Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003842.1 Corchorus capsularis cultivar CVL-1 contig03850, 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, 778

Length: 1297
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26


Found at i:109 original size:51 final size:53

Alignment explanation


    Indices: 46--159  Score: 178
    Period size: 51  Copynumber: 2.2  Consensus size: 53

         36 TGCAATTCAT

                                           *        *            
         46 TTTTTACACATGTAATAGATTCTTC-TTTTCTATAAACAAGTATTACA-ATCC
          1 TTTTTACACATGTAATAGATTCTTCTTTTTCCATAAACAAATATTACAGATCC

                                                 *           *   
         97 TTTTTACACATGTAATAGATTCTTCTTTTTCCATAAATAAATATTACAGTTCC
          1 TTTTTACACATGTAATAGATTCTTCTTTTTCCATAAACAAATATTACAGATCC

                      
        150 TTTTTACACA
          1 TTTTTACACA

        160 AATAATAAAC


Statistics
Matches: 57,  Mismatches: 4, Indels: 2
        0.90            0.06        0.03

Matches are distributed among these distances:
  51   25  0.44
  52   19  0.33
  53   13  0.23

ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45


Consensus pattern (53 bp):   
TTTTTACACATGTAATAGATTCTTCTTTTTCCATAAACAAATATTACAGATCC

Found at i:125 original size:25 final size:25

Alignment explanation


    Indices: 46--126  Score: 76
    Period size: 23  Copynumber: 3.2  Consensus size: 25

         36 TGCAATTCAT

                                     
         46 TTTTTACACATGTAATAGATTCTTC
          1 TTTTTACACATGTAATAGATTCTTC

                     *   *   *  * *     
         71 TTTTCTATAAACAAGTATTACAATC--C
          1 -TTT-T-TACACATGTAATAGATTCTTC

                                     
         97 TTTTTACACATGTAATAGATTCTTC
          1 TTTTTACACATGTAATAGATTCTTC

                 
        122 TTTTT
          1 TTTTT

        127 CCATAAATAA


Statistics
Matches: 41,  Mismatches: 10, Indels: 9
        0.68            0.17        0.15

Matches are distributed among these distances:
  23   13  0.32
  24    1  0.02
  25    9  0.22
  26    4  0.10
  27    1  0.02
  28   13  0.32

ACGTcount: A:0.30, C:0.16, G:0.06, T:0.48


Consensus pattern (25 bp):   
TTTTTACACATGTAATAGATTCTTC

Found at i:470 original size:7 final size:7

Alignment explanation


    Indices: 440--471  Score: 55
    Period size: 7  Copynumber: 4.6  Consensus size: 7

        430 AAATAGAAAG

                  *
        440 AAAACAC
          1 AAAACAA

                   
        447 AAAACAA
          1 AAAACAA

                   
        454 AAAACAA
          1 AAAACAA

                   
        461 AAAACAA
          1 AAAACAA

                
        468 AAAA
          1 AAAA

        472 AACACCATGA


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   7   24  1.00

ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00


Consensus pattern (7 bp):   
AAAACAA
Done.