Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005425.1 Corchorus capsularis cultivar CVL-1 contig05443, 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: 9702
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30


Found at i:506 original size:19 final size:19

Alignment explanation


    Indices: 464--506  Score: 59
    Period size: 19  Copynumber: 2.3  Consensus size: 19

        454 GCGGCTAGAC

                 *          *  
        464 AAATTTTTTTTTAAAATAA
          1 AAATTCTTTTTTAAAAAAA

            *                  
        483 TAATTCTTTTTTAAAAAAA
          1 AAATTCTTTTTTAAAAAAA

                 
        502 AAATT
          1 AAATT

        507 AGCCGAGCCG


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49


Consensus pattern (19 bp):   
AAATTCTTTTTTAAAAAAA

Found at i:7299 original size:3 final size:3

Alignment explanation


    Indices: 7291--7332  Score: 57
    Period size: 3  Copynumber: 13.3  Consensus size: 3

       7281 AGGTTTCTCG

                                                   *               
       7291 GAT GAT GAT GAT GAAT GAT GAAT GAT GAT GGT GAT GAT GAT G
          1 GAT GAT GAT GAT G-AT GAT G-AT GAT GAT GAT GAT GAT GAT G

       7333 GGAACGTGTT


Statistics
Matches: 35,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
   3   29  0.83
   4    6  0.17

ACGTcount: A:0.33, C:0.00, G:0.36, T:0.31


Consensus pattern (3 bp):   
GAT

Found at i:8792 original size:16 final size:16

Alignment explanation


    Indices: 8759--8815  Score: 64
    Period size: 16  Copynumber: 3.6  Consensus size: 16

       8749 CGCTCAAATG

                        *   
       8759 TTGGGTCA-TTTGGGT
          1 TTGGGTCATTTTTGGT

                            
       8774 TTGGGTCATTTTTGGT
          1 TTGGGTCATTTTTGGT

                   *          
       8790 TTGGGT-GTTTTTCGGTT
          1 TTGGGTCATTTTT-GG-T

                     
       8807 TTGGGTCAT
          1 TTGGGTCAT

       8816 ATGGTTCCAA


Statistics
Matches: 35,  Mismatches: 3, Indels: 5
        0.81            0.07        0.12

Matches are distributed among these distances:
  15   13  0.37
  16   14  0.40
  17    7  0.20
  18    1  0.03

ACGTcount: A:0.05, C:0.07, G:0.35, T:0.53


Consensus pattern (16 bp):   
TTGGGTCATTTTTGGT
Done.