T----TGGCATATAATACAT-T-TAAGGAGGATAAACTTG----ATACAAAATGAAAAGAAAATACCCAC
gi|6                          :        TATTTTATTGCCATCTTATTT-------------ACAG----------------C--AA---AT---T--------------CTCACAGC-AT--TA--GT--T--CCTG---T-------TCTCCAC--TAAAC---TAGGACTATTTATTGAGAAAACACGAC-T----TGGCATATAATACAT-T-TAAAGAGGATAAACTTG----ATATAAAATGAAAAGAAAATACCCAC
gi|9                          :        TATTTTTTCACCATATCATTT-------------ACAA----------------C--AA---AT---T--------------CTCACAAT-AT--TA--GTTAT--CC--------------CTC--C--TAAAC---TA----T-----TCGAGACAACA----------TGGC--ATAACACAT-GATAA-AAGTATAGTCTTG----ATACAAAATGAAAAGAAAATACa
gi|10                         :      caTATTTTTTCACCAT---ATT--------------ACAA----------------C--AA---AT---T--------------CTCACAAT-AT--TA--GT--TATCC--------------CTCC----TAAAC---TA--------T-TCGAGACAACA----------TGGCATA--ACACAT-GATAAA-AGTATAGTCTTG----ATACAAAATGAAAAGAAAATACac
gi|1                          :       aTATTTGATTGCCATCTTATTT-------------GCAATAGACGAGTTGGTCTAC--AA---AT---T--------------CTCACAAC-AT--TA--CT--T----TG---TACGACCCTCTCTTG--TA------TATGGCAAGTAATTGAGAAAACATGAC-A----TGG--TATAACACAT-G-ACAAAATAATAAAATTA----GTACAAAAGGAAAAAAAA
gi|11                         :   catcgTATTTTATTGCGATCTTGTTT-------------ACAG----------------C--GA-------------------------TAAAG---T--TG--G---------G---C-------TC-CCAC----AAC----------ATTAGTTGAGAAAACATGGC-A----TGGCATGCCAT--AT-TATAAAAAAGATAATCTTA----ATACAAAA--AAAAGcattc
gi|7                          :       aTATTTTATTACCATCTTATTG-------------ACAG-------------------AA---ATAGGA--------------CTCAAAAC-AT--TT--GA--T--ACCGACCC-------CCTCCCC--TGATA---TGTGATGATTAAATGAGAACATATGAC-A----TG--ATATAACAGATAT-CAACACTGTTA---TTG----ATACAGAAGGAAAAAAAAcaccta
gi|16                         :  taaccaTATTTTATTGCCGTCTTATTT-------------ACAG----------------C--AA---ca
gi|3                          : tttataaTATTTTATTGTCATCTTATTTTGTGGGTTTGGCCACAT----------------CTCGA---GT---T--------------TTCACATTTATGATAACGG--T--CCTA---C--------CTCTAA--TACATGTATATGACAAATGATTGAGAAAACGCGAC-A----TAGCACGTGATAAAA-T-C------GATAATCTTGAATTATACAAAA-GAAAAAACAACAtg
gi|2                          :        TATTTTATTGCCTTCTTATTT-------------AAAA----------------A--AA---AT---GGGGCGGGAGGCACATTCAC-CC-AT--TT--GT--T--ACGG---C-------ACTCCCCCATAATA---TATGACAAATAATTGAGAAGACATGAC-A----TGTCA-A-AATACAT-a
gi|13                         :    atcaTATTATACTGCCATCTTATTT-------------ACAG----------------C--AA---gataaaagtacatgtatacatagtgtgtacacagcaacaaaaa
gi|14                         :    atcaTATTTTATTGCACTCTTATTT-------------ACAT----------------C--AA---tggggtttgtcacatattctgacaacata
gi|15                         :          TTTTATTGCCATCATATTT-------------ACAG----------------C--AATGGGT---T--------------CTCACAAC-AT--TA--GT--T--tgcggttgggctacaaataattgagaaacatg
gi|12                         :                                                                                                                                                           aatatGAGAAAACATGACATAGCATGGCACATGATA-AT-T-------GAATCATCTTA----ATACAAAATGAAAA-ACAAGACCacagcc
2 sequences could not be aligned to this particular reference sequence:
Unaligned ( gi|4 ): GTCATATTTTACTACTATTCTATTTTCCAGTGGGGTTAGACCGCAAGGTCTCACAACGTAGTACTAAGTTACAACCCTTCCCCTTATACAAATATATGGCAAACAACTGGACAAAATCATGACATAGCATGACACATGATGAAAAGGATAATCAATTA
Unaligned ( gi|5 ): ATTGTATTGTCATCATATTGCCAGAAATAGGGCAGGGCAACAAGTTTTTACAACATTGTTAATGCACTCTCCTGATATATGACAAATACATGATAACACCTAACATGATGTAATATATGTTTTCAACGATCTTGATACAAAAAGGAAAAAAAATA






Alignments
lowQualScore                  :                            6666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666                         33333333333333        2222222222222222                                1111111      111111                                             
lowQualScore                  :                            2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222      555    77777 888   11111111111111 44  1  1111111111111111   11 8 3 1    3    0 3         2222222      111111  4444         8888        8     1           
lowQualScore                  :                            ...........................................................................................      ...    ..... ...   .............. ..  .  ................   .. . . .    .    . .         .......      ......  ....         ....        .     .           
