Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: NC_028191 Parameters: 2 7 7 80 10 50 500 Pmatch=0.80,Pindel=0.10 tuple sizes 0,4,5,7 tuple distances 0, 29, 159, 500 Length: 104741 ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30 Found at i:665 original size:2 final size:2 Alignment explanation
Indices: 653--686 Score: 50 Period size: 2 Copynumber: 17.0 Consensus size: 2 643 AGCAGGACAA * * 653 AT AT CT AT AT AT AT AT AT AG AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 687 TTTTTTTTCT Statistics Matches: 28, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47 Consensus pattern (2 bp): AT Left flanking sequence: Indices 153 -- 652 GAGCCGTATGATGGGCAACTATCACGTACGGTTCTATCAGGGGGGGGAGTCGCGCATCATGGGTA CCTTCTTATTGCTGTGAAGGGCGATATGAAAATAACCCCCTATCCAACCTCATTCTGTTGCGCGA AATCCATCATTGGCTAAGCAATTATTCGGTTATGCCATTTTAGGTTTCGCTTTAACAGAAGCTAT TGCTTTGTTTGCCTTAATGATGGCCTTTTTGATCTTATTTGTCTTTTAATTTTTCGGTGCTGGGA TTTTTTGGGAAAAAAAATATATTTTGGCTGCACCCTATTCGCAAAGCCAATAGGGCTGCGCCTAA AAAATCTAGATTTTTTGGCACCTTAGGGCCGAACGATTCGTACGTTCGAGCCCTTCACCACTTGC TACCAAAAGCATAAGCGTAAAAGAACCGAACTGACAAAGATTTTAACCTTTACAATTACTTTGGG AGCAGAGCCCTAAGGGCTGATTGGATAAAAAAAGAAGCAGGACAA Right flanking sequence: Indices 687 -- 1186 TTTTTTTTCTTTTTTAGCTGCTTCACTTCTTGTTATAAATAATCTTTAATAATCTTTGATAATGC ATAGCTTCGCGTGCTTTTCGATGGATGATAGGACCGAAGACCAAAGGCGCGAAGCGGCCGCGCGC CTGCGGCGGCCCTCGGTCTTCGTTAACTCACCAAATGCTTCCGCGTTATTCTACGCCACGTGCAC CTTTGAGCGGCCTCTTTCGTTTAATTCCCAGCTATACCTATACGAGGGCGACAGGTTACGTTTGA TTCGATATGCTAGTAAGCATATCGAATCCAGGGCTTATAGTTTAATTGGTTCAAACGCACCGCTC ATAACGGTGATATTGTAGGTTCGAGTCCTACTAAGCCTATATTCTATAGAACCAAAGTAATAAAA TTGGACTGAAATGGATGCGTAACACGTTGCGCCTTGAATCCCCCCAATATATATATATTTTTTTG CTCCGCAGGTCATTGTTGTCTTTTATCAATTTATCATCATTAAAT Found at i:1954 original size:17 final size:16 Alignment explanation
Indices: 1917--1951 Score: 61 Period size: 16 Copynumber: 2.2 Consensus size: 16 1907 GTGCTCTTCA * 1917 TTTATAGTATTTTTTC 1 TTTATACTATTTTTTC 1933 TTTATACTATTTTTTC 1 TTTATACTATTTTTTC 1949 TTT 1 TTT 1952 TATTGGCCAT Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 16 18 1.00 ACGTcount: A:0.17, C:0.09, G:0.03, T:0.71 Consensus pattern (16 bp): TTTATACTATTTTTTC Left flanking sequence: