Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010543.1 Corchorus capsularis cultivar CVL-1 contig10564, 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: 16041
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:6688 original size:22 final size:23

Alignment explanation


    Indices: 6654--6704  Score: 88
    Period size: 22  Copynumber: 2.3  Consensus size: 23

       6644 GAGATAAAAA

                                   
       6654 AAGAACAAAAAAAATGTGTGCCT
          1 AAGAACAAAAAAAATGTGTGCCT

                                   
       6677 AAGAA-AAAAAAAATGTGTGCCT
          1 AAGAACAAAAAAAATGTGTGCCT

                   
       6699 AA-AACA
          1 AAGAACA

       6705 GATGATGATG


Statistics
Matches: 27,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  21    2  0.07
  22   20  0.74
  23    5  0.19

ACGTcount: A:0.57, C:0.12, G:0.16, T:0.16


Consensus pattern (23 bp):   
AAGAACAAAAAAAATGTGTGCCT

Found at i:12674 original size:29 final size:29

Alignment explanation


    Indices: 12617--12674  Score: 71
    Period size: 29  Copynumber: 2.0  Consensus size: 29

      12607 ATCAATTTCT

                            ***    *     
      12617 AAATCTCAGTTAATTTTTTTCCTCGAAAA
          1 AAATCTCAGTTAATTTAAGTCCTAGAAAA

                                    *    
      12646 AAATCTCAGTTAATTTAAGTCCTATAAAA
          1 AAATCTCAGTTAATTTAAGTCCTAGAAAA

      12675 GTGATTTTGT


Statistics
Matches: 24,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  29   24  1.00

ACGTcount: A:0.40, C:0.16, G:0.07, T:0.38


Consensus pattern (29 bp):   
AAATCTCAGTTAATTTAAGTCCTAGAAAA

Found at i:13144 original size:30 final size:30

Alignment explanation


    Indices: 13101--13174  Score: 96
    Period size: 30  Copynumber: 2.5  Consensus size: 30

      13091 GAATTATGTG

                  *          *     *      
      13101 TTTATTTTATTTTTTTTAGTG-ATAGAGTA
          1 TTTATTCTATTTTTTTTTGTGAAAAGAGTA

                              *      *    
      13130 TTTATTCTATTTTTTTTTTTGAAAATAGTA
          1 TTTATTCTATTTTTTTTTGTGAAAAGAGTA

                           
      13160 TTTATTCTATTTTTT
          1 TTTATTCTATTTTTT

      13175 ATTACAAAGA


Statistics
Matches: 39,  Mismatches: 5, Indels: 1
        0.87            0.11        0.02

Matches are distributed among these distances:
  29   18  0.46
  30   21  0.54

ACGTcount: A:0.23, C:0.03, G:0.08, T:0.66


Consensus pattern (30 bp):   
TTTATTCTATTTTTTTTTGTGAAAAGAGTA
Done.