lowQualScore                  :                            9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999      444    77777 666   55555555555555 00  0  7777777777777777   66 6 5 5    3    2 3         8888888      777777  3333         5555        2     4           
consensus                     :        TATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------AT---T--------------CTCACA---ACAT-----TA--GTTNCTG---C-----TCT-CCCCT-----A-A-AC-----TATGACAANTAATTG-AGAAAA-CACGACATGGCATATAACACAT--GATAAAAAGGATAATCTTG----ATACAAAATGAAAAGAAAATACCCAC
Reference ( family-4013 )     :        TATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------AT---T--------------CTCACA---ACAT-----TA--GTTCCTG---C-----TCT-CCNCT-----A-A-AC-----TATGACGANTAATTG-AGAAAA-CACGACATGGCATATAACACAT--TATAAAAAGGATAATCTTG----ATACAAAATGAAAAGAAAATACCCAC
gi|1                          :        TATTTGATTGCCATCTTATT--------T--------------G--------CAATAGACGAGTTGGTCTAC--AA---------------AT---T--------------CTCACA---ACAT-----TA--CTTTGTA---CGACCCTCT-CTTGT-----A----------TATGGCAAGTAATTG-AGAAAA-CATGACATGG--TATAACACAT--GAC-AAAATAATAAAATTA----GTACAAAAGGAAAAAAAA
gi|10                         :   catcgTATTTTTTCACCAT---ATT-----------------------A--------CAA----------------C--AA---------------AT---T--------------CTCACA---ATAT-----TA--GTT-------A-----TCC-CTCCT-----A-A-AC-----TAT---------TCG-AG------ACAACATGGC--ATAACACAT--GAT-AAAAGTATAGTCTTG----ATACAAAATGAAAAGAAAATACcattc
gi|11                         :       aTATTTTATTGCGATCTTGTT--------T--------------A--------CAG----------------C--GA---------------------------------------TA---AAGT-----TG--G-----G---C-----TC--CCAC--------A-AC------------ATTAGTTG-AGAAAA-CATGGCATGGCATGC--CATAT--TATAAAAAAGATAATCTTA----ATACAAAA--AAAAG
gi|12                         :                                                                                                                                                                                                   aG-AGAAAA-CATGACATAGCATG--GCACAT--GATAATT-GAATCATCTTA----ATACAAAATGAAAA-ACAAGACCcaccta
gi|13                         :        TATTATACTGCCATCTTATT--------T--------------A--------CAG----------------C--AATGGGGTTTGTCACATAT---T--------------CTGACA---ACAT-----a
gi|15                         :      atcaTTTTATTGCCATCATATT--------T--------------A--------CAG----------------C--AATGG------------GT---T--------------CTCACA---ACAT-----TA--GTTa
gi|16                         :   aatatTATTTTATTGCCGTCTTATT--------T--------------A--------CAG----------------C--AA---------------acagcc
gi|2                          : tttataaTATTTTATTGCCTTCTTATT--------T--------------A--------AAA----------------A--AA---------------AT---GGGGCGGGAGGCACATTCACC----CAT-----TT--GTTACGG---C-----ACT-CCCCC-----ATA-ATA----TATGACAAATAATTG-AGAAGA-CATGACATGTCA-A-AATACAT--GATAAAAtg
gi|3                          :    atcaTATTTTATTGTCATCTTATT--------TTGTGGGTTTGGCC-A--------CAT----------------CTCGA---------------GT---T--------------TTCACATTTATGA-----TAACGGTCCTA---C----------CTCT-----A-ATACATGTATATGACAAATGATTG-AGAAAA-CGCGACATAG-------CACGT--GATAAAATCGATAATCTTGAATTATACAAAA-GAAAAAACAACAgtacatgtatacatagtgtgtacacagcaacaaaaa
gi|4                          :        TATTTTACTACTATTCTATT--------TTCCAGTGGGGTTAGA--------CCG----------------C--AA---------------GG---T--------------CTCACA---ACGTAGTACTAA-GTTACAA---C-----CCTTCCCCTTATACA-A-ATA----TATGGCAAACAACTGGACAAAATCATGACATAGCATG--ACACAT--GATGAAAAGGATAATCa
gi|5                          :     gtcaATTGTATTGTCATCATATTGCCAGAAAT--------------AGGGCAGGGCAA----------------C--AA---------------GT---T--------------TTTACA---ACAT-----T---GTTAATG---C-----ACT-CTCCT-----G-A-TA-----TATGACAAATACATG-ATAACA-CCTAACATG--ATGTAATATATGTTTTCAA-----CGATCTTG----ATACAAAAAGGAAAAAAAATAaatta
gi|6                          :        TATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------AT---T--------------CTCACA---GCAT-----TA--GTTCCTG---T-----TCT-CCACT-----A-A-AC-----TAGGACTATTTATTG-AGAAAA-CACGACTTGGCATATAATACAT--T-TAAAGAGGATAAACTTG----ATATAAAATGAAAAGAAAATACCCAC
gi|7                          :        TATTTTATTACCATCTTATT--------G--------------A--------CAG-------------------AA---------------ATAGGA--------------CTCAAA---ACAT-----TT--GATACCGACCC-----CCT-CCCCT-----G-A-TA-----TGTGATGATTAAATG-AGAACA-TATGACATG--ATATAACAGA---TATCAACACTGT--TATTG----ATACAGAAGGAAAAAAAAa