Indices 1417 -- 1916 TTTATGGCCGCTCACGCCTTTTTTTTTGTGAGAAAAGGCCGCGGGCCTCTAATCTAAGCTCGGAT AGTTCAAAACGCAGAGAGAGAAGTTACAAGAAGATTTCGAGCTTAGATTGGGCGAAGAGAACGCC GCAGCCTTTGATGCGGCTCTGAAAAGAGAGAAGTTGAGTAGGTGTTACCAACTACTATTCCTATT CAATTTCTCTATATTATACAATCTGCAGCAATCCTGCAGTTAAGGAGTTGTTTGATAGCAACTGT GAATAACAGTATAGATATAGATATCTTCATATTTAGCTCCCGCAAATTAATTAATATCTATGATT TTTCCATGAAGAGTGGATTCCCGTTATTTTCAAGTTGCGCTAGTAATCTACGTCACCGTCAACAT TAATTATCTATCTGTCTCTTTCATTAATTATCTAAATTATGCCAACTTATGAAACCCGGCCCGGC AATATAATCAATACTGGCGACACGATGTTGAAGCAGTGCTCTTCA Right flanking sequence: Indices 1952 -- 2451 TATTGGCCATTTATCAAAAATTTTCTGTAGTTTGAAGCTCGGCCCTGGTTCTTGTTGAAGCGAGT AGTCAGTTGTGGTGTTTGTTCGGCAGCTTCTTCATTCTACGCTAAAAATGCACCCTATGCGGAAT GCTCCTTTCATATCAACGAAGTAGTCAGAAGCTGGTAATGCAACCTTAACCATGATTGCCATAAC TGTTCAAATATCTGTCCTCGTTAGAACATCGTCTTGCTGCGCCCTCAGCATAACAAATGGAGTTG CCATATTCCAATGAATTGAGAAATTGATTACATCAAATTCCTCATTCGTTTTGTTCATCATTCGT TTTGTTCATAATGAGTTTTGGCGGCCGATGTTCCAAAAAATGAATATCTTTTTGCCATTCCTTTG CCATTACTTTGCGAGGCGGGGCTCCGCCCCCCCAATGGACTAAGTCCTTAGAGGGCAGAGCGGGT AAGTGCTTAAGTGGCACCATCTGCTAAGACGTCTAAATGCTTTCC Found at i:2274 original size:16 final size:16 Alignment explanation
Indices: 2253--2285 Score: 66 Period size: 16 Copynumber: 2.1 Consensus size: 16 2243 ATCAAATTCC 2253 TCATTCGTTTTGTTCA 1 TCATTCGTTTTGTTCA 2269 TCATTCGTTTTGTTCA 1 TCATTCGTTTTGTTCA 2285 T 1 T 2286 AATGAGTTTT Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 17 1.00 ACGTcount: A:0.12, C:0.18, G:0.12, T:0.58 Consensus pattern (16 bp): TCATTCGTTTTGTTCA Left flanking sequence: Indices 1753 -- 2252 AGTGGATTCCCGTTATTTTCAAGTTGCGCTAGTAATCTACGTCACCGTCAACATTAATTATCTAT CTGTCTCTTTCATTAATTATCTAAATTATGCCAACTTATGAAACCCGGCCCGGCAATATAATCAA TACTGGCGACACGATGTTGAAGCAGTGCTCTTCATTTATAGTATTTTTTCTTTATACTATTTTTT CTTTTATTGGCCATTTATCAAAAATTTTCTGTAGTTTGAAGCTCGGCCCTGGTTCTTGTTGAAGC GAGTAGTCAGTTGTGGTGTTTGTTCGGCAGCTTCTTCATTCTACGCTAAAAATGCACCCTATGCG GAATGCTCCTTTCATATCAACGAAGTAGTCAGAAGCTGGTAATGCAACCTTAACCATGATTGCCA TAACTGTTCAAATATCTGTCCTCGTTAGAACATCGTCTTGCTGCGCCCTCAGCATAACAAATGGA GTTGCCATATTCCAATGAATTGAGAAATTGATTACATCAAATTCC Right flanking sequence: Indices 2286 -- 2785 AATGAGTTTTGGCGGCCGATGTTCCAAAAAATGAATATCTTTTTGCCATTCCTTTGCCATTACTT