Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002704.1 Corchorus capsularis cultivar CVL-1 contig02712, 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, 672

Length: 1121
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38


Found at i:837 original size:26 final size:27

Alignment explanation


    Indices: 791--846  Score: 78
    Period size: 26  Copynumber: 2.1  Consensus size: 27

        781 TTACCACTAA

                                       
        791 TAATAATTAATATAATAATAAAAAGTT
          1 TAATAATTAATATAATAATAAAAAGTT

                     *           * *   
        818 TAATAA-TATTATAATAATAAGAGGTT
          1 TAATAATTAATATAATAATAAAAAGTT

               
        844 TAA
          1 TAA

        847 CGTGAAAAAA


Statistics
Matches: 26,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  26   20  0.77
  27    6  0.23

ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38


Consensus pattern (27 bp):   
TAATAATTAATATAATAATAAAAAGTT

Found at i:935 original size:12 final size:12

Alignment explanation


    Indices: 918--951  Score: 50
    Period size: 12  Copynumber: 2.8  Consensus size: 12

        908 TATGGAGTAA

                       *
        918 TTAATAATAATT
          1 TTAATAATAATC

                        
        930 TTAATAATAATC
          1 TTAATAATAATC

            *         
        942 ATAATAATAA
          1 TTAATAATAA

        952 GTTGTTTAAC


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  12   20  1.00

ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41


Consensus pattern (12 bp):   
TTAATAATAATC

Found at i:984 original size:114 final size:113

Alignment explanation


    Indices: 806--1012  Score: 283
    Period size: 114  Copynumber: 1.8  Consensus size: 113

        796 ATTAATATAA

                                 *                    *        *             
        806 TAATAAAAAGTTTAATAATATTATAATAATAAGAGGTTTAACGTGAAAAAAGTTGTTACCATTAT
          1 TAATAAAAAGTTTAATAATATCATAATAATAAGAGGTTTAACATGAAAAAAATTGTTACCATTA-

                                                             
        871 TTTTAGA-TTTTGTAATATGGAAAGAAAAACATAATGATATGGAGTAAT
         65 TTTTAGACTTTTGTAATATGGAAAGAAAAACATAATGATATGGAGTAAT

                  *  *                        **                         *   
        919 TAATAATAATTTTAATAATAATCATAATAATAAGTTGTTTAACAT-AAAAATAATTGTTACTATT
          1 TAATAAAAAGTTTAATAAT-ATCATAATAATAAGAGGTTTAACATGAAAAA-AATTGTTACCATT

                         *           *    
        983 ATTTTAGACTTTTTTAATATGGAAATAAAA
         64 ATTTTAGACTTTTGTAATATGGAAAGAAAA

       1013 TCTGGTTGGA


Statistics
Matches: 81,  Mismatches: 10, Indels: 5
        0.84            0.10        0.05

Matches are distributed among these distances:
 113   29  0.36
 114   52  0.64

ACGTcount: A:0.46, C:0.04, G:0.11, T:0.39


Consensus pattern (113 bp):   
TAATAAAAAGTTTAATAATATCATAATAATAAGAGGTTTAACATGAAAAAAATTGTTACCATTAT
TTTAGACTTTTGTAATATGGAAAGAAAAACATAATGATATGGAGTAAT
Done.