gi|8                          :  taaccaTATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------AT---T--------------CTCACA---GCAT-----TA--GTTCCTG---T-----TCT-CCACT-----A-A-AC-----TAGGACTATTTATTG-AGAAAA-CACGACTTGGCATATAATACAT--T-TAAGGAGGATAAACTTG----ATACAAAATGAAAAGAAAATACCCACca
gi|9                          :        TATTTTTTCACCATATCATT--------T--------------A--------CAA----------------C--AA---------------AT---T--------------CTCACA---ATAT-----TA--GTT-------A-----TCC-CTCCT-----A-A-AC-----TAT---------TCG-AG------ACAACATGGC--ATAACACAT--GAT-AAAAGTATAGTCTTG----ATACAAAATGAAAAGAAAATAC
1 sequences could not be aligned to this reference sequence:
Unaligned ( gi|14 ): TATTTTATTGCACTCTTATTTACATCAATGCGGTTGGGCTACAAATAATTGAGAAACATG






Alignments
lowQualScore                  :                            6666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666                      2222222222          2222222222222222                                     11                                                       
lowQualScore                  :                            2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222          77777 888   1111111111 1  7     1111111111111111   11 3 3 1    3    0 3         22   99       1     77          8888        8     1           
lowQualScore                  :                            ...........................................................................................          ..... ...   .......... .  .     ................   .. . . .    .    . .         ..   ..       .     ..          ....        .     .           
lowQualScore                  :                            9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999          77777 666   7777777777 2  3     1111111111111111   66 6 5 5    3    2 3         99   88       3     33          5555        2     4           
consensus                     :        TATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------AT---T--------------CTCACAACAT-----TA--GTTA---CNG---CCCT-CCCCT-----A-A-AC-----TATGACAANTAATTG-AGAAAA-CACGACATGGCATATAACACATGATAAAAAGGATAATCTTG----ATACAAAATGAAAAGAAAATACCCAC
Reference ( family-4013 )     :        TATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------AT---T--------------CTCACAACAT-----TA--GTTN---CTG---CTCT-CCCCT-----A-A-AC-----TATGACAANTAATTG-AGAAAA-CACGACATGGCATATAACACATGATAAAAAGGATAATCTTG----ATACAAAATGAAAAGAAAATACCCAC
gi|1                          :        TATTTGATTGCCATCTTATT--------T--------------G--------CAATAGACGAGTTGGTCTAC--AA---------------AT---T--------------CTCACAACAT-----TA--CTTTGTACGA---CCCT-CTCTT-----G-T-A------TATGGCAAGTAATTG-AGAAAA-CATGACATGG--TATAACACATGAC-AAAATAATAAAATTA----GTACAAAAGGAAAAAAAA
gi|10                         :   catcgTATTTTTTCACCAT---ATT-----------------------A--------CAA----------------C--AA---------------AT---T--------------CTCACAATAT-----TA--GTTA----------TCC-CTCCT-----A-A-AC-----TAT---------TCG-AGA------CAACATGGCATA--ACACATGATAAAA-GTATAGTCTTG----ATACAAAATGAAAAGAAAATACcattc
gi|11                         :       aTATTTTATTGCGATCTTGTT--------T--------------A--------CAG----------------C--GA---------------------------------------TAAAGT-----TG--G--------G---CTCC-CAC---------A-AC------------ATTAGTTG-AGAAAA-CATGGCATGGCATGC--CATATTATAAAAAAGATAATCTTA----ATACAAAA--AAAAG
gi|12                         :                                                                                                                                                                                              aG-AGAAAA-CATGACATAGCATG--GCACATGATAATT-GAATCATCTTA----ATACAAAATGAAAA-ACAAGACCcaccta
gi|13                         :        TATTATACTGCCATCTTATT--------T--------------A--------CAG----------------C--AATGGGGTTTGTCACATAT---T--------------CTGACAACAT-----a
gi|15                         :      atcaTTTTATTGCCATCATATT--------T--------------A--------CAG----------------C--AATGG------------GT---T--------------CTCACAACAT-----TA--GTTA---CAG---Ca
gi|16                         :   aatatTATTTTATTGCCGTCTTATT--------T--------------A--------CAG----------------C--AA---------------c
gi|2                          : tttataaTATTTTATTGCCTTCTTATT--------T--------------A--------AAA----------------A--AA---------------AT---GGGGCGGGAGGCACATTCACC-CAT-----TT--GTTA---CGG---CACT-CCCCC-----ATA-ATA----TATGACAAATAATTG-AGAAGA-CATGACATGTCA-A-AATACATGATAAAAtg
