Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: scaffold_1200 Parameters: 2 7 7 80 10 50 1000 Pmatch=0.80,Pindel=0.10 tuple sizes 0,4,5,7 tuple distances 0, 29, 159, 1000 Length: 34788 ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32 Found at i:102 original size:39 final size:40 Alignment explanation
Indices: 2--185 Score: 182 Period size: 39 Copynumber: 4.7 Consensus size: 40 1 G * * * 2 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT * * * 41 ATACGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT 1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT * * 82 TCCGGGCTAAG-CTCGAAGGCATTTGTGCGAGTTACTAAG 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT * * 121 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGA-TTACT-AT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT * * 159 AACCGGGCTATGTCCCGAAGGCATTTG 1 -TCCGGGCTAAGTCCCGAAGGCATTTG 186 AACGAGTAGC Statistics Matches: 119, Mismatches: 19, Indels: 13 0.79 0.13 0.09 Matches are distributed among these distances: 38 1 0.01 39 61 0.51 40 47 0.39 41 10 0.08 ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26 Consensus pattern (40 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT Found at i:204 original size:79 final size:78 Alignment explanation
Indices: 55--218 Score: 174 Period size: 79 Copynumber: 2.1 Consensus size: 78 45 GGACTAAGAT * * * ** 55 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCTCGAAGGCATTTGTGCGAGTTACTAA 1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA * 120 GTCCGGGTTAAGTC 66 GTCC-GGTTAAATC * * 134 CCGAAGGCAATTGTGCGA-TTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC 1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C * 196 TATA-TCCGGTTAAATT 63 TA-AGTCCGGTTAAATC 212 CCGAAGG 1 CCGAAGG 219 TACGTGATTT Statistics Matches: 72, Mismatches: 9, Indels: 9 0.80 0.10 0.10 Matches are distributed among these distances: 77 2 0.03 78 29 0.40 79 40 0.56 80 1 0.01 ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26 Consensus pattern (78 bp): CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA GTCCGGTTAAATC Found at i:1680 original size:48 final size:47 Alignment explanation
Indices: 1472--1737 Score: 410 Period size: 47 Copynumber: 5.6 Consensus size: 47 1462 TCCGGGTGTT 1472 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC 1 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC * * * * * * * 1519 ACATTCATCACGTTGGCCACT-CGCCCTGTCACATATATACACTTCC 1 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC 1565 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC 1 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC * 1612 ACATTCATCACATCGGCCATTAGGCCCTATCACATATATATACAC-TTC 1 ACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTC 1660 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTC 1 ACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTC 1709 ACATTCATCACATCGGCCATTAGGCCTTA 1 ACATTCATCACATCGGCCATTAGGCCTTA 1738 CTATCATTTC Statistics Matches: 199, Mismatches: 16, Indels: 6 0.90 0.07 0.03 Matches are distributed among these distances: 46 39 0.20 47 71 0.36 48 47 0.24 49 42 0.21 ACGTcount: A:0.29, C:0.31, G:0.09, T:0.30 Consensus pattern (47 bp): ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC Found at i:1697 original size:93 final size:93 Alignment explanation
