Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011011.1 Corchorus capsularis cultivar CVL-1 contig11032, 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, 894

Length: 1491
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36


Found at i:595 original size:322 final size:322

Alignment explanation


    Indices: 2--1491  Score: 1813
    Period size: 323  Copynumber: 4.6  Consensus size: 322

          1 T

                                 *         *                     *           
          2 TTTTTGG-TAAAAACGCGTTCAGGAGCCCCGACTCAATTTTGCATGATTTTTGACGCAAAGACTC
          1 TTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTC

                *               *   *             *                          
         66 CTTGTAATATCTATATTCATTGAAGCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTATG
         66 CTTGAAATATCTATATTCATCGAACCAAATGTCAGCCATATTGGATATAAGGATTTGTTTTTATG

                              *                                              
        131 AGCATCTAAATCTTGTTTTGATTTAATTACAAATTAATTCAGAAAAAATTG-AAAAACGATATTA
        131 AGCATCTAAATCTTGTTTCGATTTAATTACAAATTAATTCAGAAAAAATTGAAAAAACGATATTA

                        *     *                  *                           
        195 GAAGCGTGAAAATCCCGTTAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCA
        196 GAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAAATATATATTTTTTCTGAGTATTGTGGCA

                                                               *    *       
        260 AAAAAATTGAGAAAAAACTCTTT-GGGTCAATTTTTAGCCGAAATCGTGTAGTAACAATCACAG
        261 AAAAAA-TGAGAAAAAACT-TTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACAG

                             *        *              *                       
        323 TTTTTGGCTAAAAACGCATTCCGGAGTCCCGGCTCAATTTTCCATGATTTTTGGCGCAAAGACTC
          1 TTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTC

                *                   *             *                          
        388 CTTGTAATATCTATATTCATCGAAGCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTATG
         66 CTTGAAATATCTATATTCATCGAACCAAATGTCAGCCATATTGGATATAAGGATTTGTTTTTATG

                                                               *             
        453 AGCATCTAAATCTTGTTTCGATTTAATTACAAATTAATTCAGAAAAAATTGGAAAAACGATATTA
        131 AGCATCTAAATCTTGTTTCGATTTAATTACAAATTAATTCAGAAAAAATTGAAAAAACGATATTA

                        *     *                                              
        518 GAAGCGTGAAAATCCCGTTAATCTTTTTGGCGTTGAAATATATATTTTTTCTGAGTATTGTGGCA
        196 GAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAAATATATATTTTTTCTGAGTATTGTGGCA

                                     *   *                 *              
        583 AAAAAATGAGAAAAAA--TTTCGGGAC-AGTTTTAGCCGAAATCGTGCACTAACCATCACAG
        261 AAAAAATGAGAAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACAG

                             *        *  **    **      **                    
        642 ATTTTT-GCTAAAAACGTGTTCCGGAACCATGGCTTGATTTTGTTTGATTTTTGGCGCACAA-AC
          1 -TTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCA-AAGAC

              *     *                       *                   *            
        705 TCTTTGAATTATCTATATTCATCGAACCAAATTTCAGCCATATTGGATATAATGA-TTGTTTTT-
         64 TCCTTGAAATATCTATATTCATCGAACCAAATGTCAGCCATATTGGATATAAGGATTTGTTTTTA

              *       *           *     *   *            *                   
        768 TCAAGCATCTCAATCTTGTTTCAATTTATTTAGAAATTAATTC-GGAAAAATATGAAAAAACGAT
        129 T-GAGCATCTAAATCTTGTTTCGATTTAATTACAAATTAATTCAGAAAAAAT-TGAAAAAACGAT

                              *                *   * *                       
        832 ATTAGAAGCGTGAAAAGCTCGTCAATCTTTTTGGCATTGGATTATATATTTTTTCCTGAGTATTG
        192 ATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAAATATATATTTTTT-CTGAGTATTG

              *       *                 **    *      *                       
        897 TGTCAAAAAATTGAGAAAAAAACTTTTCAAGTCAGTTTTTAACCGAAATCGTGTACTAACCATCA
        256 TGGCAAAAAAATGAG-AAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCA

               
        962 CAG
        320 CAG

                  *       *        *       *             *        **        *
        965 TTTTTGCCTAAAAATGCGTTCCGAAGCCCCGACTCAATTTTGCATTATTTTTGGTACAAAGACTT
          1 TTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTC

                      *      *          *                 *      *           
       1030 CTTGAAATATTTATATTTATCGAACCAATTGTCAGCCATATTGGATCTAAGGACTTGTTTTTATG
         66 CTTGAAATATCTATATTCATCGAACCAAATGTCAGCCATATTGGATATAAGGATTTGTTTTTATG

             *     *                 *   *           *       * *             
       1095 ATCATCTGAATCTTGTTTCGATTTATTTAGAAATTAATTCAAAAAAAGAATAAAAAAACGATATT
        131 AGCATCTAAATCTTGTTTCGATTTAATTACAAATTAATTCAGAAAAA-ATTGAAAAAACGATATT

                                          *               *      * *      *  
       1160 AGAAGCGTGAAAAGCCCGTCAATCTTTTTGACGTTGAATTATATATTTTTTTTATTAGTATTATG
        195 AGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAA--ATATATATTTTTTCTGAGTATTGTG

              * *   *         *              *        *                     *
       1225 GCGAGAAATTGAGAAAAATCTTTTCGGG-CAAGCTTTTAGCCAAAATCGTGTACTAACCATCACG
        258 GCAAAAAAATGAGAAAAAACTTTTCGGGTCAA-TTTTTAGCCGAAATCGTGTACTAACCATCACA

             
       1289 G
        322 G

                    *        *     *           *               *       *     
       1290 TTTTTGAGATAAAAACGTGTTTCGGGAGCCCCGGCCCAATTTTGCATGATTCTTGG-GAGAAAGA
          1 TTTTTG-GCTAAAAACGCG-TTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCG-CAAAGA

                                              *        *         *           
       1354 CTCCTTGAAATATCTATATTCATCGAA-CAAAGTCTCAGCCATTTTGGATATATGGATTTGTTTT
         63 CTCCTTGAAATATCTATATTCATCGAACCAAA-TGTCAGCCATATTGGATATAAGGATTTGTTTT

             *          *           **        *                   *          
       1418 TTTCGAGCATCTCAATCTTGTTTCTTTTTAATTATAAATTAATT-AGGAAAAAAATGAAAAAACG
        127 TAT-GAGCATCTAAATCTTGTTTCGATTTAATTACAAATTAATTCA-GAAAAAATTGAAAAAACG

                      
       1482 ATATTAGAAG
        190 ATATTAGAAG


Statistics
Matches: 1006,  Mismatches: 136, Indels: 48
        0.85            0.11        0.04

Matches are distributed among these distances:
 317    8  0.01
 318  103  0.10
 319  147  0.15
 320   17  0.02
 321    7  0.01
 322  188  0.19
 323  198  0.20
 324   47  0.05
 325  100  0.10
 326   31  0.03
 327  121  0.12
 328   39  0.04

ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36


Consensus pattern (322 bp):   
TTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTC
CTTGAAATATCTATATTCATCGAACCAAATGTCAGCCATATTGGATATAAGGATTTGTTTTTATG
AGCATCTAAATCTTGTTTCGATTTAATTACAAATTAATTCAGAAAAAATTGAAAAAACGATATTA
GAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAAATATATATTTTTTCTGAGTATTGTGGCA
AAAAAATGAGAAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCACAG
Done.