gi|3                          :    atcaTATTTTATTGTCATCTTATT--------TTGTGGGTTTGGCC-A--------CAT----------------CTCGA---------------GT---T--------------TTCACAT--T-----TATGATAA---CGG---TCCTACCTCT-----A-ATACATGTATATGACAAATGATTG-AGAAAA-CGCGACATAG-------CACGTGATAAAATCGATAATCTTGAATTATACAAAA-GAAAAAACAACAgtacatgtatacatagtgtgtacacagcaacaaaaa
gi|4                          :        TATTTTACTACTATTCTATT--------TTCCAGTGGGGTTAGA--------CCG----------------C--AA---------------GG---T--------------CTCACAACGTAGTACTAA-GTTA---CAA---CCCTTCCCCTTATACA-A-ATA----TATGGCAAACAACTGGACAAAATCATGACATAGCATG--ACACATGATGAAAAGGATAATCa
gi|5                          :     gtcaATTGTATTGTCATCATATTGCCAGAAAT--------------AGGGCAGGGCAA----------------C--AA---------------GT---T--------------TTTACAACAT-----T---GTTA---ATG---CACT-CTCCT-----G-A-TA-----TATGACAAATACATG-ATAACA-CCTAACATG--ATGTAATATATGTTTTCAACG---ATCTTG----ATACAAAAAGGAAAAAAAATAaatta
gi|6                          :        TATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------AT---T--------------CTCACAGCAT-----TA--GTTC---CTG---TTCT-CCACT-----A-A-AC-----TAGGACTATTTATTG-AGAAAA-CACGACTTGGCATATAATACATT-TAAAGAGGATAAACTTG----ATATAAAATGAAAAGAAAATACCCAC
gi|7                          :        TATTTTATTACCATCTTATT--------G--------------A--------CAG-------------------AA---------------ATAGGA--------------CTCAAAACAT-----TT--GATA---CCGACCCCCT-CCCCT-----G-A-TA-----TGTGATGATTAAATG-AGAACA-TATGACATG--ATATAACA---GATATCAACACTGTTATTG----ATACAGAAGGAAAAAAAAa
gi|8                          :  taaccaTATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------AT---T--------------CTCACAGCAT-----TA--GTTC---CTG---TTCT-CCACT-----A-A-AC-----TAGGACTATTTATTG-AGAAAA-CACGACTTGGCATATAATACATT-TAAGGAGGATAAACTTG----ATACAAAATGAAAAGAAAATACCCACca
gi|9                          :        TATTTTTTCACCATATCATT--------T--------------A--------CAA----------------C--AA---------------AT---T--------------CTCACAATAT-----TA--GTTA----------TCC-CTCCT-----A-A-AC-----TAT---------TCG-AGA------CAACATGGCATA--ACACATGATAAAA-GTATAGTCTTG----ATACAAAATGAAAAGAAAATAC
1 sequences could not be aligned to this reference sequence:
Unaligned ( gi|14 ): TATTTTATTGCACTCTTATTTACATCAATGCGGTTGGGCTACAAATAATTGAGAAACATG






Alignments
lowQualScore                  :                            6666666666666666666666666666666666666666666666666666666666666666666666666666666666666666                      1111111111          2222222222222222                                     11                                                       
lowQualScore                  :                            2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222       0  888888888   1111111111 1  7  0  7777777777777777   0  444 1    3    0 3         22   33       1 2   22          8888        8     1           
lowQualScore                  :                            ........................................................................................       .  .........   .......... .  .  .  ................   .  ... .    .    . .         ..   ..       . .   ..          ....        .     .           
lowQualScore                  :                            9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999       2  000000000   2222222222 0  3  5  7777777777777777   5  888 5    3    2 3         99   77       3 6   88          5555        2     4           
consensus                     :        TATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------ATT--------------CTCACAACAT-----TA--GTT---ACGG---CCCT-CCCCT-----A-A-AC-----TATGACAANTAATTG-AGAAAA-CACGACATGGCATATAACACATGATAAAAAGGATAATCTTG----ATACAAAATGAAAAGAAAATACCCAC
Reference ( family-4013 )     :        TATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------ATT--------------CTCACAACAT-----TA--GTT---ACNG---CCCT-CCCCT-----A-A-AC-----TATGACAANTAATTG-AGAAAA-CACGACATGGCATATAACACATGATAAAAAGGATAATCTTG----ATACAAAATGAAAAGAAAATACCCAC
gi|1                          :        TATTTGATTGCCATCTTATT--------T--------------G--------CAATAGACGAGTTGGTCTAC--AA---------------ATT--------------CTCACAACAT-----TA--CTTTGTACGA---CCCT-CTCTT-----G-T-A------TATGGCAAGTAATTG-AGAAAA-CATGACATGG--TATAACACATGAC-AAAATAATAAAATTA----GTACAAAAGGAAAAAAAA
gi|10                         :   catcgTATTTTTTCACCAT---ATT-----------------------A--------CAA----------------C--AA---------------ATT--------------CTCACAATAT-----TA--GTT---AT-----CCCT-CC--T-----A-A-AC-----TAT---------TCG-AGA------CAACATGGCATA--ACACATGATAAAA-GTATAGTCTTG----ATACAAAATGAAAAGAAAATACcattc