TGCGAGGCGGGGCTCCGCCCCCCCAATGGACTAAGTCCTTAGAGGGCAGAGCGGGTAAGTGCTTA AGTGGCACCATCTGCTAAGACGTCTAAATGCTTTCCTTGATAACCGGAAGTTCTGAAAAAGTGTG AAATGCCGGAGGGCTTTTGACCATCCATTCAAGTGTCGTTGAATTCTGTTCAACAGCCCAAGGAC TTGAAGCACACTTGTTTTCACTGGTTAGAGTAAAAAAAACCACTACAAAGAAACACAAAATTCCT ACTACAGAAACATACGAGCCGAAACTACTAAAGGCATTCCATCCAGCGTAAGCATCTGGATAATC TGGAATGCGACGTGGCATACCTGCAAGACCTAAAAAATGCATAGGAAAAAAAGTCAAGTTCACAC CAAAGAAAGTGATCCAAAAATGAATTTGACCTAAAGTCTCTGGAT Found at i:18039 original size:15 final size:14 Alignment explanation
Indices: 18003--18044 Score: 50 Period size: 13 Copynumber: 3.0 Consensus size: 14 17993 AAAATGCATT * * 18003 TTTTTTATTTTCTA 1 TTTTTCATTTTCAA 18017 -TTTTCATTTTCAA 1 TTTTTCATTTTCAA 18030 TTTTTCCATTTTCAA 1 TTTTT-CATTTTCAA 18045 ATTTATGGGA Statistics Matches: 24, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 13 11 0.46 14 4 0.17 15 9 0.38 ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67 Consensus pattern (14 bp): TTTTTCATTTTCAA Left flanking sequence: Indices 17503 -- 18002 ATTTGCTATGCGAAGGCTCCGCGCCTTCCAGGAGCTATGGCTACGGAGGTAGCGTACCGGGGGCG CAAAGCCTTCGCCGAAGGCCGAAGAAGATAAAATAAAGCCCAAAAATTAATCATTTTTTTGTTTA AATTTTGAGTTTTTTTATCTTGTATTCTTTTATTCGGAAAAGCAAAATCCTAAAAACAAATAGAG CAGATGGTCCAACTACAGAACTTTTTTTTTTTTCTTATTTTCATGGTTGTGCTTTGTGGTACGGC AGCACCCATACTATTTCAATGGTTGGTAAGTAGAGATGTTCCCACAGGTGCTCCTTTTTCTCATG GTACTATAATACCTATTTTTACCTCTTTATTATTGCTTCTAGTTCATGTACATTCCAGGGGATTC ATACGCTCTATGGATAAAACAGAAAGAATAGTTTTGGTAAGAGCAAAACCCATTTTATTACTCAA CATAATTGAAAAAAGCTCCCCAAAAACTAGAGCTAAAAATGCATT Right flanking sequence: Indices 18045 -- 18544 ATTTATGGGAGACTTGTCATATTTAGAATCTTTCTATGGTGTGCTTTGTTTTTTATTATTTTGTA CATTTTTCTTATCATCTAAATATAGGCGCGATACGTGGGCAAACAAGGAGCGTAGGCTTGGAATA GAAGAAAAAATAAAACCGCGTAAGCGGGCACAGAGAAGAAAGCGCCAAGCGCTTTGTTGGCCTAA CAAAAAGAAGAAACAAAGAAATAAAAAGAAAGAAAATTTTTACTTTTTATTTCTTGCAAATAAAT CAAAAATATTTTTGATTTATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAAAAAGCCAAA ATTTTGGCTTTTTCTTCTCTGCTTGCTTTTTCGCAAGCTTATTCTTTCGTCCTTGAAAATATTTG GAATAGATTTTTTCTCGTTCGCGCCTTACCAAAAAGACTGATGGATGTTGGTCATGACTTTCGAA AAGTTCCCATGACTATGAAAATTTCACATGGAGGAGTTTGCATCT Found at i:18529 original size:19 final size:20 Alignment explanation
