Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005653.1 Corchorus capsularis cultivar CVL-1 contig05671, whole genome shotgun sequence

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: 3076
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30


Found at i:590 original size:324 final size:325

Alignment explanation

Indices: 1--813 Score: 1278 Period size: 324 Copynumber: 2.5 Consensus size: 325 * 1 TCGTGTACTAACCATCACGGGTTTTTGCTAAAAACGCAGTCCGATGCCCCGGCTCAGTTTTGCCA 1 TCGTGTACTAACCATCACGGGTTTTTGCTAAAAACGCAGTCCGATGCCCCGGCTCAGTTTTGCCT * * 66 AATTTTTTGCGTAAAGACTCCTTGAGATATCTATATTTATCGAACCAAATCTCAACCACATTGGA 66 AATTTTTTGCGTAAAGACTCCTTGAGATATCTATATTTATCGAACTAAATCTCAACCACATTGAA * ** * * * 131 T-TTACAGATTTATTTTTTTGAGCATCTCAA-TTTGATTTCGGTTTAATTAGAATTAATTAGGAA 131 TATTA-AGATTTCTTTTTACGAGCATCTGAATTTTGATTTCGATTTAATTAAAATTAATTAGGAA * 194 AAAAATGGGTAAACGATATTAGAAGCGTGAAAAACCTTTCAATTTTTTTGACATTGAATTATATA 195 AAAAATGGGTAAACGATATTAGAAGCGTGAAAAACCTTTCAATGTTTTTGACATTGAATTATATA * ** 259 TATTTTTTCTGTGTTTTTTGGCGAAAAAATTGAGAAAAAAATTTTCGGGTCAATTTTTTGTCAAA 260 TATTTTTTCTGTGTATTTTGGCGAAAAAATTGAGAAAAAAATTTTCGGGTCAATTTTTTACCAAA 324 A 325 A * * * * 325 TCGTGTACTAACCATCACGGGATTTTGCTAAGAACGAAGCCCGATGCCCCGGCTCAGTTTTGCCT 1 TCGTGTACTAACCATCACGGGTTTTTGCTAAAAACGCAGTCCGATGCCCCGGCTCAGTTTTGCCT * 390 AATTTTTTGCGTAAAGACTTCTTGAGATATCTATATTTATCGAACTAAATCTCAACCACATTGAA 66 AATTTTTTGCGTAAAGACTCCTTGAGATATCTATATTTATCGAACTAAATCTCAACCACATTGAA * * 455 TATTAAGATTTCTTTTTACAAGCATCTGAATTTTG-TTTCGATTTAATTGAAAATTAATTCGGAA 131 TATTAAGATTTCTTTTTACGAGCATCTGAATTTTGATTTCGATTTAATT-AAAATTAATTAGG-A ** * 519 AAAAAGATTTGTAAACGATATTAGAAGCGTGAAAAACCTTTTAA-GTTTTTGACATTGAA-T-TA 194 AAAAA-ATGGGTAAACGATATTAGAAGCGTGAAAAACCTTTCAATGTTTTTGACATTGAATTATA * * 581 TATATTTTTTCTGTGTATTTTGGCGAAAAATTTGAGAAAAAAATTTTCGGGTCAATTTTTTACCG 258 TATATTTTTTCTGTGTATTTTGGCGAAAAAATTGAGAAAAAAATTTTCGGGTCAATTTTTTACCA 646 AAA 323 AAA * * * 649 TCATGTACTAACCATCACGGGTTTTTGCTAAAAACGCAGTTCGATGCCCCGACTCAGTTTTGCCT 1 TCGTGTACTAACCATCACGGGTTTTTGCTAAAAACGCAGTCCGATGCCCCGGCTCAGTTTTGCCT * * 714 AATATTTTGCGTAAACACTCCTTGAGATATCTATATTTATCGAACTAAATCTCAACCACATTGAA 66 AATTTTTTGCGTAAAGACTCCTTGAGATATCTATATTTATCGAACTAAATCTCAACCACATTGAA 779 TATTAAGATTTCTTTTTACGAGCATCTGAATTTTG 131 TATTAAGATTTCTTTTTACGAGCATCTGAATTTTG 814 GTTAAAAACC Statistics Matches: 448, Mismatches: 36, Indels: 10 0.91 0.07 0.02 Matches are distributed among these distances: 324 374 0.83 325 19 0.04 326 20 0.04 327 35 0.08 ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37 Consensus pattern (325 bp): TCGTGTACTAACCATCACGGGTTTTTGCTAAAAACGCAGTCCGATGCCCCGGCTCAGTTTTGCCT AATTTTTTGCGTAAAGACTCCTTGAGATATCTATATTTATCGAACTAAATCTCAACCACATTGAA TATTAAGATTTCTTTTTACGAGCATCTGAATTTTGATTTCGATTTAATTAAAATTAATTAGGAAA AAAATGGGTAAACGATATTAGAAGCGTGAAAAACCTTTCAATGTTTTTGACATTGAATTATATAT ATTTTTTCTGTGTATTTTGGCGAAAAAATTGAGAAAAAAATTTTCGGGTCAATTTTTTACCAAAA Found at i:1072 original size:268 final size:267 Alignment explanation

