Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022617.1 Corchorus olitorius cultivar O-4 contig22650, 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: 6573
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33


Found at i:490 original size:64 final size:64

Alignment explanation


    Indices: 210--566  Score: 484
    Period size: 64  Copynumber: 5.6  Consensus size: 64

        200 CCGGTGCATC

                *       *                         *          *            *  
        210 TCTTAACAAGATTGTCTTCCGATCAACTTCTGAAAACTTTTCGAGAAACTATCTTCTGGTGTGCT
          1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTT-GAGAAACCATCTTCTGGTGTACT

             *  *                   *             *       *           *   * 
        275 TTTTAACAAGATCGTCTTCCGATCGACTTCTGAAAA-TTTTGAGAATCCATCTTCTGGCGTAGT
          1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT

                                                                            
        338 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTC-GGTGTACT
          1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT

                         *            *               *                     
        401 TCTTGACAAGATCATCTTCCGATCAATTTCTGAAAACTGTTGGGAAACCATCTTCTGGTGTACT
          1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT

              **  *             *                 *                      *  
        465 TCACGATAAGATCGTCTTCCAATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTCCT
          1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT

                  *     *                         
        529 TCTTGATAAGATTGTCTTCCGATCAACTTCTGAAAACT
          1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACT

        567 CTTTTTTAGC


Statistics
Matches: 259,  Mismatches: 31, Indels: 5
        0.88            0.11        0.02

Matches are distributed among these distances:
  63  109  0.42
  64  117  0.45
  65   33  0.13

ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34


Consensus pattern (64 bp):   
TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACT

Found at i:548 original size:191 final size:191

Alignment explanation


    Indices: 210--566  Score: 500
    Period size: 191  Copynumber: 1.9  Consensus size: 191

        200 CCGGTGCATC

                        **                        *          *            *  
        210 TCTTAACAAGATTGTCTTCCGATCAACTTCTGAAAACTTTTCGAGAAACTATCTTCTGGTGTGCT
          1 TCTTAACAAGATCATCTTCCGATCAACTTCTGAAAACTGTTCGAGAAACCATCTTCTGGTGTACT

             ***                *   *            *       *               *   
        275 TTTTAACAAGATCGTCTTCCGATCGACTTCTGAAAATTTTGAGAATCCATCTTCTGGCGTAGTTC
         66 TCACAACAAGATCGTCTTCCAATCAACTTCTGAAAATCTTGAGAAACCATCTTCTGGCGTACTTC

                                                                         
        340 TTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCGGTGTACT
        131 TTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCGGTGTACT

                *                     *                *                     
        401 TCTTGACAAGATCATCTTCCGATCAATTTCTGAAAACTGTT-GGGAAACCATCTTCTGGTGTACT
          1 TCTTAACAAGATCATCTTCCGATCAACTTCTGAAAACTGTTCGAGAAACCATCTTCTGGTGTACT

                * *                                                   *  *   
        465 TCACGATAAGATCGTCTTCCAATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTCCTT
         66 TCACAACAAGATCGTCTTCCAATCAACTTCTGAAAA-TCTTGAGAAACCATCTTCTGGCGTACTT

                 *     *                         
        530 CTTGATAAGATTGTCTTCCGATCAACTTCTGAAAACT
        130 CTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACT

        567 CTTTTTTAGC


Statistics
Matches: 143,  Mismatches: 22, Indels: 2
        0.86            0.13        0.01

Matches are distributed among these distances:
 190   49  0.34
 191   94  0.66

ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34


Consensus pattern (191 bp):   
TCTTAACAAGATCATCTTCCGATCAACTTCTGAAAACTGTTCGAGAAACCATCTTCTGGTGTACT
TCACAACAAGATCGTCTTCCAATCAACTTCTGAAAATCTTGAGAAACCATCTTCTGGCGTACTTC
TTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCGGTGTACT

Done.