gi|11                         :       aTATTTTATTGCGATCTTGTT--------T--------------A--------CAG----------------C--GA------------------------------------TAA---------A--GTT---G-GG---C--T-CCC-------------------ACAACA-TTAGTTG-AGAAAA-CATGGCATGGCATGC--CATATTATAAAAAAGATAATCTTA----ATACAAAA--AAAAG
gi|12                         :                                                                                                                                                                                           aG-AGAAAA-CATGACATAGCATG--GCACATGATAATT-GAATCATCTTA----ATACAAAATGAAAA-ACAAGACCcaccta
gi|13                         :        TATTATACTGCCATCTTATT--------T--------------A--------CAG----------------C--AATGGGGTTTGTCACATATT--------------CTGACAACAT-----a
gi|15                         :      atcaTTTTATTGCCATCATATT--------T--------------A--------CAG----------------C--AATGG------------GTT--------------CTCACAACAT-----TA--GTT---ACAG---CCa
gi|16                         :   aatatTATTTTATTGCCGTCTTATT--------T--------------A--------CAG----------------C--AA---------------
gi|2                          : tttataaTATTTTATTGCCTTCTTATT--------T--------------A--------AAA----------------A--AA---------------ATGGGGCGGGAGGCACATTCACC-CAT-----TT--GTT---ACGG---CACT-CCCCC-----ATA-ATA----TATGACAAATAATTG-AGAAGA-CATGACATGTCA-A-AATACATGATAAAAtg
gi|3                          :    atcaTATTTTATTGTCATCTTATT--------TTGTGGGTTTGGCC-A--------CAT----------------CTCGA---------------GTT--------------TTCACAT--T-----TATGATA---ACGG---TCCTACCTCT-----A-ATACATGTATATGACAAATGATTG-AGAAAA-CGCGACATAG-------CACGTGATAAAATCGATAATCTTGAATTATACAAAA-GAAAAAACAACAgtacatgtatacatagtgtgtacacagcaacaaaaa
gi|4                          :        TATTTTACTACTATTCTATT--------TTCCAGTGGGGTTAGA--------CCG----------------C--AA---------------GGT--------------CTCACAACGTAGTACTAA-GTT---ACAA---CCCTTCCCCTTATACA-A-ATA----TATGGCAAACAACTGGACAAAATCATGACATAGCATG--ACACATGATGAAAAGGATAATCa
gi|5                          :     gtcaATTGTATTGTCATCATATTGCCAGAAAT--------------AGGGCAGGGCAA----------------C--AA---------------GTT--------------TTTACAACAT-----T---GTT---AATG---CACT-CTCCT-----G-A-TA-----TATGACAAATACATG-ATAACA-CCTAACATG--ATGTAATATATGTTTTCAACG---ATCTTG----ATACAAAAAGGAAAAAAAATAaatta
gi|6                          :        TATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------ATT--------------CTCACAGCAT-----TA--GTT---CCTG---TTCT-CCACT-----A-A-AC-----TAGGACTATTTATTG-AGAAAA-CACGACTTGGCATATAATACATT-TAAAGAGGATAAACTTG----ATATAAAATGAAAAGAAAATACCCAC
gi|7                          :        TATTTTATTACCATCTTATT--------G--------------A--------CAG-------------------AA---------------ATAGGA-----------CTCAAAACAT-----TT--GAT---ACCGACCCCCT-CCCCT-----G-A-TA-----TGTGATGATTAAATG-AGAACA-TATGACATG--ATATAACA---GATATCAACACTGTTATTG----ATACAGAAGGAAAAAAAAa
gi|8                          :  taaccaTATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------ATT--------------CTCACAGCAT-----TA--GTT---CCTG---TTCT-CCACT-----A-A-AC-----TAGGACTATTTATTG-AGAAAA-CACGACTTGGCATATAATACATT-TAAGGAGGATAAACTTG----ATACAAAATGAAAAGAAAATACCCACca
gi|9                          :        TATTTTTTCACCATATCATT--------T--------------A--------CAA----------------C--AA---------------ATT--------------CTCACAATAT-----TA--GTT---AT-----CCCT---CCT-----A-A-AC-----TAT---------TCG-AG------ACAACATGGC--ATAACACATGAT-AAAAGTATAGTCTTG----ATACAAAATGAAAAGAAAATAC
1 sequences could not be aligned to this reference sequence:
Unaligned ( gi|14 ): TATTTTATTGCACTCTTATTTACATCAATGCGGTTGGGCTACAAATAATTGAGAAACATG






Alignments
lowQualScore                  :                            6666666666666666666666666666666666666666666666666666666666666666666666666666666666666666                      1111111111          2222222222222222                                     11                                                       
lowQualScore                  :                            2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222       0  888888888   3333333333 1  7  0  7777777777777777   0  444 1    3    0 3         22   33       1 2   22          8888        8     1           
lowQualScore                  :                            ........................................................................................       .  .........   .......... .  .  .  ................   .  ... .    .    . .         ..   ..       . .   ..          ....        .     .           
