Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011634.1 Corchorus capsularis cultivar CVL-1 contig11655, 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: 20861
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36


Found at i:4944 original size:6 final size:6

Alignment explanation


    Indices: 4933--4972  Score: 80
    Period size: 6  Copynumber: 6.7  Consensus size: 6

       4923 GTTTAGACTT

                                                          
       4933 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATAT
          1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATAT

       4973 TTCAAGATTC


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   34  1.00

ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35


Consensus pattern (6 bp):   
ATATAG

Found at i:12707 original size:25 final size:26

Alignment explanation


    Indices: 12656--12707  Score: 63
    Period size: 26  Copynumber: 2.0  Consensus size: 26

      12646 TTACTCAATT

                               **     
      12656 AAAAACTCTATTTTATTTTTCTGTAA
          1 AAAAACTCTATTTTATTTTAATGTAA

                                       
      12682 AAAAACTCTATTTT-TATTTAAT-TAA
          1 AAAAACTCTATTTTAT-TTTAATGTAA

             
      12707 A
          1 A

      12708 TCTAATATCC


Statistics
Matches: 23,  Mismatches: 2, Indels: 3
        0.82            0.07        0.11

Matches are distributed among these distances:
  25    5  0.22
  26   18  0.78

ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48


Consensus pattern (26 bp):   
AAAAACTCTATTTTATTTTAATGTAA

Found at i:15002 original size:13 final size:13

Alignment explanation


    Indices: 14984--15016  Score: 57
    Period size: 13  Copynumber: 2.5  Consensus size: 13

      14974 TATTCCATAT

                         
      14984 TTTAATAATTAAA
          1 TTTAATAATTAAA

                         
      14997 TTTAATAATTAAA
          1 TTTAATAATTAAA

              *    
      15010 TTAAATA
          1 TTTAATA

      15017 GCGTAAAATA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   19  1.00

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (13 bp):   
TTTAATAATTAAA
Done.