Indices: 18487--18529 Score: 52 Period size: 19 Copynumber: 2.2 Consensus size: 20 18477 GGATGTTGGT * * 18487 CATGACTTTCGAAAAGTTCC 1 CATGACTATCGAAAAGTTCA * 18507 CATGACTAT-GAAAATTTCA 1 CATGACTATCGAAAAGTTCA 18526 CATG 1 CATG 18530 GAGGAGTTTG Statistics Matches: 20, Mismatches: 3, Indels: 1 0.83 0.12 0.04 Matches are distributed among these distances: 19 12 0.60 20 8 0.40 ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30 Consensus pattern (20 bp): CATGACTATCGAAAAGTTCA Left flanking sequence: Indices 17987 -- 18486 GAGCTAAAAATGCATTTTTTTTATTTTCTATTTTCATTTTCAATTTTTCCATTTTCAAATTTATG GGAGACTTGTCATATTTAGAATCTTTCTATGGTGTGCTTTGTTTTTTATTATTTTGTACATTTTT CTTATCATCTAAATATAGGCGCGATACGTGGGCAAACAAGGAGCGTAGGCTTGGAATAGAAGAAA AAATAAAACCGCGTAAGCGGGCACAGAGAAGAAAGCGCCAAGCGCTTTGTTGGCCTAACAAAAAG AAGAAACAAAGAAATAAAAAGAAAGAAAATTTTTACTTTTTATTTCTTGCAAATAAATCAAAAAT ATTTTTGATTTATTTGCTGCAATTTTCAAAAACCTTCGGCTTCAACGAAAAAGCCAAAATTTTGG CTTTTTCTTCTCTGCTTGCTTTTTCGCAAGCTTATTCTTTCGTCCTTGAAAATATTTGGAATAGA TTTTTTCTCGTTCGCGCCTTACCAAAAAGACTGATGGATGTTGGT Right flanking sequence: Indices 18530 -- 19029 GAGGAGTTTGCATCTTTATTATGGGTGTTATTCTGTCGTGCGACCCGGCAGCTTATGCGCGACCA TCTCGTGTTTAAGCTCACGCCATGTGGGCGTGAACTCTGGTTGAATTCGGGTTCTAAATCCCGCC GCTGAGATGCTCAGTCGACTCTTGGACCTTGATAAGAAGACGGCTTCTTCTCAAATTAGTGCAAA AGGTTCAAGGACTTAGGATGAACTTAATGTGAATGGGTATAAGCTTCGCTGCTCAAAAACACCCA GTATTGACCACACTGAGAGACTTGCCAATGGCAAAAAAGGCCGCGGGTAACGCTAGTTGGCGAAA TGGCGTTAAGCATTCCTAGCAATACGAAAAGAGAGGTCGTGATGATATCATCTACGTTCGTACTG TTCCTCGTGGAGTAAATCTCACATCCAAAAATCTAACCAGGGAACGGAATAATTCCCATTGAGTT CCAGTAAAACTGGCAGGCCAGCCGGGCCGTAAGCTAGTGGGAACA Found at i:41636 original size:81 final size:81 Alignment explanation
Indices: 41501--41650 Score: 248 Period size: 81 Copynumber: 1.9 Consensus size: 81 41491 AAAATACTCG * * 41501 CTATCGGATTCGAACCGATAACCCGTAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC 1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC 41566 CAAGCGAGTATGCTCA 66 CAAGCGAGTATGCTCA * * 41582 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA 1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA 41646 CCAAG 65 CCAAG 41651 TGAGCTCAAG Statistics Matches: 64, Mismatches: 4, Indels: 2 0.91 0.06 0.03 Matches are distributed