Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007113.1 Corchorus capsularis cultivar CVL-1 contig07134, 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: 16262
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31


Found at i:10832 original size:49 final size:48

Alignment explanation


    Indices: 10704--11033  Score: 248
    Period size: 50  Copynumber: 6.7  Consensus size: 48

      10694 AAAGTGAACT

                  *       *      *    **           *         
      10704 TGCCTTTCGTCCGGAAAGGGCGTTTTAAGAAAAAGCAAGCAAAACT-AA
          1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGTAAAA-TAAA

            *     *              *    *                   * *
      10752 CGCCTTTCGTCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAAAGTTAG
          1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGTAAAA-TAAA

                                  *            * *         *
      10801 TGCCTTCCGTCCGGGAAGGGCACTTTGGGAAAAAGTAGGTAAAATAAG
          1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGTAAAATAAA

            * **        *                **                   *
      10849 CGTTTTCCGTCCAGGAAGGGCATTTTTTGAAAAAATAGCAAGTAAAATAAG
          1 TGCCTTCCGTCCGGGAAGGGCA--TTTTGGGAAAA-AGCAAGTAAAATAAA

              *   *                   *           *           
      10900 TGTCTTTCGTCCGGGAAGGGCATTTTTGGAAAATAGCAGGTAAAAGTAAA
          1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAA-AGCAAGTAAAA-TAAA

                    *     *     *     *        *  *       *   
      10950 TGCCTTCCATCCGGAAAGGGTATTTTTGGAAAATAACAGGTAAAAACAAA
          1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAA-AGCAAGT-AAAATAAA

                   *     *                    
      11000 TGCCTTCTGTCCGAGAAGGGCATTTTGGGAAAAA
          1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAA

      11034 AATTTGACAG


Statistics
Matches: 231,  Mismatches: 45, Indels: 11
        0.80            0.16        0.04

Matches are distributed among these distances:
  48   62  0.27
  49   58  0.25
  50   76  0.33
  51   35  0.15

ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24


Consensus pattern (48 bp):   
TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGTAAAATAAA

Found at i:10870 original size:48 final size:49

Alignment explanation


    Indices: 10707--10982  Score: 188
    Period size: 48  Copynumber: 5.6  Consensus size: 49

      10697 GTGAACTTGC

                        *      *    **       * * *           *
      10707 CTTT-CGTCCGGAAAGGGCGTTTTAAGAAAAAGCAAGCAAAACTAA-CGC
          1 CTTTCCGTCCGGGAAGGGCATTTTTGGAAAAAGTAGGTAAAA-TAAGCGT

                               *    *        * *        *  *  
      10755 CTTT-CGTCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAAAGTTAGTG-
          1 CTTTCCGTCCGGGAAGGGCATTTTTGGAAAAAGTAGGTAAAA-TAAGCGT

             *                  *   *                        
      10803 CCTTCCGTCCGGGAAGGGCACTTTGGGAAAAAGTAGGTAAAATAAGCGT
          1 CTTTCCGTCCGGGAAGGGCATTTTTGGAAAAAGTAGGTAAAATAAGCGT

                      *              *      *                *  
      10852 -TTTCCGTCCAGGAAGGGCATTTTTTGAAAAAATAGCAAGTAAAATAAGTGT
          1 CTTTCCGTCCGGGAAGGGCATTTTTGGAAAAAGTAG---GTAAAATAAGCGT

                                              *            **  
      10903 CTTT-CGTCCGGGAAGGGCATTTTTGGAAAATAGCAGGTAAAAGTAAATG-
          1 CTTTCCGTCCGGGAAGGGCATTTTTGGAAAA-AGTAGGTAAAA-TAAGCGT

             *    *     *     *            
      10952 CCTTCCATCCGGAAAGGGTATTTTTGGAAAA
          1 CTTTCCGTCCGGGAAGGGCATTTTTGGAAAA

      10983 TAACAGGTAA


Statistics
Matches: 188,  Mismatches: 30, Indels: 18
        0.80            0.13        0.08

Matches are distributed among these distances:
  48   76  0.40
  49   42  0.22
  50   28  0.15
  51   36  0.19
  52    6  0.03

ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25


Consensus pattern (49 bp):   
CTTTCCGTCCGGGAAGGGCATTTTTGGAAAAAGTAGGTAAAATAAGCGT

Done.