Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024187.1 Corchorus olitorius cultivar O-4 contig24220, 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: 13715
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26


Found at i:13022 original size:35 final size:35

Alignment explanation


    Indices: 12964--13267  Score: 403
    Period size: 35  Copynumber: 8.7  Consensus size: 35

      12954 CTCAGGAATA

                          **           *   *    
      12964 CAGATGACTCGGTGCGGCATCTTCAAAAAT-GATCT
          1 CAGATGACTCGGTGTAGCATCTTCAAAGATAAAT-T

             *                *      *      *  
      12999 CGGATGACTCGGTGTAGCGTCTTCATAGATAAGTT
          1 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATT

                                     *         
      13034 CAGATGACTCGGTGTAGCATCTTCATAGATAAATT
          1 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATT

                              *      *         
      13069 CAGATGACTCGGTGTAGCGTCTTCATAGATAAATT
          1 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATT

                              *      *        *
      13104 CAGATGACTCGGTGTAGCGTCTTCATAGATAAATC
          1 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATT

                 *                            *
      13139 CAGATTACTCGGTGTAGCATCTTCAAAGATAAATC
          1 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATT

                                               
      13174 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATT
          1 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATT

            *        *                    *    
      13209 TAGATGACTTGGTGTAGCATCTTCAAAGATGAATT
          1 CAGATGACTCGGTGTAGCATCTTCAAAGATAAATT

            *         *             
      13244 TAGATGACTCAGTGTAGCATCTTC
          1 CAGATGACTCGGTGTAGCATCTTC

      13268 GATATGAACT


Statistics
Matches: 245,  Mismatches: 23, Indels: 2
        0.91            0.09        0.01

Matches are distributed among these distances:
  35  244  1.00
  36    1  0.00

ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30


Consensus pattern (35 bp):   
CAGATGACTCGGTGTAGCATCTTCAAAGATAAATT

Found at i:13566 original size:28 final size:28

Alignment explanation


    Indices: 13526--13599  Score: 130
    Period size: 28  Copynumber: 2.6  Consensus size: 28

      13516 GTCACTTAAG

                    *                   
      13526 GGGGCATTCTGGTCATTTTACATGTCCA
          1 GGGGCATTTTGGTCATTTTACATGTCCA

                               *        
      13554 GGGGCATTTTGGTCATTTTGCATGTCCA
          1 GGGGCATTTTGGTCATTTTACATGTCCA

                              
      13582 GGGGCATTTTGGTCATTT
          1 GGGGCATTTTGGTCATTT

      13600 CAAATGCACT


Statistics
Matches: 44,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  28   44  1.00

ACGTcount: A:0.15, C:0.18, G:0.28, T:0.39


Consensus pattern (28 bp):   
GGGGCATTTTGGTCATTTTACATGTCCA
Done.