Indices: 550--1081 Score: 886 Period size: 268 Copynumber: 2.0 Consensus size: 267 540 TAGAAGCGTG * * 550 AAAAACCTTTTAAGTTTTTGACATTGAATTATATATTTTTTCTGTGTATTTTGGCGAAAAATTTG 1 AAAAACCTTTCAAGTTTTTGACATTGAATTATATATTTTTTCTGAGTATTTTGGCGAAAAATTTG 615 AGAAAAAAATTTTCGGGTCAATTTTTTACCGAAATCATGTACTAACCATCACGGGTTTTTGCTAA 66 AGAAAAAAATTTTCGGGTCAATTTTTTACCGAAATCATGTACTAACCATCACGGGTTTTTGCTAA * 680 AAACGCAGTTCGATGCCCCGACTCAGTTTTGCCTAATATTTTGCGTAAACACTCCTTGAGATATC 131 AAACGCAGTCCGATGCCCCGACTCAGTTTTGCCTAATATTTTGCGTAAACACTCCTTGAGATATC * * 745 TATATTTATCGAACTAAATCTCAACCACATTGAATATTAAGATTTCTTTTTACGAGCATCTGAAT 196 TATATTTATCGAACCAAATCTCAACCACATTGAATATTAAGATTTATTTTTACGAGCATCTGAAT 810 TTTGGTT 261 TTTGGTT * * * 817 AAAAACCTTTCAATTTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTTTTGCGAAAAATTT 1 AAAAACCTTTCAA-GTTTTTGACATTGAATTATATATTTTTTCTGAGTATTTTGGCGAAAAATTT * * 882 GAGAGAAAAATTTTCGGGTCAATTTTTTACCGAAATCGTGTACTAACCATCACGGGTTTTTGCTA 65 GAGAAAAAAATTTTCGGGTCAATTTTTTACCGAAATCATGTACTAACCATCACGGGTTTTTGCTA * * * * 947 AAAACGCAGTCCGATGCCCCGGCTCAGTTTTGCCTAATTTTTTGCGTCAAGACTCCTTGAGATAT 130 AAAACGCAGTCCGATGCCCCGACTCAGTTTTGCCTAATATTTTGCGTAAACACTCCTTGAGATAT * ** 1012 CTATATTTATCGAACCAAATCTCAACCACATTGGAT-TTACAGATTTATTTTTTTGAGCATCTGA 195 CTATATTTATCGAACCAAATCTCAACCACATTGAATATTA-AGATTTATTTTTACGAGCATCTGA 1076 ATTTTG 259 ATTTTG 1082 TTTCGGTTTA Statistics Matches: 246, Mismatches: 17, Indels: 3 0.92 0.06 0.01 Matches are distributed among these distances: 267 15 0.06 268 231 0.94 ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39 Consensus pattern (267 bp): AAAAACCTTTCAAGTTTTTGACATTGAATTATATATTTTTTCTGAGTATTTTGGCGAAAAATTTG AGAAAAAAATTTTCGGGTCAATTTTTTACCGAAATCATGTACTAACCATCACGGGTTTTTGCTAA AAACGCAGTCCGATGCCCCGACTCAGTTTTGCCTAATATTTTGCGTAAACACTCCTTGAGATATC TATATTTATCGAACCAAATCTCAACCACATTGAATATTAAGATTTATTTTTACGAGCATCTGAAT TTTGGTT Found at i:1405 original size:325 final size:321 Alignment explanation

