Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010453.1 Corchorus capsularis cultivar CVL-1 contig10474, 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: 6480
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.36


Found at i:2269 original size:24 final size:24

Alignment explanation


    Indices: 2242--2288  Score: 85
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       2232 CTCTCTTAAT

                                    
       2242 TGACTAAATAGAAGTAAAAAAGTG
          1 TGACTAAATAGAAGTAAAAAAGTG

                     *             
       2266 TGACTAAATTGAAGTAAAAAAGT
          1 TGACTAAATAGAAGTAAAAAAGT

       2289 ACAAAGACAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.53, C:0.04, G:0.19, T:0.23


Consensus pattern (24 bp):   
TGACTAAATAGAAGTAAAAAAGTG

Found at i:2548 original size:14 final size:13

Alignment explanation


    Indices: 2529--2558  Score: 51
    Period size: 13  Copynumber: 2.2  Consensus size: 13

       2519 CCCACCAATA

                          
       2529 AAAAGTTAAAAGTT
          1 AAAAGTT-AAAGTT

                         
       2543 AAAAGTTAAAGTT
          1 AAAAGTTAAAGTT

               
       2556 AAA
          1 AAA

       2559 TAAAATTTTA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    9  0.56
  14    7  0.44

ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27


Consensus pattern (13 bp):   
AAAAGTTAAAGTT

Found at i:2555 original size:6 final size:7

Alignment explanation


    Indices: 2529--2558  Score: 53
    Period size: 7  Copynumber: 4.4  Consensus size: 7

       2519 CCCACCAATA

                   
       2529 AAAAGTT
          1 AAAAGTT

                   
       2536 AAAAGTT
          1 AAAAGTT

                   
       2543 AAAAGTT
          1 AAAAGTT

                   
       2550 -AAAGTT
          1 AAAAGTT

               
       2556 AAA
          1 AAA

       2559 TAAAATTTTA


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
   6    6  0.27
   7   16  0.73

ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27


Consensus pattern (7 bp):   
AAAAGTT

Found at i:6007 original size:58 final size:58

Alignment explanation


    Indices: 5918--6027  Score: 184
    Period size: 58  Copynumber: 1.9  Consensus size: 58

       5908 GAGGTCAAAC

                          ***                                         
       5918 TTTTTTTCTCCCCTTTGTTTACGTTCAAAGATTAATATCAATCCAATAACTTCAACTT
          1 TTTTTTTCTCCCCTCCCTTTACGTTCAAAGATTAATATCAATCCAATAACTTCAACTT

                                      *                         
       5976 TTTTTTTCTCCCCTCCCTTTACGTTCCAAGATTAATATCAATCCAATAACTT
          1 TTTTTTTCTCCCCTCCCTTTACGTTCAAAGATTAATATCAATCCAATAACTT

       6028 ATGGCCAAAA


Statistics
Matches: 48,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  58   48  1.00

ACGTcount: A:0.26, C:0.25, G:0.05, T:0.44


Consensus pattern (58 bp):   
TTTTTTTCTCCCCTCCCTTTACGTTCAAAGATTAATATCAATCCAATAACTTCAACTT
Done.