Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003270.1 Corchorus capsularis cultivar CVL-1 contig03278, 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, 994

Length: 1658
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32


Found at i:81 original size:22 final size:22

Alignment explanation


    Indices: 53--616  Score: 157
    Period size: 22  Copynumber: 25.7  Consensus size: 22

         43 TCAGGGAGGA

                                  
         53 TATCAAAATTTCATATGAAGGT
          1 TATCAAAATTTCATATGAAGGT

                             **    
         75 TATCAAAATTTCATAGTTTA-GT
          1 TATCAAAATTTCATA-TGAAGGT

             *           * *  *   
         97 TTTCAAAATTTCACAAGAGGGT
          1 TATCAAAATTTCATATGAAGGT

                   *         * *  
        119 TATCAAAGTTTCATA-GTATGT
          1 TATCAAAATTTCATATGAAGGT

             *    *         * *  * 
        140 AGATCACAATTTCATAGGGAGAT
          1 -TATCAAAATTTCATATGAAGGT

                            *          
        163 TAATTAACAAAATTTCGTAATG-AGGT
          1 T-A-T--CAAAATTTCAT-ATGAAGGT

                    **     * *    
        189 TATCAAAAAATCATAGGGAGGT
          1 TATCAAAATTTCATATGAAGGT

                             *    
        211 TATCAAAA--T--T-TGTA-GT
          1 TATCAAAATTTCATATGAAGGT

                  *        *   *  
        227 TATCAAGATTTCATAAGAAAGT
          1 TATCAAAATTTCATATGAAGGT

                       *   * *     
        249 TATCAAAATTTTATAGGGAGGTT
          1 TATCAAAATTTCATATGAAGG-T

                       *   *     * 
        272 TATCAAAATTTTATAGGAAGATT
          1 TATCAAAATTTCATATGAAG-GT

                            *      
        295 TATCAAAATTTCATAACG-AGGT
          1 TATCAAAATTTCAT-ATGAAGGT

                 *             * * 
        317 TATCACAATTTCATA-GTATGAT
          1 TATCAAAATTTCATATG-AAGGT

                         *     * * 
        339 TATCAAAATTTCAGA-GTATGAT
          1 TATCAAAATTTCATATG-AAGGT

                               *    
        361 TA-CTAACAA-TTCATATGGAGGT
          1 TATC-AA-AATTTCATATGAAGGT

             * *   *        *  *   
        383 TTTTAAATTTTCATAACG-TGGT
          1 TATCAAAATTTCAT-ATGAAGGT

                  *  *   *   *    
        405 TATCAATATATCAAATGGAGGT
          1 TATCAAAATTTCATATGAAGGT

                  *  *        **   
        427 TATCAACATCTCATAGTGTTGGT
          1 TATCAAAATTTCATA-TGAAGGT

                                    
        450 TATCAAAATTTCAT-TGGGAA-GT
          1 TATCAAAATTTCATAT--GAAGGT

                                   
        472 TATCAAAATTTCATATTG-AGGT
          1 TATCAAAATTTCATA-TGAAGGT

                       * *  * *    
        494 CT-TCAAAATTCCTTAGGGAGGT
          1 -TATCAAAATTTCATATGAAGGT

              * **                
        516 TAACCGAATTTCATA-GAAGGT
          1 TATCAAAATTTCATATGAAGGT

               *    *      **     
        537 TA-AAAAAATT-ATAAAAAGGT
          1 TATCAAAATTTCATATGAAGGT

             *  *     *        **  
        557 TCTCGAAATTGCATA-GTATCGT
          1 TATCAAAATTTCATATG-AAGGT

               *            *      
        579 TATTAAAATTTCATAGGGAAGGT
          1 TATCAAAATTTCATA-TGAAGGT

                           
        602 TATCAAAATTTCATA
          1 TATCAAAATTTCATA

        617 ATGGGGTCAT


Statistics
Matches: 395,  Mismatches: 104, Indels: 85
        0.68            0.18        0.15

Matches are distributed among these distances:
  16    9  0.02
  17    2  0.01
  18    2  0.01
  19    3  0.01
  20   13  0.03
  21   27  0.07
  22  234  0.59
  23   83  0.21
  24    6  0.02
  25    1  0.00
  26   13  0.03
  27    2  0.01

ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36


Consensus pattern (22 bp):   
TATCAAAATTTCATATGAAGGT

Done.