Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011648.1 Corchorus olitorius cultivar O-4 contig11681, 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: 2294
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21


Found at i:1127 original size:154 final size:154

Alignment explanation

Indices: 1--2294 Score: 3198 Period size: 154 Copynumber: 14.8 Consensus size: 154 * * * * 1 AAACAATGGAAAGAAAAACATTGGGGTTTTGCTAAATCGAAGACGATTCAAAACAG-AACTCATG 1 AAACAATGGAAAGAAAAGCATTGAGG-TTTGCCAAATCGAAGACGATTCAAAAC-GTAACTAATG * * * * 65 GGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAAGGAGGTGAAAACTTCACAGTGGACTAATCT 64 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT * 130 TACCAAAATGATTATTATAGTTAGGCCAT 129 CACCAAAATG---ATTATAGTTAGGCCAT * * * 159 AAACAATGGAAAAAAAAGCATTGAGGTTTGCCAAATTC-ACGACGATTCAAAACATAACTAATGG 1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA-TCGAAGACGATTCAAAACGTAACTAATGG * * * * * 223 GTCCCGAAAGGCCCCAAAAATAACATGTGTTCCAAATGAGCTAAAAACTTCCCAGTGGACTAATT 65 GCCCCGATAGG-CCC-AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC * 288 TCACCAAAAGGATTATAGTTAGGCCAT 128 TCACCAAAATGATTATAGTTAGGCCAT * * * * 315 AAACAAAT-GAAAGAAAAGCATTGGGGTTTGGCAAATCGAAGGCGATTCAAAAACAG-AACGAAT 1 AAAC-AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC-AAAAC-GTAACTAAT * * 378 GAGCCCCGAAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTACACAGTGGACTAA 63 GGGCCCCG-ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT-CACAGTGGACTAA 443 TCTCACCAAAATGATTAGTAGTTAGGCCAT 126 TCTCACCAAAATGATTA-TAGTTAGGCCAT * * * 473 AAACAATGG-AAGGAAAGCCATCGAAGG-TTGACCAAATCGAAGACGATTCAAAACGTCACTAAT 1 AAACAATGGAAAGAAAAG-CATTG-AGGTTTG-CCAAATCGAAGACGATTCAAAACGTAACTAAT * * 536 GGTCCCCGATAGGCCCAAAATAACAAGTGTTCCGAATGAGCTAAAAACTTCACAGTTGGACTAAT 63 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG-TGGACTAAT 601 CTCACCAAAATGATTATAGTTAGGCCAT 127 CTCACCAAAATGATTATAGTTAGGCCAT * * * 629 ACACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGT 1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGG * 694 CCCCGATAGGCCCAAAATAACAAGTGTTACAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA 66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA ** 759 CC-AAATGATTATAGTCGGGCCAT 131 CCAAAATGATTATAGTTAGGCCAT * * * * 782 AAACAATGGAAAGAAAAGCATCGAAGGTTT-CAAAATCGAAGACGATTCAAAATGGAACTAATGG 1 AAACAATGGAAAGAAAAGCATTG-AGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGG * * 846 GCCCCGATAGGGCCAAAATAACAAGTGTTCCCAATGAGCT-AAAACTTCACAGTGGACTAATCTC 65 GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC * 910 ACCAAAATGATTATAGTTAGCCCAT 130 ACCAAAATGATTATAGTTAGGCCAT * * * * * 935 AAACAATGGAAAGAAAGGCGTCGAAGG-TTGCCAAATCGAAGACGATTCAAAATGGAACTAATGG 1 AAACAATGGAAAGAAAAGCATTG-AGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGG * * 999 TCCTCGATAGGCCCAAAAT-ACAAGTGTTCCAAATGAGCTAAAAACTTGCACAGTGGACTAATCT 65 GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT-CACAGTGGACTAATCT 1063 CACCAAAATGATTATAGTTAGGCCAT 129 CACCAAAATGATTATAGTTAGGCCAT * * * * * 1089 AAACAACT-TAAGGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCGAAACGTCACTAATGG 1 AAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGG * * * * 1153 GCCCCGATAGTCCCAAAATAACAACTGTTCCAAATGAGCTAAAAACTTCACAGTGGACAAATCTA 65 GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC * 1218 ACCAAAATGATTATAGTGAGGCCAT 130 ACCAAAATGATTATAGTTAGGCCAT * * 1243 AAACACTGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG 1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGG * * 1308 CCCCGATAGGCCCAAAATAACATGTTTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA 66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA * * 1373 CCAAAATGATTATAATTAGGCGAT 131 CCAAAATGATTATAGTTAGGCCAT * * * 1397 AAACAATGGAAAGAAAAAGCATTTATGG-TTGCCAAATCGAAGACGTTTCAAAACGGAACTAATG 1 AAACAATGGAAAG-AAAAGCATTGA-GGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATG ** * * * 1461 CTCCCCGAAAGGCCCAAAATAACAAATGTTCCAAATGAGCTAAAACCTTCACAGTGGACTAATCT 64 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT * 1526 CACCAAAATTATTATAGTTAGGCCAT 129 CACCAAAATGATTATAGTTAGGCCAT * * 1552 AAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG 1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGG * * * 1617 CCCCGATAGGCCCAAAATAACATGTGTTCCAATTGAGCTAAAAACTTCACAATGGACTAATCTCA 