lowQualScore                  :                            9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999       2  000000000   0000000000 0  3  5  7777777777777777   5  888 5    3    2 3         99   77       3 6   88          5555        2     4           
consensus                     :        TATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------ATT--------------CTCACAACAT-----TA--GTT---ACGG---CCCT-CCCCT-----A-A-AC-----TATGACAANTAATTG-AGAAAA-CACGACATGGCATATAACACATGATAAAAAGGATAATCTTG----ATACAAAATGAAAAGAAAATACCCAC
Reference ( family-4013 )     :        TATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------ATT--------------CTCACAACAT-----TA--GTT---ACGG---CCCT-CCCCT-----A-A-AC-----TATGACAANTAATTG-AGAAAA-CACGACATGGCATATAACACATGATAAAAAGGATAATCTTG----ATACAAAATGAAAAGAAAATACCCAC
gi|1                          :        TATTTGATTGCCATCTTATT--------T--------------G--------CAATAGACGAGTTGGTCTAC--AA---------------ATT--------------CTCACAACAT-----TA--CTTTGTACGA---CCCT-CTCTT-----G-T-A------TATGGCAAGTAATTG-AGAAAA-CATGACATGG--TATAACACATGAC-AAAATAATAAAATTA----GTACAAAAGGAAAAAAAA
gi|10                         :   catcgTATTTTTTCACCAT---ATT-----------------------A--------CAA----------------C--AA---------------ATT--------------CTCACAATAT-----TA--GTT---AT-----CCCT-CC--T-----A-A-AC-----TAT---------TCG-AGA------CAACATGGCATA--ACACATGATAAAA-GTATAGTCTTG----ATACAAAATGAAAAGAAAATACcattc
gi|11                         :       aTATTTTATTGCGATCTTGTT--------T--------------A--------CAG----------------C--GA------------------------------------TAA---------A--GTT---G-GG---C--T-CCC-------------------ACAACA-TTAGTTG-AGAAAA-CATGGCATGGCATGC--CATATTATAAAAAAGATAATCTTA----ATACAAAA--AAAAG
gi|12                         :                                                                                                                                                                                           aG-AGAAAA-CATGACATAGCATG--GCACATGATAATT-GAATCATCTTA----ATACAAAATGAAAA-ACAAGACCcaccta
gi|13                         :        TATTATACTGCCATCTTATT--------T--------------A--------CAG----------------C--AATGGGGTTTGTCACATATT--------------CTGACAACAT-----a
gi|15                         :      atcaTTTTATTGCCATCATATT--------T--------------A--------CAG----------------C--AATGG------------GTT--------------CTCACAACAT-----TA--GTT---ACAG---CCa
gi|16                         :   aatatTATTTTATTGCCGTCTTATT--------T--------------A--------CAG----------------C--AA---------------
gi|2                          : tttataaTATTTTATTGCCTTCTTATT--------T--------------A--------AAA----------------A--AA---------------ATGGGGCGGGAGGCACATTCACC-CAT-----TT--GTT---ACGG---CACT-CCCCC-----ATA-ATA----TATGACAAATAATTG-AGAAGA-CATGACATGTCA-A-AATACATGATAAAAtg
gi|3                          :    atcaTATTTTATTGTCATCTTATT--------TTGTGGGTTTGGCC-A--------CAT----------------CTCGA---------------GTT--------------TTCACAT--T-----TATGATA---ACGG---TCCTACCTCT-----A-ATACATGTATATGACAAATGATTG-AGAAAA-CGCGACATAG-------CACGTGATAAAATCGATAATCTTGAATTATACAAAA-GAAAAAACAACAgtacatgtatacatagtgtgtacacagcaacaaaaa
gi|4                          :        TATTTTACTACTATTCTATT--------TTCCAGTGGGGTTAGA--------CCG----------------C--AA---------------GGT--------------CTCACAACGTAGTACTAA-GTT---ACAA---CCCTTCCCCTTATACA-A-ATA----TATGGCAAACAACTGGACAAAATCATGACATAGCATG--ACACATGATGAAAAGGATAATCa
gi|5                          :     gtcaATTGTATTGTCATCATATTGCCAGAAAT--------------AGGGCAGGGCAA----------------C--AA---------------GTT--------------TTTACAACAT-----T---GTT---AATG---CACT-CTCCT-----G-A-TA-----TATGACAAATACATG-ATAACA-CCTAACATG--ATGTAATATATGTTTTCAACG---ATCTTG----ATACAAAAAGGAAAAAAAATAaatta
gi|6                          :        TATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------ATT--------------CTCACAGCAT-----TA--GTT---CCTG---TTCT-CCACT-----A-A-AC-----TAGGACTATTTATTG-AGAAAA-CACGACTTGGCATATAATACATT-TAAAGAGGATAAACTTG----ATATAAAATGAAAAGAAAATACCCAC
gi|7                          :        TATTTTATTACCATCTTATT--------G--------------A--------CAG-------------------AA---------------ATAGGA-----------CTCAAAACAT-----TT--GAT---ACCGACCCCCT-CCCCT-----G-A-TA-----TGTGATGATTAAATG-AGAACA-TATGACATG--ATATAACA---GATATCAACACTGTTATTG----ATACAGAAGGAAAAAAAAa
gi|8                          :  taaccaTATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------ATT--------------CTCACAGCAT-----TA--GTT---CCTG---TTCT-CCACT-----A-A-AC-----TAGGACTATTTATTG-AGAAAA-CACGACTTGGCATATAATACATT-TAAGGAGGATAAACTTG----ATACAAAATGAAAAGAAAATACCCACca
gi|9                          :        TATTTTTTCACCATATCATT--------T--------------A--------CAA----------------C--AA---------------ATT--------------CTCACAATAT-----TA--GTT---AT-----CCCT---CCT-----A-A-AC-----TAT---------TCG-AG------ACAACATGGC--ATAACACATGAT-AAAAGTATAGTCTTG----ATACAAAATGAAAAGAAAATAC


blockSeqs                     :                            GCCAGAAATAGGGCAGGGCAACAAGTT                                                                       AGTACTAA    ACCGACC    C  A     AATACATGTA            AAA A    G      T         GC   TA       A A   AA          AATT        T     G