Indices: 817--2038 Score: 1681 Period size: 325 Copynumber: 3.8 Consensus size: 321 807 AATTTTGGTT 817 AAAAACCTTTCAATTTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTTTTGCGAAAAATTT 1 AAAAACCTTTCAATTTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTTTTGCGAAAAA-TT * * * 882 GAGAGAAAAATTTTCGGGTCAATTTTTTACCGAAATCGTGTACTAACCATCACGGGTTTTTGCTA 65 GAGAAAAAAAATTTCGGGTCAATTTTTTGCCGAAATCGTGTACTAACCATCACGGGTTTTTGCTA * * 947 AAAACGCAGTCCGATGCCCCGGCTCAGTTTTGCCTAATTTTTTGCGTCAAGACTCCTTGAGATAT 130 AAAACGCAGTCCGATGCCCCGACTCAGTTTTGCCTAATTTTTTGCGTAAAGACTCCTTGAGATAT * * * * ** 1012 CTATATTTATCGAACCAAATCTCAACCACATTGGATTTACAGATTTATTTTTTTGAGCATCTGAA 195 CTATATTTATCGAACCAAATCTCAACCACATTGAATATAAAGATTTCTTTTTACGAGCATCTGAA * 1077 TTTTGTTTCGGTTTAATTAGAAATTAATTCGGGAAAAAATGGGTAAACGATATTAGAAGTGTG 260 TTTTGTTTCGGTTTAATTAGAAATTAATTCGGAAAAAAATGGGTAAACGATATTAGAAG-GTG * 1140 AAAAACCTTTCAATTTTTTTGGCATTGAATTATATATATTTATT-TGAGTATTTTTTCGAAAAAT 1 AAAAACCTTTCAATTTTTTTGGCATTGAATTATATAT-TTT-TTCTGAGTATTTTTGCGAAAAAT * * 1204 TGAGAAAAAAAAAATTTCGGGTCAATTTTTTGCCGAAATCGTGTATTAACCATCATGGGTTTTTG 64 TGAG--AAAAAAAATTTCGGGTCAATTTTTTGCCGAAATCGTGTACTAACCATCACGGGTTTTTG * ** * 1269 CTAAAAACGCAGT-CGAATACCATGATTCAGTTTTGCC-AGATTTTTTGCGTAAAGACTCCTTGA 127 CTAAAAACGCAGTCCG-ATGCCCCGACTCAGTTTTGCCTA-ATTTTTTGCGTAAAGACTCCTTGA * * * 1332 GATATCTATATTTATTGAACCAGATCTCAACCTCATTAGAAT-TAAAGATTTCTTTTTACGAGCA 190 GATATCTATATTTATCGAACCAAATCTCAACCACATT-GAATATAAAGATTTCTTTTTACGAGCA * 1396 TCTGAATTTTGTTTCGGTTTAATTAGAAATTAATTCGGAAAAAAATGGGTAAACGTTATTAGAAG 254 TCTGAATTTTGTTTCGGTTTAATTAGAAATTAATTCGGAAAAAAATGGGTAAACGATATTAGAAG 1461 GATG 319 G-TG * * * * * * 1465 AAAAACCTTTCAATATTTTTGACATTGAATTATTTATTTTTGCAGAGTATTTTGGCGAAAAATTG 1 AAAAACCTTTCAATTTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTTTTGCGAAAAATTG * * * 1530 AGAAAAAAATTTTCGGGTCATTTTTTTGCCGAAATCGTGTACTAACAAATCACGGGTTTTTGCTA 66 AGAAAAAAAATTTCGGGTCAATTTTTTGCCGAAATCGTGTACTAAC-CATCACGGGTTTTTGCTA * * 1595 AAAATGCAGTCCGATGCCCCGGCTCAGTTTTGCCTAATTTTTTGCGTAAAGACTCCTTGAGATAT 130 AAAACGCAGTCCGATGCCCCGACTCAGTTTTGCCTAATTTTTTGCGTAAAGACTCCTTGAGATAT * * 1660 CTATATTTATCGAACCAAATCTCAACCACATTGAATATTAAGA-TT-TTTTTACGAGTATCTGAA 195 CTATATTTATCGAACCAAATCTCAACCACATTGAATATAAAGATTTCTTTTTACGAGCATCTGAA * * * * * * * 1723 TTTTGTTTCGATTTAATTAGAAACTATTTC-TAAATAAATGGGTAAACGATATTAGAAGCATT 260 TTTTGTTTCGGTTTAATTAGAAATTAATTCGGAAAAAAATGGGTAAACGATATTAGAAG-GTG * * 1785 AAAAACCTTTAAATTTTTTTGGCATTGAATTATATATTTTTTCTCAGTA-TTTT--G-------G 1 AAAAACCTTTCAATTTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTTTTGCGAAAAATTG * * * * * * 1840 CG--AAAAAATTCTCGGGTCAATTTTTTGCTGAAATCTTGTATTAACTATCACAGGTTTTTGCTA 66 AGAAAAAAAATT-TCGGGTCAATTTTTTGCCGAAATCGTGTACTAACCATCACGGGTTTTTGCTA * * * 1903 AAAACGCATTCCGATGCCCCGACTCAGTTTTGCCTAATTTTTTTGCGTCAACACTCCTTGAGATA 130 AAAACGCAGTCCGATGCCCCGACTCAGTTTTGCCTAA-TTTTTTGCGTAAAGACTCCTTGAGATA * * 1968 TCTATATTTATCGAACTAAATCTCAACCACATTGAATATTAAGATTTCTTTTTACGAGCATCTGA 194 TCTATATTTATCGAACCAAATCTCAACCACATTGAATATAAAGATTTCTTTTTACGAGCATCTGA 2033 ATTTTG 259 ATTTTG 2039 GTTAAAAACC Statistics Matches: 805, Mismatches: 76, Indels: 48 0.87 0.08 0.05 Matches are distributed among these distances: 308 57 0.07 309 98 0.12 310 4 0.00 311 22 0.03 317 1 0.00 319 3 0.00 320 68 0.08 321 44 0.05 322 47 0.06 323 147 0.18 324 52 0.06 325 259 0.32 326 3 0.00 ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38 Consensus pattern (321 bp): AAAAACCTTTCAATTTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTTTTGCGAAAAATTG AGAAAAAAAATTTCGGGTCAATTTTTTGCCGAAATCGTGTACTAACCATCACGGGTTTTTGCTAA AAACGCAGTCCGATGCCCCGACTCAGTTTTGCCTAATTTTTTGCGTAAAGACTCCTTGAGATATC TATATTTATCGAACCAAATCTCAACCACATTGAATATAAAGATTTCTTTTTACGAGCATCTGAAT TTTGTTTCGGTTTAATTAGAAATTAATTCGGAAAAAAATGGGTAAACGATATTAGAAGGTG Found at i:2220 original size:32 final size:32 Alignment explanation

