Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012177.1 Corchorus olitorius cultivar O-4 contig12210, 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: 1901
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29


Found at i:89 original size:29 final size:29

Alignment explanation


    Indices: 46--299  Score: 228
    Period size: 29  Copynumber: 8.7  Consensus size: 29

         36 CGCATGCTCA

                *               *      *  
         46 GGGGAATTTTGGGTCATTTTTGCATATATG
          1 GGGGCATTTT-GGTCATTTTCGCATATCTG

                              * *        
         76 GGGGCATTTTGGTCATTTCCACATATCTG
          1 GGGGCATTTTGGTCATTTTCGCATATCTG

                     *                   * 
        105 GGGGCAGTTCTGGTCATTTTCGCATATTCGG
          1 GGGGCA-TTTTGGTCATTTTCGCATA-TCTG

                              * *        
        136 GGGGCATTTTGGTCATTTCCACATATCTG
          1 GGGGCATTTTGGTCATTTTCGCATATCTG

                    *           *         
        165 GGGGCATTCTGGTCATTTTCACATAT-TCG
          1 GGGGCATTTTGGTCATTTTCGCATATCT-G

                               *   *    *
        194 GGGGCATTTTGGTCATTTTTGCACATCTA
          1 GGGGCATTTTGGTCATTTTCGCATATCTG

              *                         **
        223 GGAGCATTTTGGTCATTCTT-GCATATCCA
          1 GGGGCATTTTGGTCATT-TTCGCATATCTG

                     *            *        
        252 GGGGCATTTCGGTCATCTTTACACAT-TCT-
          1 GGGGCATTTTGGTCAT-TTT-CGCATATCTG

                  *      *     
        281 GGGGCAGTTTGGTTATTTT
          1 GGGGCATTTTGGTCATTTT

        300 TTGCATACTC


Statistics
Matches: 186,  Mismatches: 30, Indels: 18
        0.79            0.13        0.08

Matches are distributed among these distances:
  28    4  0.02
  29  123  0.66
  30   47  0.25
  31   12  0.06

ACGTcount: A:0.17, C:0.18, G:0.26, T:0.39


Consensus pattern (29 bp):   
GGGGCATTTTGGTCATTTTCGCATATCTG

Found at i:175 original size:59 final size:59

Alignment explanation


    Indices: 57--299  Score: 266
    Period size: 58  Copynumber: 4.2  Consensus size: 59

         47 GGGAATTTTG

                     *                                                  
         57 GGTCATTTTTGCATATAT-GGGGGCATTTTGGTCATTTCCACATATCTGGGGGCAGTTCT
          1 GGTCATTTTCGCATAT-TCGGGGGCATTTTGGTCATTTCCACATATCTGGGGGCAGTTCT

                                                                        
        116 GGTCATTTTCGCATATTCGGGGGGCATTTTGGTCATTTCCACATATCTGGGGGCA-TTCT
          1 GGTCATTTTCGCATATTC-GGGGGCATTTTGGTCATTTCCACATATCTGGGGGCAGTTCT

                      *                          ***  *    *  *      * 
        175 GGTCATTTTCACATATTCGGGGGCATTTTGGTCATTTTTGCACATCTAGGAGCA-TTTT
          1 GGTCATTTTCGCATATTCGGGGGCATTTTGGTCATTTCCACATATCTGGGGGCAGTTCT

                             * *         *          *                     
        233 GGTCATTCTT-GCATATCCAGGGGCATTTCGGTCATCTTTACACAT-TCT-GGGGCAGTT-T
          1 GGTCATT-TTCGCATATTCGGGGGCATTTTGGTCA--TTTCCACATATCTGGGGGCAGTTCT

               *     
        291 GGTTATTTT
          1 GGTCATTTT

        300 TTGCATACTC


Statistics
Matches: 159,  Mismatches: 19, Indels: 14
        0.83            0.10        0.07

Matches are distributed among these distances:
  57    2  0.01
  58   73  0.46
  59   43  0.27
  60   41  0.26

ACGTcount: A:0.17, C:0.19, G:0.25, T:0.40


Consensus pattern (59 bp):   
GGTCATTTTCGCATATTCGGGGGCATTTTGGTCATTTCCACATATCTGGGGGCAGTTCT

Done.