Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006577.1 Corchorus capsularis cultivar CVL-1 contig06598, 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, 720

Length: 1201
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37


Found at i:835 original size:327 final size:327

Alignment explanation


    Indices: 10--1201  Score: 1554
    Period size: 334  Copynumber: 3.6  Consensus size: 327

          1 TGTACTATC

                                                   *   *                  *  
         10 CATCACGATTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCGGTTTTTCATGATTTTTTATGC
          1 CATCACGATTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAGTTTTTCATGATTTTTTACGC

                   *        *              *         *                       
         75 CAAGACTTCTTGAAATGTCTATATTTATCTAGCCAAATTTCTGCCAGATTGGATTTAAGGATTTG
         66 CAAGACTCCTTGAAATATCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAGGATTTG

                      *                                              *       
        140 TTTTTACGAGAATCTGAATCATATTTCAATTTTCTTAGAATTTAATTCATAAAAAATTGGAAAAA
        131 TTTTTACGAGCATCTGAATCATATTTCAATTTTCTTAGAATTTAATTCATAAAAAATAGGAAAAA

                                   *                                         
        205 CGATATTGAAAGCGTGAAAAGCCGTTCAATCTTTTTGGCATTGAATTATATATTTTTTTACGAGT
        196 CGATATTGAAAGCGTGAAAAGCCTTTCAATCTTTTT-GCATTGAATTATATA-TTTTTTACGAGT

                   *                 *     *                                 
        270 ATTGTGTTCAAAAATTGAGGAAAATTTTTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCAA
        259 ATTGTGTCCAAAAATTGAGGAAAA-ATTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATC-A

                    
        335 TGTACTAT
        322 TG-A-TAT

                   *              *            *     *                     * 
        343 CCATCACAATTTTTGGCTAAAACCGCGTTCCGGGGTCCCGAATCAGTTTTTCATGATTTTTTAGG
          1 -CATCACGATTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAGTTTTTCATGATTTTTTACG

                    *                                 *  * *    *      *     
        408 CCAAGACTTCTTGAAATATCTATATTTATCTAACCAAATTTCCGCTATATTGAATTTAAAGATTT
         65 CCAAGACTCCTTGAAATATCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAGGATTT

                          *             *                                    
        473 GTTTTTACGAGCATATGAATCATATTTCGATTTTCTTAGAATTTAATTCATAAAAAATAGGAAAA
        130 GTTTTTACGAGCATCTGAATCATATTTCAATTTTCTTAGAATTTAATTCATAAAAAATAGGAAAA

                                                       *                     
        538 ACGATATTGAAAGCGTGAAAAGCCTTTCAATCTTTTTGCATTGGATTATATATTTTTTACGAGTA
        195 ACGATATTGAAAGCGTGAAAAGCCTTTCAATCTTTTTGCATTGAATTATATATTTTTTACGAGTA

                                          *                                  
        603 TTGTGTCCAAAAATTGAGGAAAAATTCTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATG
        260 TTGTGTCCAAAAATTGAGGAAAAATT-TTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCATG

                
        668 -TA-
        324 ATAT

                    *        *      *               *                  *     
        670 CATCACGAGTTTTGGCAAAAAAACTCGTTCCGGGGCCCCGGCTCAG-TTTTCATTGATTGTTTAC
          1 CATCACGATTTTTGGC-TAAAAACGCGTTCCGGGGCCCCGACTCAGTTTTTCA-TGATTTTTTAC

              *   *                                      *   *               
        734 GCGAAGGCTCCTTGAAATATCTATATTTATCTAACCAAATTTCAGTCAGGTTGGATTTAAGGATT
         64 GCCAAGACTCCTTGAAATATCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAGGATT

             *  *     *                  *                  *            *   
        799 TATTCTTACGGGCATCTGAATCATATTTCGATTTTCTTAGAATTTAATCCATAAAAAATAGAAAA
        129 TGTTTTTACGAGCATCTGAATCATATTTCAATTTTCTTAGAATTTAATTCATAAAAAATAGGAAA

                                   *          *    *                   *     
        864 AACGATATT-AGAAGCGTGAAAATCCTTTCAATAATTTTGGCATTGAATTATATATTTTATACGA
        194 AACGATATTGA-AAGCGTGAAAAGCCTTTCAAT-CTTTTTGCATTGAATTATATATTTTTTACGA

                   *                          *        *                     
        928 GTATTGTATCC--AAATTGAGGAAAAACTTTTCATGTCAATTTCTGCAAAATTTTAGCCGAAATC
        257 GTATTGTGTCCAAAAATTGAGGAAAAA-TTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATC

            *        
        991 GTGTACTAT
        321 ATG-A-TAT

                                     *     * *         * *    *          *   
       1000 CTATCACGATTTTTGGCTAAAAACGTGTTCCAGTGCCCCGACTTAATTTTACATGATTTTTGACG
          1 C-ATCACGATTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAGTTTTTCATGATTTTTTACG

                 *   *     *          *       *    *       *        *   *    
       1065 CCAAGCCTCATTGAATTATCTATATTCATCTAACTAAATCTCAGCCACATTGGATTGAAGAATTT
         65 CCAAGACTCCTTGAAATATCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAGGATTT

                                              *      *                       
       1130 GTTTTTACGAGCATCTGAATCATATTTCAATTTTATTAGAAATTAATTCAGT--AAAATAGGAAA
        130 GTTTTTACGAGCATCTGAATCATATTTCAATTTTCTTAGAATTTAATTCA-TAAAAAATAGGAAA

                     
       1193 AACGATATT
        194 AACGATATT


Statistics
Matches: 754,  Mismatches: 91, Indels: 31
        0.86            0.10        0.04

Matches are distributed among these distances:
 326   69  0.09
 327  177  0.23
 328   39  0.05
 329   21  0.03
 330  128  0.17
 331   25  0.03
 332   69  0.09
 333   14  0.02
 334  212  0.28

ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37


Consensus pattern (327 bp):   
CATCACGATTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAGTTTTTCATGATTTTTTACGC
CAAGACTCCTTGAAATATCTATATTTATCTAACCAAATTTCAGCCAGATTGGATTTAAGGATTTG
TTTTTACGAGCATCTGAATCATATTTCAATTTTCTTAGAATTTAATTCATAAAAAATAGGAAAAA
CGATATTGAAAGCGTGAAAAGCCTTTCAATCTTTTTGCATTGAATTATATATTTTTTACGAGTAT
TGTGTCCAAAAATTGAGGAAAAATTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGAT
AT
Done.