Indices: 2184--2801 Score: 536 Period size: 31 Copynumber: 19.9 Consensus size: 32 2174 AACGGCAATT * * * ** 2184 GGCAAATGCCAACGCCACGGCCAAAGAACATC 1 GGCAAATGCCGACGCCAAGGCCAATGGGCATC * * 2216 GGCAATTGCCAACGCCAAGGCC-ATGGGCATC 1 GGCAAATGCCGACGCCAAGGCCAATGGGCATC * 2247 GGCAAATGCCGACGTCAAGGCC-ATGGGCATC 1 GGCAAATGCCGACGCCAAGGCCAATGGGCATC * 2278 AGCAAATGCCGACGCCAAGGCCAA-GGGCCATC 1 GGCAAATGCCGACGCCAAGGCCAATGGG-CATC * * 2310 GGCAAATGCCGACGCCAAGGCCAAGGGGACA-A 1 GGCAAATGCCGACGCCAAGGCCAATGGG-CATC * * * * ** * 2342 GGGACAT--C-A-TCAAATTCCAA--CGCAATC 1 GGCAAATGCCGACGCCAAGGCCAATGGGC-ATC ** * 2369 GGCAAATGCCGATACCAAGG-CAACGGGCCATC 1 GGCAAATGCCGACGCCAAGGCCAATGGG-CATC * 2401 GGCAATTGCCGACG-CATAGGCC-ATGGGCATC 1 GGCAAATGCCGACGCCA-AGGCCAATGGGCATC * * 2432 GCCAAATGCCGACGCCAAGGCC-ATGCGCATC 1 GGCAAATGCCGACGCCAAGGCCAATGGGCATC * * * 2463 GGCAAATACAGACGCCAAGGCCAA-GGGCATT 1 GGCAAATGCCGACGCCAAGGCCAATGGGCATC * 2494 GGCAAATGCCGACGCCAAGGCC-TTGGGCCATC 1 GGCAAATGCCGACGCCAAGGCCAATGGG-CATC 2526 GGCAAATGCCGACGCCAAGGCC-ATGGGCCATC 1 GGCAAATGCCGACGCCAAGGCCAATGGG-CATC * 2558 GGCAAATGCCG-TGCCAAGGCC-ATGGGCATC 1 GGCAAATGCCGACGCCAAGGCCAATGGGCATC * * 2588 GGTAAATGCCGACGCCAAAGCCAA-GGG---C 1 GGCAAATGCCGACGCCAAGGCCAATGGGCATC * * * 2616 GACAAATGCCCACACCAAGGCC-ATGGGCATC 1 GGCAAATGCCGACGCCAAGGCCAATGGGCATC * * * 2647 GTCAAATGCCGACGCCAAGACCAA-GGGCCACC 1 GGCAAATGCCGACGCCAAGGCCAATGGG-CATC * 2679 GGCAAATGCCGACGCCAAGACCAA-GGGCCATC 1 GGCAAATGCCGACGCCAAGGCCAATGGG-CATC * * * 2711 GGCAAATCCCGACGCCAAGGCTAA-GGGCATG 1 GGCAAATGCCGACGCCAAGGCCAATGGGCATC * * 2742 GGCAAATGTCGACGCCAAGGCCTA-GGGACATC 1 GGCAAATGCCGACGCCAAGGCCAATGGG-CATC * * * 2774 GGCAAATGCCGATGCCAATGCGAATGGG 1 GGCAAATGCCGACGCCAAGGCCAATGGG 2802 ACAAGTGACA Statistics Matches: 483, Mismatches: 75, Indels: 55 0.79 0.12 0.09 Matches are distributed among these distances: 25 1 0.00 26 2 0.00 27 6 0.01 28 28 0.06 29 2 0.00 30 19 0.04 31 211 0.44 32 204 0.42 33 10 0.02 ACGTcount: A:0.29, C:0.31, G:0.29, T:0.10 Consensus pattern (32 bp): GGCAAATGCCGACGCCAAGGCCAATGGGCATC Found at i:2253 original size:63 final size:64 Alignment explanation

