Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023721.1 Corchorus olitorius cultivar O-4 contig23754, 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: 8561
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:3795 original size:29 final size:29

Alignment explanation


    Indices: 3761--3957  Score: 180
    Period size: 29  Copynumber: 6.8  Consensus size: 29

       3751 TTCGCACGCT

                  *                      
       3761 CAGGGGAATTTTGGTCATTTTTGCACATC
          1 CAGGGGCATTTTGGTCATTTTTGCACATC

              *                  ***  *   
       3790 CGGGGGGCATTTTGGTCATTTCCACATATC
          1 C-AGGGGCATTTTGGTCATTTTTGCACATC

            *         *          *   *   
       3820 TAGGGGCATTCTGGTCATTTTCGCATA-C
          1 CAGGGGCATTTTGGTCATTTTTGCACATC

                                          
       3848 TCAGGGGCATTTTGGTCATTTTTGCACATC
          1 -CAGGGGCATTTTGGTCATTTTTGCACATC

            *   *              *     *   
       3878 TAGGAGCATTTTGGTCATTCTTGCATATC
          1 CAGGGGCATTTTGGTCATTTTTGCACATC

                       *      *   *     *
       3907 CAGGGGCATTTCGGTCATCTTTACACATT
          1 CAGGGGCATTTTGGTCATTTTTGCACATC

             *      *      *      
       3936 CTGGGGCAGTTTGGTTATTTTT
          1 CAGGGGCATTTTGGTCATTTTT

       3958 TGCATACTCT


Statistics
Matches: 133,  Mismatches: 32, Indels: 6
        0.78            0.19        0.04

Matches are distributed among these distances:
  28    1  0.01
  29  109  0.82
  30   23  0.17

ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39


Consensus pattern (29 bp):   
CAGGGGCATTTTGGTCATTTTTGCACATC

Found at i:3942 original size:87 final size:87

Alignment explanation


    Indices: 3760--3957  Score: 224
    Period size: 87  Copynumber: 2.3  Consensus size: 87

       3750 ATTCGCACGC

                   *                        *  *                        *    
       3760 TCAGGGGAATTTTGGTCATTTTTGCACATCCGGGGGGCATTTTGGTCATTTCCACATATCTAGGG
          1 TCAGGGGCATTTTGGTCATTTTTGCACATCCGAGGAGCATTTTGGTCATTTCCACATATCCAGGG

                             *    
       3825 GCATTCTGGTCATTTTCGCATA
         66 GCATTCTGGTCATTTTCACATA

                                            *                     **         
       3847 CTCAGGGGCATTTTGGTCATTTTTGCACAT-CTAGGAGCATTTTGGTCA-TTCTTGCATATCCAG
          1 -TCAGGGGCATTTTGGTCATTTTTGCACATCCGAGGAGCATTTTGGTCATTTC-CACATATCCAG

                                       
       3910 GGGCATT-TCGGTCATCTTTACACAT-
         64 GGGCATTCT-GGTCAT-TTT-CACATA

              *      *      *      
       3935 TCTGGGGCAGTTTGGTTATTTTT
          1 TCAGGGGCATTTTGGTCATTTTT

       3958 TGCATACTCT


Statistics
Matches: 95,  Mismatches: 11, Indels: 9
        0.83            0.10        0.08

Matches are distributed among these distances:
  86    4  0.04
  87   56  0.59
  88   31  0.33
  89    4  0.04

ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39


Consensus pattern (87 bp):   
TCAGGGGCATTTTGGTCATTTTTGCACATCCGAGGAGCATTTTGGTCATTTCCACATATCCAGGG
GCATTCTGGTCATTTTCACATA
Done.