Indices: 1472--1734 Score: 404 Period size: 93 Copynumber: 2.8 Consensus size: 93 1462 TCCGGGTGTT * * 1472 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACGTTGGCC 1 ACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATACACTTTCACATTCATCACATCGGCC * * * 1537 ACT-CGCCCTGTCACATATATACACTTCC 65 ATTAGGCCCTATCACATATATACACTTCC 1565 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCC 1 ACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATACACTTTCACATTCATCACATCGGCC 1630 ATTAGGCCCTATCACATATATATACACTT-C 65 ATTAGGCCCTATCAC--ATATATACACTTCC 1660 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGG 1 ACATTCATCACATCGGCCATTAGGCCTTATCAC--A-ATATACACTTTCACATTCATCACATCGG 1725 CCATTAGGCC 63 CCATTAGGCC 1735 TTACTATCAT Statistics Matches: 160, Mismatches: 5, Indels: 6 0.94 0.03 0.04 Matches are distributed among these distances: 93 65 0.41 94 9 0.06 95 34 0.21 96 12 0.08 97 40 0.25 ACGTcount: A:0.29, C:0.32, G:0.10, T:0.30 Consensus pattern (93 bp): ACATTCATCACATCGGCCATTAGGCCTTATCACAATATACACTTTCACATTCATCACATCGGCCA TTAGGCCCTATCACATATATACACTTCC Found at i:1734 original size:144 final size:140 Alignment explanation
Indices: 1472--1737 Score: 408 Period size: 144 Copynumber: 1.9 Consensus size: 140 1462 TCCGGGTGTT * * * 1472 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACGTTGGCC 1 ACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACTTTCACATTCATCACATCGGCC * 1537 ACTCGCCCTGTCACATATATACACTTCCACATTCATCACATCGGCCATTAGGCCTTATCACATAT 66 ACTCGCCCTATCACATATATACACTTCCACATTCATCACATCGGCCATTAGGCCTTATCACATAT 1602 ATACACTTTC 131 ATACACTTTC 1612 ACATTCATCACATCGGCCATTAGGCCCTATCACATATATATACAC-TTCACATTCATCACATCGG 1 ACATTCATCACATCGGCCATTAGGCCCTATCAC--ATATATACACTTTCACATTCATCACATCGG * * * * 1676 CCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA 64 CCACT-CGCCCTATCAC--ATATATACACTTCCACATTCATCACATCGGCCATTAGGCCTTA 1738 CTATCATTTC Statistics Matches: 113, Mismatches: 8, Indels: 6 0.89 0.06 0.05 Matches are distributed among these distances: 140 32 0.28 141 21 0.19 142 18 0.16 144 42 0.37 ACGTcount: A:0.29, C:0.31, G:0.09, T:0.30 Consensus pattern (140 bp): ACATTCATCACATCGGCCATTAGGCCCTATCACATATATACACTTTCACATTCATCACATCGGCC ACTCGCCCTATCACATATATACACTTCCACATTCATCACATCGGCCATTAGGCCTTATCACATAT ATACACTTTC Found at i:12721 original size:119 final size:120 Alignment explanation
Indices: 12539--12761 Score: 283 Period size: 119 Copynumber: 1.9 Consensus size: 120 12529 TCCTCGTTCA * * 12539 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT 1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCGGAT * * * 12604 TTAGTAAC-TCGCACAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC 66 ATAGTAACTTAGCACAA-AGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC * * ** 12659 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATACCTTC-GGATCTTAGTCCGG 1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATACCTTCGGGA-CTTAACCCGG * * * 12721 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA 64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA 12762 CATCATTCAA Statistics Matches: 88, Mismatches: 12, Indels: 7 0.82 0.11 0.07 Matches are distributed among these distances: 118 4 0.05 119 65 0.74 120 19 0.22 ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25 Consensus pattern (120 bp): AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCGGAT ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC Found at i:12761 original size:40 final size:40 Alignment explanation
Indices: 12537--12761 Score: 269 Period size: 40 Copynumber: 5.7 Consensus size: 40 12527 GCTCCTCGTT * * 12537 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA * * 12577 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA * * * 12617 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA * * 12657 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA * * * * * 12696 CAAATACCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA 1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA 12737 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGA 12762 CATCATTCAA Statistics Matches: 160, Mismatches: 19, Indels: 12 0.84 0.10 0.06 Matches are distributed among these distances: 38 2 0.01 39 30 0.19 40 116 0.73 41 12 0.08 ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25 Consensus pattern (40 bp): CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA Found at i:15203 original size:40 final size:40 Alignment explanation