Indices: 2163--2333 Score: 204 Period size: 63 Copynumber: 2.7 Consensus size: 64 2153 GTTTTTGCTA * * * * * * * 2163 AACGCCAA-GCCAACGGCAATTGGCAAATGCCAACGCCACGGCCAAAGAACATCGGCAATTGCC 1 AACGCCAAGGCCAAGGGCCATCGGCAAATGCCGACGCCAAGGCCAAAGAACATCAGCAAATGCC * * * ** 2226 AACGCCAAGGCCATGGG-CATCGGCAAATGCCGACGTCAAGGCC-ATGGGCATCAGCAAATGCC 1 AACGCCAAGGCCAAGGGCCATCGGCAAATGCCGACGCCAAGGCCAAAGAACATCAGCAAATGCC * 2288 GACGCCAAGGCCAAGGGCCATCGGCAAATGCCGACGCCAAGGCCAA 1 AACGCCAAGGCCAAGGGCCATCGGCAAATGCCGACGCCAAGGCCAA 2334 GGGGACAAGG Statistics Matches: 90, Mismatches: 15, Indels: 5 0.82 0.14 0.05 Matches are distributed among these distances: 62 29 0.32 63 54 0.60 64 7 0.08 ACGTcount: A:0.32, C:0.33, G:0.27, T:0.09 Consensus pattern (64 bp): AACGCCAAGGCCAAGGGCCATCGGCAAATGCCGACGCCAAGGCCAAAGAACATCAGCAAATGCC Found at i:2864 original size:32 final size:32 Alignment explanation