among these distances: 81 62 0.97 82 2 0.03 ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29 Consensus pattern (81 bp): CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC CAAGCGAGTATGCTCA Left flanking sequence: Indices 41001 -- 41500 CGGACAACTTCAATCTACTTTAGTCAATCATATGGATATAAAAAAAGCGGCTAATTTAGAAATAA CATCAGTATTTCAACAACTTTTTGAGCTCATTTTTTACCCATATAATTCTTTATGTTTTTGTTTG AACAAGCCAATTTATGCTTCACCCACTATACAAGAAAAGACGCAAGGAGGGTTACTTAGTCACCA GAGGATAACCACTTAGTAACTTGGGCCCCCACTTTGCCAATTAAGGCCGCAGGCTTTATTAACAG AACTGGAGCGCGTAGTTTATAGCGAAGCTTTTTTTTTTTTAATATTTTGGGAAATCCCCCAAAAG TATTTTTTGCTGCGAAAAGCAGCGCCCTCGAAGATTGTAAAGATTTAAGCTAATGGATGATTTGT TTTTTTGGCGAATAACGGGATTCGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTAT TAAGTTATACTCGCCCTTTTTCCAATTCAGACATTAAAATACTCG Right flanking sequence: Indices 41651 -- 42150 TGAGCTCAAGGAAACAAAGCGCAGAATGGAAACACAATCTTTTTGTTTCGTTTTATTTTTGCCAT TTCATTTTATCGACATCTCCGGCTTATTCCGGCTCGGCTGAATCTGCGGCATTTTTTCAAATATT CGAAAAATCTATAGTCCTCTGTCTTAAGGTGTGTAGAGACTCCTTTTTTATTGATTTATACCAAT CTATCTTAGATCCGAGATAGTGCCGAAAAAATGATTCAATTTAATCTAACCATGGTTGCCTTGGC AATGGCAATGACTTTTATACAATATGCAGAATACTCCAAAACCTCTATTTAGAACTAAAAGAAGA TAATGCTTCTTTATAAAAAAATCATAAAGTGCAAAGGTTAAAATTTTGAGCTTTGTTTTACGTAG TTTTGCCATCTATATAATAGAATATAGTAAGAAATAATAAGTTGGCGAGGAAGTAAAAAAATATA TATATCTATATATATATATAGATATATATATTTTTTTTTATTCTG Found at i:42106 original size:2 final size:2 Alignment explanation
Indices: 42101--42136 Score: 54 Period size: 2 Copynumber: 18.0 Consensus size: 2 42091 AAGTAAAAAA * * 42101 AT AT AT AT AT CT AT AT AT AT AT AT AG AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 42137 TTTTTTTTAT Statistics Matches: 30, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47 Consensus pattern (2 bp): AT Left flanking sequence: Indices 41601 -- 42100 AACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCACCAAGTGAGCTCAAGGAAAC AAAGCGCAGAATGGAAACACAATCTTTTTGTTTCGTTTTATTTTTGCCATTTCATTTTATCGACA TCTCCGGCTTATTCCGGCTCGGCTGAATCTGCGGCATTTTTTCAAATATTCGAAAAATCTATAGT CCTCTGTCTTAAGGTGTGTAGAGACTCCTTTTTTATTGATTTATACCAATCTATCTTAGATCCGA GATAGTGCCGAAAAAATGATTCAATTTAATCTAACCATGGTTGCCTTGGCAATGGCAATGACTTT TATACAATATGCAGAATACTCCAAAACCTCTATTTAGAACTAAAAGAAGATAATGCTTCTTTATA