Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006313.1 Corchorus capsularis cultivar CVL-1 contig06334, 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: 3922
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.34


Found at i:2513 original size:34 final size:33

Alignment explanation


    Indices: 2413--2518  Score: 124
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       2403 TTGAAAAGAG

                    *               *        
       2413 TGTTTTAGATGTTGTTTGCGATGATACTAAATC
          1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC

             **                 *    *        
       2446 TAATTT-GAGTGTTGTTTGCAATGACACTAAATC
          1 TGTTTTAG-GTGTTGTTTGCGATGAAACTAAATC

                               *              
       2479 TGTTTTAGGTGTTGTTTAGTGATGAAACTAAATC
          1 TGTTTTAGGTGTTGTTT-GCGATGAAACTAAATC

                  
       2513 TGTTTT
          1 TGTTTT

       2519 GGATGCTAAT


Statistics
Matches: 60,  Mismatches: 10, Indels: 5
        0.80            0.13        0.07

Matches are distributed among these distances:
  32    1  0.02
  33   39  0.65
  34   20  0.33

ACGTcount: A:0.25, C:0.08, G:0.21, T:0.45


Consensus pattern (33 bp):   
TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC

Found at i:2624 original size:33 final size:31

Alignment explanation


    Indices: 2545--2655  Score: 109
    Period size: 33  Copynumber: 3.5  Consensus size: 31

       2535 GAAAAACAAT

                                    *       
       2545 TCTGTTTTGGTTGAACATAGCATTAAAAATAA
          1 TCTGTTTTGGTTG-ACATAGCATTGAAAATAA

              * *    *                *      
       2577 TTTTATTTTAGTTGATCATAGCATTGCAAATAA
          1 -TCTGTTTTGGTTGA-CATAGCATTGAAAATAA

                                             
       2610 TCCTGTTTTGGTTG--ATAGCATTGAAAATAAA
          1 T-CTGTTTTGGTTGACATAGCATTGAAAAT-AA

                      *    
       2641 TCTGTTTTGGGTGAC
          1 TCTGTTTTGGTTGAC

       2656 GAGAAAGAGA


Statistics
Matches: 63,  Mismatches: 10, Indels: 11
        0.75            0.12        0.13

Matches are distributed among these distances:
  30   24  0.38
  31    3  0.05
  32    2  0.03
  33   34  0.54

ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41


Consensus pattern (31 bp):   
TCTGTTTTGGTTGACATAGCATTGAAAATAA

Found at i:2630 original size:30 final size:30

Alignment explanation


    Indices: 2594--2650  Score: 89
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       2584 TTAGTTGATC

                     *                     
       2594 ATAGCATTGCAAAT-AATCCTGTTTTGGTTG
          1 ATAGCATTGAAAATAAAT-CTGTTTTGGTTG

                                       
       2624 ATAGCATTGAAAATAAATCTGTTTTGG
          1 ATAGCATTGAAAATAAATCTGTTTTGG

       2651 GTGACGAGAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  30   22  0.88
  31    3  0.12

ACGTcount: A:0.32, C:0.11, G:0.19, T:0.39


Consensus pattern (30 bp):   
ATAGCATTGAAAATAAATCTGTTTTGGTTG

Found at i:3036 original size:30 final size:30

Alignment explanation


    Indices: 2995--3052  Score: 82
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       2985 AAGGGGGAGG

                                           
       2995 GAATGATGCGCCCAAGG-CTTATCATGGAAA
          1 GAATGATGCG-CCAAGGACTTATCATGGAAA

                *                 *     
       3025 GAATTATGCGCCAAGGACTTATTATGGA
          1 GAATGATGCGCCAAGGACTTATCATGGA

       3053 CTTGAAGACA


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  29    6  0.24
  30   19  0.76

ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24


Consensus pattern (30 bp):   
GAATGATGCGCCAAGGACTTATCATGGAAA
Done.