Indices: 2810--2880 Score: 90 Period size: 32 Copynumber: 2.2 Consensus size: 32 2800 GGACAAGTGA * 2810 CATGGGCCATCGGCATTCGCCGACACCAAGGC 1 CATGGGCCATCGGCAATCGCCGACACCAAGGC * * 2842 CATGGGCCATCGGCAAAT-GCCGACGCTAAGGC 1 CATGGGCCATCGGC-AATCGCCGACACCAAGGC * 2874 CAAGGGC 1 CATGGGC 2881 ATCATCAAAT Statistics Matches: 34, Mismatches: 4, Indels: 2 0.85 0.10 0.05 Matches are distributed among these distances: 32 32 0.94 33 2 0.06 ACGTcount: A:0.24, C:0.34, G:0.31, T:0.11 Consensus pattern (32 bp): CATGGGCCATCGGCAATCGCCGACACCAAGGC Found at i:2941 original size:32 final size:32 Alignment explanation

Indices: 2900--3020 Score: 156 Period size: 32 Copynumber: 3.8 Consensus size: 32 2890 TTCCGATGCA * * * 2900 ATCGGCAAATACCGATGCCAAGGCAACGGGCC 1 ATCGGCAAATGCCGATGCCAAGGCCATGGGCC 2932 ATCGGCAAATGCCGATGCCAAGGCCATGGG-C 1 ATCGGCAAATGCCGATGCCAAGGCCATGGGCC * 2963 ATCGGCAAATGCCGACT-CCAAGGCCATGGGCA 1 ATCGGCAAATGCCGA-TGCCAAGGCCATGGGCC ** * 2995 ATCGGCAAATGCTTATGCCAACGCCA 1 ATCGGCAAATGCCGATGCCAAGGCCA 3021 AGTGGACTAG Statistics Matches: 79, Mismatches: 7, Indels: 6 0.86 0.08 0.07 Matches are distributed among these distances: 31 30 0.38 32 49 0.62 ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13 Consensus pattern (32 bp): ATCGGCAAATGCCGATGCCAAGGCCATGGGCC Found at i:2985 original size:63 final size:63 Alignment explanation

Indices: 2900--3020 Score: 163 Period size: 63 Copynumber: 1.9 Consensus size: 63 2890 TTCCGATGCA * * 2900 ATCGGCAAATACCGATGCCAAGGCAACGGGCCATCGGCAAATGCCGATGCCAAGGCCATGGGC 1 ATCGGCAAATACCGATGCCAAGGCAACGGGCAATCGGCAAATGCCGATGCCAACGCCATGGGC * * * ** 2963 ATCGGCAAATGCCGACT-CCAAGGCCATGGGCAATCGGCAAATGCTTATGCCAACGCCA 1 ATCGGCAAATACCGA-TGCCAAGGCAACGGGCAATCGGCAAATGCCGATGCCAACGCCA 3021 AGTGGACTAG Statistics Matches: 50, Mismatches: 7, Indels: 2 0.85 0.12 0.03 Matches are distributed among these distances: 63 49 0.98 64 1 0.02 ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13 Consensus pattern (63 bp): ATCGGCAAATACCGATGCCAAGGCAACGGGCAATCGGCAAATGCCGATGCCAACGCCATGGGC Done.