66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA * 1682 GCAAAATGATTATAGTTAGGCCAT 131 CCAAAATGATTATAGTTAGGCCAT * * * * * * * * 1706 AAACACTAGAAAGAAAAGCAATGAGGTTTGCCAAATCGACGATGATTCAAAACGTCACAAATGAG 1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGG * * * * 1771 CCCCGATAGGCCCAAAATAACAAGTGTTGCAATTTAGCTAAAAACTTCACAATGGACTAATCTCA 66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA * 1836 CCAAAATGATTATAATTAGGCCAT 131 CCAAAATGATTATAGTTAGGCCAT * * * 1860 AAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGT 1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGG * * * 1925 CCCCGAAAGACCCAAAATAAGAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA 66 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA * 1990 CTAAAATGATTATAGTTAGGCCAT 131 CCAAAATGATTATAGTTAGGCCAT * * ** 2014 AAACAACT-TAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATAGAAAACGTCAA-TAATG 1 AAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGT-AACTAATG * * 2077 GGCCCCGATAGGCCCAAAATAATAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATAT 64 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT * 2142 CACCAAAATGATTATAATTAGGCCAT 129 CACCAAAATGATTATAGTTAGGCCAT * * 2168 AAACAATGGAAAGAAAAAGCATTTAAGG-TTGCCAAATCGAAGACGATTCAAAACGTCACTAATG 1 AAACAATGGAAAG-AAAAGCA-TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATG * * * * * 2232 GACCTCGATATGCCCAAAATATCAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAAT 64 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT Statistics Matches: 1913, Mismatches: 186, Indels: 77 0.88 0.09 0.04 Matches are distributed among these distances: 152 48 0.03 153 212 0.11 154 861 0.45 155 352 0.18 156 124 0.06 157 173 0.09 158 73 0.04 159 70 0.04 ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21 Consensus pattern (154 bp): AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGG CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA CCAAAATGATTATAGTTAGGCCAT Found at i:1614 original size:617 final size:615 Alignment explanation

Indices: 1--2294 Score: 3216 Period size: 617 Copynumber: 3.7 Consensus size: 615 * * * * 1 AAACAATGGAAAGAAAAACATTGGGGTTTTGCTAAATCGAAGACGATTCAAAACAG-AACTCATG 1 AAACAATGGAAAGAAAAGCATTGAGG-TTTGCCAAATCGAAGACGATTCAAAAC-GTAACTAATG * * * 65 GGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAAGGAGGTGAAAACTTCACAGTGGACTAATCT 64 GGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT * * 130 TACCAAAATGATTATTATAGTTAGGCCATAAACAATGGAAAAAAAAGCATTGAGGTTTGCCAAAT 129 CACCAAAATGATTA-TA-A-TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA- * ** * * 195 TC-ACGACGATTCAAAACATAACTAATGGGTCCCGAAAGGCCCCAAAAATAACATGTGTTCCAAA 190 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGG-CCC-AAAATAACAAGTGTTCCAAA * * * 259 TGAGCTAAAAACTTCCCAGTGGACTAATTTCACCAAAAGGATTATAGTTAGGCCATAAACAAAT- 253 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC-AATG * * * * * 323 GAAAGAAAAGCATTGGGGTTTGGCAAATCGAAGGCGATTCAAAAACAG-AACGAATGAGCCCCGA 317 GAAAGAAAAGCTTTGAGG-TTGCCAAATCGAAGACGATTC-AAAAC-GTAACTAATG-GCCCCG- * * 387 AAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTACACAGTGGACTAATCTCACCAA 377 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT-CACAATGGACTAATCTCACCAA * * 452 AATGATTAGTAGTTAGGCCATAAACAA-TGGAAGG-AAAGCCATCGAAGG-TTGACCAAATCGAA 441 AATGATTA-TAGTTAGGCCATAAACAACTAGAAGGAAAAG-CATTG-AGGTTTG-CCAAATCGAA * * 514 GACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCGAATGAGCTA 502 GACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTA 579 AAAACTTCACAGTTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT 567 AAAACTTCACAG-TGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT * * * 629 ACACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGT 1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGG * * 694 CCCCGATAGGCCCAAAATAACAAGTGTTACAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA 66 CCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA * ** * * 759 CC-AAATGATTATAGTCGGGCCATAAACAATGGAAAGAAAAGCATCGAAGGTTT-CAAAATCGAA 131 CCAAAATGATTATAATTAGGCCATAAACAATGGAAAGAAAAGCATTG-AGGTTTGCCAAATCGAA * * * * 822 GACGATTCAAAATGGAACTAATGGGCCCCGATAGGGCCAAAATAACAAGTGTTCCCAATGAGCT- 195 GACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTA * 886 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGCCCATAAACAATGGAAAGAAA 260 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA * * * * * * 951 GGCGTCGAAGGTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGTCCTCGATAGGCCCAAA 325 AGCTTTG-AGGTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGG-CCCCGATAGGCCCAAA * 1016 AT-ACAAGTGTTCCAAATGAGCTAAAAACTTGCACAGTGGACTAATCTCACCAAAATGATTATAG 388 ATAACAAGTGTTCCAAATGAGCTAAAAACTT-CACAATGGACTAATCTCACCAAAATGATTATAG * * * 1080 TTAGGCCATAAACAACT-TAAGGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCGAAACGT 452 TTAGGCCATAAACAACTAGAAGGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGT * * 1144 CACTAATGGGCCCCGATAGTCCCAAAATAACAACTGTTCCAAATGAGCTAAAAACTTCACAGTGG 517 CACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG * * * 1209 ACAAATCTAACCAAAATGATTATAGTGAGGCCAT 582 ACTAATCTCACCAAAATGATTATAGTTAGGCCAT * * 1243 AAACACTGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG 1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGG * * * 1308 CCCCGATAGGCCCAAAATAACATGTTTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA 66 CCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA * * 1373 CCAAAATGATTATAATTAGGCGATAAACAATGGAAAGAAAAAGCATTTATGG-TTGCCAAATCGA 131 CCAAAATGATTATAATTAGGCCATAAACAATGGAAAG-AAAAGCATTGA-GGTTTGCCAAATCGA * ** * 1437 AGACGTTTCAAAACGGAACTAATGCTCCCCGAAAGGCCCAAAATAACAAATGTTCCAAATGAGCT 194 AGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCT * * 1502 AAAACCTTCACAGTGGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAACAATGGAAAGAA 259 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA * 1567 AAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAA 324 AAGCTTTGAGG-TTGCCAAATCGAAGACGATTCAAAACGTAACTAAT-GGCCCCGATAGGCCCAA * * * 1632 AATAACATGTGTTCCAATTGAGCTAAAAACTTCACAATGGACTAATCTCAGCAAAATGATTATAG 387 AATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAG * * * * 1697 TTAGGCCATAAAC-ACTAGAAAGAAAAGCAATGAGGTTTGCCAAATCGACGATGATTCAAAACGT 452 TTAGGCCATAAACAACTAGAAGGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGT * * * * * * 1761 CACAAATGAGCCCCGATAGGCCCAAAATAACAAGTGTTGCAATTTAGCTAAAAACTTCACAATGG 517 CACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGG * 1826 ACTAATCTCACCAAAATGATTATAATTAGGCCAT 582 ACTAATCTCACCAAAATGATTATAGTTAGGCCAT * * * 1860 AAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGT 1 AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGG * * 1925 CCCCGAAAGACCCAAAATAAGAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA 66 CCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA * * * * 1990 CTAAAATGATTATAGTTAGGCCATAAACAACT-TAAAGAAAAGCTTTGAGGTTTGCCAAATCGAA 131 CCAAAATGATTATAATTAGGCCATAAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAA ** * * * 2054 GACGATAGAAAACGTCAA-TAATGGGCCCCGATAGGCCCAAAATAATAAGTGTTCCAAATGAGCT 195 GACGATTCAAAACG-GAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCT * * 2118 AAAAACTTCACAGTGGACTAATATCACCAAAATGATTATAATTAGGCCATAAACAATGGAAAGAA 259 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG-A * * * * 2183 AAAGCATTTAAGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGACCTCGATATGCCCA 323 AAAGC-TTTGAGGTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGG-CCCCGATAGGCCCA * 2248 AAATATCAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAAT 386 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAAT Statistics Matches: 1498, Mismatches: 143, Indels: 61 0.88 0.08 0.04 Matches are distributed among these distances: 614 160 0.11 615 120 0.08 616 244 0.16 617 599 0.40 618 49 0.03 619 18 0.01 620 80 0.05 621 26 0.02 622 4 0.00 623 63 0.04 624 6 0.00 625 2 0.00 626 10 0.01 627 94 0.06 628 23 0.02 ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21 Consensus pattern (615 bp): AAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGG CCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA CCAAAATGATTATAATTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG ACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA AAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA GCTTTGAGGTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGCCCCGATAGGCCCAAAATA ACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAG GCCATAAACAACTAGAAGGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACT AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA ATCTCACCAAAATGATTATAGTTAGGCCAT Done.