Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009771.1 Corchorus olitorius cultivar O-4 contig09803, 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: 2950
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39


Found at i:171 original size:6 final size:6

Alignment explanation


    Indices: 160--189  Score: 51
    Period size: 6  Copynumber: 5.0  Consensus size: 6

        150 ACCTTTAATT

                                 *            
        160 TTTTTC TTTTTC TTTTTC CTTTTC TTTTTC
          1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC

        190 CCTCTTTTTC


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   6   22  1.00

ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80


Consensus pattern (6 bp):   
TTTTTC

Found at i:1569 original size:22 final size:22

Alignment explanation


    Indices: 1544--1919  Score: 181
    Period size: 22  Copynumber: 16.9  Consensus size: 22

       1534 GTTATATATG

                          *     * 
       1544 TATGAAATTTTGATGACCTCCC
          1 TATGAAATTTTGATAACCTCAC

                               *   
       1566 TATGGAAA-TTTGATAACCACAC
          1 TAT-GAAATTTTGATAACCTCAC

             *              * *  *
       1588 TGTGAAATTTTGATAATCACAT
          1 TATGAAATTTTGATAACCTCAC

                       *         *
       1610 TATGAAATTTTAATAACCTCAG
          1 TATGAAATTTTGATAACCTCAC

             *              *   * 
       1632 TGTGAAATTTTGATAATCTCTC
          1 TATGAAATTTTGATAACCTCAC

               *            * *   
       1654 TATAAAATTTTGATAATCACAC
          1 TATGAAATTTTGATAACCTCAC

                    *   *     *   
       1676 TAT-AAA-ATTGGTAACCGCAC
          1 TATGAAATTTTGATAACCTCAC

            *     *   *           
       1696 CATGAAGTTTCGATAACCTC-C
          1 TATGAAATTTTGATAACCTCAC

                            *     * *  * 
       1717 TTATGAGAATGAAACTGTGATATCTTCTC
          1 -TATGA-AAT-----TTTGATAACCTCAC

                *               * 
       1746 TATGTAATTTTGATAACCTCTC
          1 TATGAAATTTTGATAACCTCAC

            *  *       *        * 
       1768 CATAAAATTTTCATAACCTCCC
          1 TATGAAATTTTGATAACCTCAC

                               * ***
       1790 TA-GTAAATTTTGATAACATTTTT
          1 TATG-AAATTTTGATAAC-CTCAC

               *        *       **
       1813 TATAAAATTTTGGTAACCTCTT
          1 TATGAAATTTTGATAACCTCAC

                                 * 
       1835 TATGAAATTTTGATAA-CTACGC
          1 TATGAAATTTTGATAACCT-CAC

                  *          *    
       1857 TATGAAGTTTTGATAACTTC-C
          1 TATGAAATTTTGATAACCTCAC

                         *     * * 
       1878 ATATGAAATTTTGGTAACCACGC
          1 -TATGAAATTTTGATAACCTCAC

                   *           
       1901 TATGAAAATTTGATAACCT
          1 TATGAAATTTTGATAACCT

       1920 TCCTGTGTAC


Statistics
Matches: 266,  Mismatches: 69, Indels: 38
        0.71            0.18        0.10

Matches are distributed among these distances:
  20   12  0.05
  21   13  0.05
  22  202  0.76
  23   23  0.09
  27    3  0.01
  28   12  0.05
  29    1  0.00

ACGTcount: A:0.35, C:0.16, G:0.12, T:0.38


Consensus pattern (22 bp):   
TATGAAATTTTGATAACCTCAC

Done.