AAAAAATCATAAAGTGCAAAGGTTAAAATTTTGAGCTTTGTTTTACGTAGTTTTGCCATCTATAT AATAGAATATAGTAAGAAATAATAAGTTGGCGAGGAAGTAAAAAA Right flanking sequence: Indices 42137 -- 42636 TTTTTTTTATTCTGTGGTCTTGCAATTGTGCTTAAAGCTAAGGGCCCCAGCCCCCTATTTCCTAT CGTTTTCGTCAATCAAATAAAGGCTTCGTTTAGCCAGGGGTTATTCTTCTCTCCTGCTGAATTGC TTCGCGAACAAAGTAGGCGAAAAAAATAAAGATTTTTTTTGTCCGCCTTATTATCTAAATGGCCC TATGAGCTTTTACCAAGCAAAATATTTATTGCATAAGCCATCGGCTTCTACAAAGACCAATAAAG TGATAACAGCAGCGTAGCCAAGCTTGTTCCGCCCGCTGTGCGCAAAAAAAGTGTTTTTTTCCAGC ACTTAGTAAAACAAAATTTCGACACTCCTTGCGTTGCGGATGGTGAGTGGATTACTAATAAAATG GAGTGATCCAAGATGACCTCTCTTTCAATTTCAATTATGTCATTATATAGTAATGGCATGCGGCG AACTCTATTGGATGCGCCAAAAACTTGATTTGTTGGGCTGTGTCA Found at i:77120 original size:18 final size:18 Alignment explanation
Indices: 77097--77132 Score: 72 Period size: 18 Copynumber: 2.0 Consensus size: 18 77087 GGAGCGCAGC 77097 AACATAAGTACGGCAATG 1 AACATAAGTACGGCAATG 77115 AACATAAGTACGGCAATG 1 AACATAAGTACGGCAATG 77133 CCCGGCTCCG Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17 Consensus pattern (18 bp): AACATAAGTACGGCAATG Left flanking sequence: Indices 76597 -- 77096 TCTAATTGCGCCACTTTTCAAACCCATCATTGCACTTTGTGAAGATTGGAAAAAAATTCTAGAGG ATTTGGACAAGTATCCTTGCCGGGATTGCTCTAGCAATTACAGCGGGTATTTGAGGAATCCAGCG TCGGTCAAGAATTCCGGATCAAACGAAGTTTCTGTCCAAAATTCTTGACCTATGAAACTTCGCCG AAGTTTCTTCGCTCATAGTTCACAAGAGATTTTAACAAACGGATTAAGATAAAAGGAGAGGTTTT GCGCTGCGGCTTCTCTGTACTAAATTTATTGGAGCTTACGCCCTGACTGGAGAAGTTGTAGTAGA AAAGGGTATTATGGCCCAGGCGTGCCGCTGTGTTGTTTTTTTTGTTGATTTGGTTCCTTTGTTGT CCAGCTACGATGCAAAAAACGTCTATGCCGCTTCACTACTCAATTAGCTACTTTTATGCGCAGAT TTATTATACTGGGAAGTCATAGAGGGCGGCCCGAAGGAGCGCAGC Right flanking sequence: Indices 77133 -- 77632 CCCGGCTCCGAAGGAGCCAATAGCACGCTCCTTCGGAGCCCTTACTTGATAACGAATCGTTTAGA GCTTTACACTCTTCTATCCCCAGTGCAAATTGACGGATCCTGCGACTGAAGAAGCTTATTTCAGT TCTTCGTATATTTCTATCTTACTTAATCGACGGTTTAGAAGAGATGCCATTCTAGTTTCATAGCA TAGTCTCAAAATACGATAGAACACTTAAAAAAAAAGAAATAAATTACTCTATTCGTTTCTAGCAT CTTTTCTACTTCAATTTAGGTTTTGGCTGGTTGTTTATTTTGATTTTTTTCTTGCCTTATCGCGG GCAAGTAAATAATCTACTGCGGCTCTATGAAAAACCATTTATAAAAAAATCTAGATTTTTTTTTG CGTCGTGTTTTCCGGATTTATCAAGTTTACTAAGTTTACAAGCTCGAATCGGTTGAATTCGTAGC AGAGCACTCTATAACATTTTAACATTTGCACTAGAGACTAAATGC Done.