Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014562.1 Corchorus capsularis cultivar CVL-1 contig14583, 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, 945

Length: 1575
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34


Found at i:1027 original size:322 final size:319

Alignment explanation


    Indices: 296--1575  Score: 1210
    Period size: 322  Copynumber: 4.0  Consensus size: 319

        286 TACGCATAAA

                     *              *   *      *         *             **    
        296 ATAATTCAACGCCAAAAATATTGAAGGATTTTTCACGCATT-TAAGATCGTTTTTCTTTTTTTAT
          1 ATAATTCAATGCCAAAAATATTGACGGACTTTT-AGGC-TTCTAATATCGTTTTTC---CATT-T

                  *   *       *           *       * *  *    *               *
        360 TTTTCCAAATTAATTTCTCATTAAATCGAACCAAGATTCAAATACTCGTAAAAACAAATCCTTAA
         60 TTTTCCGAATAAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGAAAAAACAAATCCTTAT

              *    * *    *     *       * *           *    *        *  **    
        425 ATGCAATGTGGCTGCGATTTAG-TTAGATGAATATAGATATTCCAAGAAGTC-TTGGAGTAAAAA
        125 ATCCAATATTGCTGAGATTTGGTTTA-AAGTATATAGATATTTCAAGGAGTCTTTGCA-CCAAAA

                 *     *                                              *      
        488 ATCATTCAAAACTGAGCCGGGGC-CCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTCAGTACA
        188 ATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA

                    *             *          **                   *          
        552 CAATTTTGACTAAAACA-TACCCAAAATTTTTTTTTCAATTTTTTGCCACAATACACAGAAAAAA
        253 CAATTTTGGCTAAAA-ATTACCAAAAATTTTTTCCTCAATTTTTTGCCACAATAAACAGAAAAAA

               
        616 TAT
        317 TAT

                                      *        *  *  *                       
        619 ATAATTCAATGCCAAAAATATTGACGAACTTTTTAAGCATCCAATATCGTTTTTCCATTTTTTTC
          1 ATAATTCAATGCCAAAAATATTGACGGAC-TTTTAGGCTTCTAATATCGTTTTTCCATTTTTTTC

            *   **                    *                               *    * 
        684 TGAACCAATTTCTAATTAAATCGAAATAAGATTTAGATGCTCGAAAAAACAAATCCTTTTATCTA
         65 CGAATAAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGAAAAAACAAATCCTTATATCCA

                 *    *                                 *     *              
        749 ATATTTCTGATATTTGGTTTAAAGTATATAGATATTTCAAGGAGCCTTTGTACCAAAAATCATGC
        130 ATATTGCTGAGATTTGGTTTAAAGTATATAGATATTTCAAGGAGTCTTTGCACCAAAAATCATGC

                     *       *                                              *
        814 AAAATTGAGTCGGGGCTACGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTC
        195 AAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTT

                                                            **  *       *  
        879 GGCTAAAAATTGACTCAAAAATTTTTTCCTCAATTTTTTGCCACAATAGGCAAAAAAAAGCAT
        260 GGCTAAAAATT-AC-CAAAAATTTTTTCCTCAATTTTTTGCCACAATAAACAGAAAAAA-TAT

                           * *   *      *     *                              
        942 ATAATT-AACTGCCATATATAATGACGGGCTTTTCGCGCTTCTAATATCGTTTTTCCA-TTTTTT
          1 ATAATTCAA-TGCCAAAAATATTGACGGACTTTTAG-GCTTCTAATATCGTTTTTCCATTTTTTT

                        *                     *       *             * *      
       1005 CCGAATAAATTTTTAATTAAATCGAAACAAGATTGAGATGCTTGAAAAAACAAATCGTGATATCC
         64 CCGAATAAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGAAAAAACAAATCCTTATATCC

                                ** * *   *                *   *              
       1070 AATATTGCTGAGATTTGGTTCGATGAATAAAGATATTTCAAGGAGTTTTTACACCAAAAATCATG
        129 AATATTGCTGAGATTTGGTTTAAAGTATATAGATATTTCAAGGAGTCTTTGCACCAAAAATCATG

            *             *      *    **     *                               
       1135 TAAAATTGAGCCGGTGCTCCGAAACGAATTTTTTGCC----A-----A-----A--ACACAATTT
        194 CAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTT

                        *                  *               *               
       1184 TGGCTAAAAACTGACCAAAAAGTTTTTT-CTTAATTTTTTGCCACAACAAACAGAAAAAATAT
        259 TGGCTAAAAA-TTACCAAAAA-TTTTTTCCTCAATTTTTTGCCACAATAAACAGAAAAAATAT

                                         *          *                        
       1246 ATAATTCAATGCCAAAAATATTGACGGATTTTTTAGGCTTATAATATCGTTTTTCCATTTTTTTT
          1 ATAATTCAATGCCAAAAATATTGACGGA-CTTTTAGGCTTCTAATATCGTTTTTCCA-TTTTTTT

             *    *      *                        *        *                 
       1311 CGGAATTAATTTCCAATTAAATCGAAACAAGATTTAGAAGCTCGAAATAACAAATCCTTATATCC
         64 CCGAATAAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGAAAAAACAAATCCTTATATCC

                     *           **        *        *           **       *   
       1376 AATATTGCTAAGATTTGG-TTCGA-TATATATATATTTCATGGAGTCTTTGCGTCAAAAATTATG
        129 AATATTGCTGAGATTTGGTTTAAAGTATATAGATATTTCAAGGAGTCTTTGCACCAAAAATCATG

             *        *  * *  * *                       *                    
       1439 CCAAATTGAGTCGAGACTTCAGAACGCGTTTTTAGCCAAAAACCATGATGGTTAGTACACAATTT
        194 CAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTT

                                  *      *                 *               
       1504 TGGCTAAAAACTTACCAAAAAAATTTTTCAT-AATTTTTTGCCACAACAAACAGAAAAAATAT
        259 TGGCTAAAAA-TTACC-AAAAATTTTTTCCTCAATTTTTTGCCACAATAAACAGAAAAAATAT

                      
       1566 ATAATTCAAT
          1 ATAATTCAAT


Statistics
Matches: 776,  Mismatches: 146, Indels: 73
        0.78            0.15        0.07

Matches are distributed among these distances:
 304   99  0.13
 305   40  0.05
 306  104  0.13
 307    1  0.00
 308    2  0.00
 313    2  0.00
 318    2  0.00
 319  112  0.14
 320  132  0.17
 321    8  0.01
 322  188  0.24
 323   82  0.11
 324    4  0.01

ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34


Consensus pattern (319 bp):   
ATAATTCAATGCCAAAAATATTGACGGACTTTTAGGCTTCTAATATCGTTTTTCCATTTTTTTCC
GAATAAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGAAAAAACAAATCCTTATATCCAA
TATTGCTGAGATTTGGTTTAAAGTATATAGATATTTCAAGGAGTCTTTGCACCAAAAATCATGCA
AAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTTG
GCTAAAAATTACCAAAAATTTTTTCCTCAATTTTTTGCCACAATAAACAGAAAAAATAT
Done.