blockSeqs                     :                            TACAGCAATGGGGTTTGTCACATATT                                                                        TATG        ACAG       C  T     TATACAAATA            AAA A    .      .         GC   TA       A A   TC          .           T     G
blockSeqs                     :                            TTGTGGGTTTGGCCACATCTCGAGTT                                                                        TA          ACGG       A  .     ATAATA                AAA G    .      .         GC   TA       A A   AG          .           A     A
blockSeqs                     :                            TAAAAAAAATGGGGCGGGAGGCACA                                                                         TA          ACGG       C  .     AAAC                  AAA A    .      .         TC   TA       A A   AC          .           T     A
blockSeqs                     :                            TTCCAGTGGGGTTAGACCGCAAGGT                                                                         TT          ACAA       C  .     GATA                  TAT A    .      .         GC   TA       A A   AG          .           G     G
blockSeqs                     :                            TACAGCAATGGGTT                                                                                    TA          AATG       A  .     AAAC                  GAT T    .      .         GC   C        A G   AC          .           T     A
blockSeqs                     :                            GACAGAAATAGGA                                                                                     TT          CCTG       T  .     GATA                  TAT A    .      .         GC   A        T T   AG          .           T     G
blockSeqs                     :                            TACAGCAAATT                                                                                       TA          CCTG       C  .     AAAC                  AT  T    .      .         GC   .        A A   AG          .           .     G
blockSeqs                     :                            TACAGCAAATT                                                                                       TA          GGG        T  .     AAAC                  .   .    .      .         G    .        A A   G           .           .     .
blockSeqs                     :                            TACAACAAATT                                                                                       A           AT         C  .     .                     .   .    .      .         .    .        . A   G                              
blockSeqs                     :                            ACAACAAATT                                                                                        T           AT         .                                       .      .         .    .        . .                                  
blockSeqs                     :                            TACAGCGA                                                                                                                                                                                                                             


blockSeqCons                  :                                                                                                                                          ACNG******          AAAC************                                GC
originalCons                  :        TATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------ATT--------------CTCACAACAT-----TA--GTT---ACGG---CCCT-CCCCT-----A-A-AC-----TATGACAANTAATTG-AGAAAA-CACGACATGGCATATAACACATGATAAAAAGGATAATCTTG----ATACAAAATGAAAAGAAAATACCCAC
finalCons                     :        TATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------ATT--------------CTCACAACAT-----TA--GTTACNG------CCCT-CCCCTAAAC------------TATGACAANTAATTG-AGAAAA-CACGACATGGCATATAACACATGATAAAAAGGATAATCTTG----ATACAAAATGAAAAGAAAATACCCAC
1 sequences could not be aligned to this reference sequence:
Unaligned ( gi|14 ): TATTTTATTGCACTCTTATTTACATCAATGCGGTTGGGCTACAAATAATTGAGAAACATG






Alignments
lowQualScore                  :                            6666666666666666666666666666666666666666666666666666666666666666666666666666666666666666                      1111111111          2222222222222222                                     11                                                       
lowQualScore                  :                            2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222       0  888888888   1111111111 1  7  0  7777777777777777   0  444 1    3    0 3         22   33       1 2   22          8888        8     1           
lowQualScore                  :                            ........................................................................................       .  .........   .......... .  .  .  ................   .  ... .    .    . .         ..   ..       . .   ..          ....        .     .           