Indices: 15120--15305 Score: 234 Period size: 40 Copynumber: 4.7 Consensus size: 40 15110 TTGAATGATG * * * * * 15120 TCCGGGCTAAGTCCTGAAGGC-TTTGTGCTAAGTGACCATA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA * 15160 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA 1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA * 15200 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA * 15240 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA * * 15281 -CTGGGCTATGTCCCGAAGGCATTTG 1 TCCGGGCTAAGTCCCGAAGGCATTTG 15306 AACGAGTAGC Statistics Matches: 131, Mismatches: 11, Indels: 8 0.87 0.07 0.05 Matches are distributed among these distances: 39 1 0.01 40 120 0.92 41 10 0.08 ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27 Consensus pattern (40 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA Found at i:15312 original size:80 final size:79 Alignment explanation
Indices: 15173--15338 Score: 219 Period size: 80 Copynumber: 2.1 Consensus size: 79 15163 GGACTAAGAT * ** 15173 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT 1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAG-TAGCT * 15237 AAATCCGGGTTAAGTC 65 AAATCC-GGTTAAATC * * 15253 CCGAAGGCATTTGTGCGAGTTACTATAA-CTGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCT 1 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTAGCT * * 15317 ATATCCGGTTAAATT 65 AAATCCGGTTAAATC 15332 CCGAAGG 1 CCGAAGG 15339 TACGTGATTT Statistics Matches: 76, Mismatches: 8, Indels: 5 0.85 0.09 0.06 Matches are distributed among these distances: 79 16 0.21 80 58 0.76 81 2 0.03 ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27 Consensus pattern (79 bp): CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTAGCTA AATCCGGTTAAATC Found at i:22501 original size:19 final size:18 Alignment explanation
Indices: 22477--22512 Score: 54 Period size: 19 Copynumber: 1.9 Consensus size: 18 22467 TTAAATTTAG * 22477 TGAATTAATTGAATTATGT 1 TGAATTAAATG-ATTATGT 22496 TGAATTAAATGATTATG 1 TGAATTAAATGATTATG 22513 GTGCCAAGTT Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 18 6 0.38 19 10 0.62 ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44 Consensus pattern (18 bp): TGAATTAAATGATTATGT Found at i:22963 original size:68 final size:66 Alignment explanation
Indices: 22889--23035 Score: 163 Period size: 64 Copynumber: 2.2 Consensus size: 66 22879 CATCATGTCT * * * * 22889 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA 1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA 22952 TGTAG 62 TGTAG ** * * 22957 ACAAGAGAGCTACGGTATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT 1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT 23022 AG 65 AG 23024 ACAAGAGAGCTA 1 ACAAGAGAGCTA 23036 TGAGATAAAT Statistics Matches: 68, Mismatches: 8, Indels: 7 0.82 0.10 0.08 Matches are distributed among these distances: 64 24 0.35 65 3 0.04 66 4 0.06 67 24 0.35 68 13 0.19 ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22 Consensus pattern (66 bp): ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA G Found at i:22994 original size:64 final size:64 Alignment explanation
Indices: 22913--23096 Score: 178 Period size: 67 Copynumber: 2.8 Consensus size: 64 22903 AGACATTATG * * 22913 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACG-GTATAT 1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAG-ATAA * * * * * * 22977 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTATGAGAT 1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT 23042 AA 63 AA * * * * 23044 AT-TGGCTAGGTCACATGGGAGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC 1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC 23097 CGAACTATAT Statistics Matches: 97, Mismatches: 17, Indels: 13 0.76 0.13 0.10 Matches are distributed among these distances: 62 1 0.01 63 19 0.20 64 25 0.26 66 20 0.21 67 31 0.32 68 1 0.01 ACGTcount: A:0.29, C:0.16, G:0.30, T:0.24 Consensus pattern (64 bp): ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA Found at i:29974 original size:27 final size:26 Alignment explanation
