Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011683.1 Corchorus capsularis cultivar CVL-1 contig11704, 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: 16281
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33


Found at i:9596 original size:24 final size:24

Alignment explanation


    Indices: 9571--9638  Score: 82
    Period size: 24  Copynumber: 2.8  Consensus size: 24

       9561 TCCAACAGTC

                    *            *   
       9571 TTTTCTTTTTCCTGTTGCTCATTCT
          1 TTTTC-TTCTCCTGTTGCTCACTCT

                     *              
       9596 TTTTCTTCTGCTGTTGCTCACTCT
          1 TTTTCTTCTCCTGTTGCTCACTCT

                     *   *     
       9620 TTTTCTTCTTCTGCTGCTC
          1 TTTTCTTCTCCTGTTGCTC

       9639 TTTTGCTTTC


Statistics
Matches: 38,  Mismatches: 5, Indels: 1
        0.86            0.11        0.02

Matches are distributed among these distances:
  24   33  0.87
  25    5  0.13

ACGTcount: A:0.03, C:0.28, G:0.10, T:0.59


Consensus pattern (24 bp):   
TTTTCTTCTCCTGTTGCTCACTCT

Found at i:10618 original size:5 final size:5

Alignment explanation


    Indices: 10608--10640  Score: 59
    Period size: 5  Copynumber: 6.8  Consensus size: 5

      10598 TATTTTTTGT

                                                    
      10608 TTATA TTATA TTATA TTATA TTATA -TATA TTAT
          1 TTATA TTATA TTATA TTATA TTATA TTATA TTAT

      10641 GATGTTATAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   4    4  0.15
   5   23  0.85

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (5 bp):   
TTATA

Found at i:13412 original size:78 final size:78

Alignment explanation


    Indices: 13330--13492  Score: 281
    Period size: 78  Copynumber: 2.1  Consensus size: 78

      13320 TTTATAGTTT

                                                             *               
      13330 TATTTTACTAAACTAAAAACTCTATTTTTATTTAATCAAATATAATATCTTTAAAACTATTTTAT
          1 TATTTTACTAAACTAAAAACTCTATTTTTATTTAATCAAATATAATATCCTTAAAACTATTTTAT

                         
      13395 TTTACCATTTTAC
         66 TTTACCATTTTAC

                     **                         *                *           
      13408 TATTTTACTCGACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACTATTTTAT
          1 TATTTTACTAAACTAAAAACTCTATTTTTATTTAATCAAATATAATATCCTTAAAACTATTTTAT

                         
      13473 TTTACCATTTTAC
         66 TTTACCATTTTAC

                   
      13486 TATTTTA
          1 TATTTTA

      13493 ATTGAAAACT


Statistics
Matches: 80,  Mismatches: 5, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  78   80  1.00

ACGTcount: A:0.36, C:0.13, G:0.01, T:0.50


Consensus pattern (78 bp):   
TATTTTACTAAACTAAAAACTCTATTTTTATTTAATCAAATATAATATCCTTAAAACTATTTTAT
TTTACCATTTTAC
Done.