lowQualScore                  :                            9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999       2  000000000   2222222222 0  3  5  7777777777777777   5  888 5    3    2 3         99   77       3 6   88          5555        2     4           
consensus                     :        TATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------ATT--------------CTCACAACAT-----TA--GTT---ACGG---CCCT-CCCCT-----A-A-AC-----TATGACAANTAATTG-AGAAAA-CACGACATGGCATATAACACATGATAAAAAGGATAATCTTG----ATACAAAATGAAAAGAAAATACCCAC
Reference ( family-4013 )     :        TATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------ATT--------------CTCACAACAT-----TA--GTT---ACNG---CCCT-CCCCT-----A-A-AC-----TATGACAANTAATTG-AGAAAA-CACGACATGGCATATAACACATGATAAAAAGGATAATCTTG----ATACAAAATGAAAAGAAAATACCCAC
gi|1                          :        TATTTGATTGCCATCTTATT--------T--------------G--------CAATAGACGAGTTGGTCTAC--AA---------------ATT--------------CTCACAACAT-----TA--CTTTGTACGA---CCCT-CTCTT-----G-T-A------TATGGCAAGTAATTG-AGAAAA-CATGACATGG--TATAACACATGAC-AAAATAATAAAATTA----GTACAAAAGGAAAAAAAA
gi|10                         :   catcgTATTTTTTCACCAT---ATT-----------------------A--------CAA----------------C--AA---------------ATT--------------CTCACAATAT-----TA--GTT---AT-----CCCT-CC--T-----A-A-AC-----TAT---------TCG-AGA------CAACATGGCATA--ACACATGATAAAA-GTATAGTCTTG----ATACAAAATGAAAAGAAAATACcattc
gi|11                         :       aTATTTTATTGCGATCTTGTT--------T--------------A--------CAG----------------C--GA------------------------------------TAA---------A--GTT---G-GG---C--T-CCC-------------------ACAACA-TTAGTTG-AGAAAA-CATGGCATGGCATGC--CATATTATAAAAAAGATAATCTTA----ATACAAAA--AAAAG
gi|12                         :                                                                                                                                                                                           aG-AGAAAA-CATGACATAGCATG--GCACATGATAATT-GAATCATCTTA----ATACAAAATGAAAA-ACAAGACCcaccta
gi|13                         :        TATTATACTGCCATCTTATT--------T--------------A--------CAG----------------C--AATGGGGTTTGTCACATATT--------------CTGACAACAT-----a
gi|15                         :      atcaTTTTATTGCCATCATATT--------T--------------A--------CAG----------------C--AATGG------------GTT--------------CTCACAACAT-----TA--GTT---ACAG---CCa
gi|16                         :   aatatTATTTTATTGCCGTCTTATT--------T--------------A--------CAG----------------C--AA---------------
gi|2                          : tttataaTATTTTATTGCCTTCTTATT--------T--------------A--------AAA----------------A--AA---------------ATGGGGCGGGAGGCACATTCACC-CAT-----TT--GTT---ACGG---CACT-CCCCC-----ATA-ATA----TATGACAAATAATTG-AGAAGA-CATGACATGTCA-A-AATACATGATAAAAtg
gi|3                          :    atcaTATTTTATTGTCATCTTATT--------TTGTGGGTTTGGCC-A--------CAT----------------CTCGA---------------GTT--------------TTCACAT--T-----TATGATA---ACGG---TCCTACCTCT-----A-ATACATGTATATGACAAATGATTG-AGAAAA-CGCGACATAG-------CACGTGATAAAATCGATAATCTTGAATTATACAAAA-GAAAAAACAACAgtacatgtatacatagtgtgtacacagcaacaaaaa
gi|4                          :        TATTTTACTACTATTCTATT--------TTCCAGTGGGGTTAGA--------CCG----------------C--AA---------------GGT--------------CTCACAACGTAGTACTAA-GTT---ACAA---CCCTTCCCCTTATACA-A-ATA----TATGGCAAACAACTGGACAAAATCATGACATAGCATG--ACACATGATGAAAAGGATAATCa
gi|5                          :     gtcaATTGTATTGTCATCATATTGCCAGAAAT--------------AGGGCAGGGCAA----------------C--AA---------------GTT--------------TTTACAACAT-----T---GTT---AATG---CACT-CTCCT-----G-A-TA-----TATGACAAATACATG-ATAACA-CCTAACATG--ATGTAATATATGTTTTCAACG---ATCTTG----ATACAAAAAGGAAAAAAAATAaatta
gi|6                          :        TATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------ATT--------------CTCACAGCAT-----TA--GTT---CCTG---TTCT-CCACT-----A-A-AC-----TAGGACTATTTATTG-AGAAAA-CACGACTTGGCATATAATACATT-TAAAGAGGATAAACTTG----ATATAAAATGAAAAGAAAATACCCAC
gi|7                          :        TATTTTATTACCATCTTATT--------G--------------A--------CAG-------------------AA---------------ATAGGA-----------CTCAAAACAT-----TT--GAT---ACCGACCCCCT-CCCCT-----G-A-TA-----TGTGATGATTAAATG-AGAACA-TATGACATG--ATATAACA---GATATCAACACTGTTATTG----ATACAGAAGGAAAAAAAAa
gi|8                          :  taaccaTATTTTATTGCCATCTTATT--------T--------------A--------CAG----------------C--AA---------------ATT--------------CTCACAGCAT-----TA--GTT---CCTG---TTCT-CCACT-----A-A-AC-----TAGGACTATTTATTG-AGAAAA-CACGACTTGGCATATAATACATT-TAAGGAGGATAAACTTG----ATACAAAATGAAAAGAAAATACCCACca
gi|9                          :        TATTTTTTCACCATATCATT--------T--------------A--------CAA----------------C--AA---------------ATT--------------CTCACAATAT-----TA--GTT---AT-----CCCT---CCT-----A-A-AC-----TAT---------TCG-AG------ACAACATGGC--ATAACACATGAT-AAAAGTATAGTCTTG----ATACAAAATGAAAAGAAAATAC
1 sequences could not be aligned to this reference sequence:
Unaligned ( gi|14 ): TATTTTATTGCACTCTTATTTACATCAATGCGGTTGGGCTACAAATAATTGAGAAACATG