Indices: 29937--29989 Score: 97 Period size: 27 Copynumber: 2.0 Consensus size: 26 29927 TTATGTCAGT 29937 GCTACGGGGTTACCTCCTAACTGTGA 1 GCTACGGGGTTACCTCCTAACTGTGA 29963 GCTACCGGGGTTACCTCCTAACTGTGA 1 GCTA-CGGGGTTACCTCCTAACTGTGA 29990 AGTTGAGTTC Statistics Matches: 26, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 26 4 0.15 27 22 0.85 ACGTcount: A:0.19, C:0.28, G:0.26, T:0.26 Consensus pattern (26 bp): GCTACGGGGTTACCTCCTAACTGTGA Found at i:30669 original size:6 final size:6 Alignment explanation
Indices: 30639--30732 Score: 68 Period size: 6 Copynumber: 15.3 Consensus size: 6 30629 AAGAAACATT * * * 30639 ATCAGA A-CTAGA ATCAAA ATAAGA ATCAGA ATCAGA ATCAG- GTGACAGA 1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA * * * 30688 ATTAGA ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA AT 1 ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT 30733 GTGAATGCAA Statistics Matches: 68, Mismatches: 12, Indels: 16 0.71 0.12 0.17 Matches are distributed among these distances: 5 4 0.06 6 55 0.81 7 7 0.10 8 2 0.03 ACGTcount: A:0.50, C:0.14, G:0.17, T:0.19 Consensus pattern (6 bp): ATCAGA Found at i:30697 original size:31 final size:31 Alignment explanation
Indices: 30660--30732 Score: 110 Period size: 31 Copynumber: 2.4 Consensus size: 31 30650 AATCAAAATA * * 30660 AGAATCAGAATCAGAATCAGGTGACAGAATT 1 AGAATCAGAATCAGAATCAGGTAACAGAATC * 30691 AGAATCAGAATCAGTATCAGGTAACAGAATC 1 AGAATCAGAATCAGAATCAGGTAACAGAATC * 30722 AAAATCAGAAT 1 AGAATCAGAAT 30733 GTGAATGCAA Statistics Matches: 38, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 31 38 1.00 ACGTcount: A:0.48, C:0.14, G:0.19, T:0.19 Consensus pattern (31 bp): AGAATCAGAATCAGAATCAGGTAACAGAATC Found at i:30894 original size:29 final size:29 Alignment explanation
Indices: 30855--30933 Score: 106 Period size: 29 Copynumber: 2.7 Consensus size: 29 30845 CTTAATAATC * 30855 AACCACGCACACTTAGTGCCATGTACTTT-A 1 AACC-CGCACACTTAGTGCCATGCA-TTTCA * 30885 AACTCGCACACTTAGTGCCATGCATTTCA 1 AACCCGCACACTTAGTGCCATGCATTTCA * 30914 AGCCCGCACACTTAGTGCCA 1 AACCCGCACACTTAGTGCCA 30934 ATCTCACAAC Statistics Matches: 44, Mismatches: 4, Indels: 3 0.86 0.08 0.06 Matches are distributed among these distances: 28 3 0.07 29 38 0.86 30 3 0.07 ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24 Consensus pattern (29 bp): AACCCGCACACTTAGTGCCATGCATTTCA Found at i:30976 original size:43 final size:43 Alignment explanation
Indices: 30915--31103 Score: 360 Period size: 43 Copynumber: 4.4 Consensus size: 43 30905 TGCATTTCAA 30915 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT 1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT * 30958 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACAATTATT 1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT * 31001 GCCCGCACACTTAGTGTCAATCTCACAACCGTGAACACTTATT 1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT 31044 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT 1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT 31087 GCCCGCACACTTAGTGC 1 GCCCGCACACTTAGTGC 31104 TGAAAACCAA Statistics Matches: 142, Mismatches: 4, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 43 142 1.00 ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23 Consensus pattern (43 bp): GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT Done.