Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008638.1 Corchorus capsularis cultivar CVL-1 contig08659, 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: 20083
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:8366 original size:87 final size:87

Alignment explanation


    Indices: 8183--8359  Score: 212
    Period size: 87  Copynumber: 2.0  Consensus size: 87

       8173 TGCAGGGTTA

                         *                               *                *  
       8183 AAAAAAATGATGTTTTACTCATGTCATGAATTCATATAACAATTATGTACTAAGTCAAATCTTCA
          1 AAAAAAA--ATGTCTTACTCATGTCATGAATTCATATAACAATTACGTACTAAGTCAAATCTCCA

                    *     *** *  * *
       8248 ATCTTTAATAAAAAGTTATCGGTT
         64 ATCTTTAAGAAAAACCAAGCGATG

                                                                             
       8272 AAAAAAAATGTCTTACTCATGTCATGAATTCATATAACAATTACGTACTAAGTCAAATCTCCCAA
          1 AAAAAAAATGTCTTACTCATGTCATGAATTCATATAACAATTACGTACTAAGTCAAATCT-CCAA

             *          *          
       8337 TTTTTAAGAAAATCCAAGC-ATG
         65 TCTTTAAGAAAAACCAAGCGATG

             
       8359 A
          1 A

       8360 TTAAAAAGAA


Statistics
Matches: 75,  Mismatches: 12, Indels: 4
        0.82            0.13        0.04

Matches are distributed among these distances:
  87   53  0.71
  88   15  0.20
  89    7  0.09

ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33


Consensus pattern (87 bp):   
AAAAAAAATGTCTTACTCATGTCATGAATTCATATAACAATTACGTACTAAGTCAAATCTCCAAT
CTTTAAGAAAAACCAAGCGATG

Found at i:8428 original size:14 final size:15

Alignment explanation


    Indices: 8401--8433  Score: 50
    Period size: 14  Copynumber: 2.3  Consensus size: 15

       8391 TGACTAAAAA

                           
       8401 TAATATTAATTAAAT
          1 TAATATTAATTAAAT

                   *       
       8416 TAATATTCA-TAAAT
          1 TAATATTAATTAAAT

                
       8430 TAAT
          1 TAAT

       8434 TTTTAAAAAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  14    9  0.53
  15    8  0.47

ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45


Consensus pattern (15 bp):   
TAATATTAATTAAAT

Found at i:19392 original size:17 final size:17

Alignment explanation


    Indices: 19370--19404  Score: 70
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      19360 AGAGTTTTGT

                             
      19370 AAATTGACATGCTAAGC
          1 AAATTGACATGCTAAGC

                             
      19387 AAATTGACATGCTAAGC
          1 AAATTGACATGCTAAGC

             
      19404 A
          1 A

      19405 GTTATACGTG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23


Consensus pattern (17 bp):   
AAATTGACATGCTAAGC

Found at i:19839 original size:25 final size:25

Alignment explanation


    Indices: 19805--19854  Score: 100
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      19795 AAGTGAAGCC

                                     
      19805 CAGATCATGCACAAAACCCAGATCA
          1 CAGATCATGCACAAAACCCAGATCA

                                     
      19830 CAGATCATGCACAAAACCCAGATCA
          1 CAGATCATGCACAAAACCCAGATCA

      19855 TGTTGCAGCA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   25  1.00

ACGTcount: A:0.44, C:0.32, G:0.12, T:0.12


Consensus pattern (25 bp):   
CAGATCATGCACAAAACCCAGATCA
Done.