Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011136.1 Corchorus capsularis cultivar CVL-1 contig11157, 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: 12435
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:5761 original size:7 final size:7

Alignment explanation


    Indices: 5749--5776  Score: 56
    Period size: 7  Copynumber: 4.0  Consensus size: 7

       5739 GTTTTAAGTT

                   
       5749 AAAAATA
          1 AAAAATA

                   
       5756 AAAAATA
          1 AAAAATA

                   
       5763 AAAAATA
          1 AAAAATA

                   
       5770 AAAAATA
          1 AAAAATA

       5777 GTCTTTACAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   21  1.00

ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14


Consensus pattern (7 bp):   
AAAAATA

Found at i:8656 original size:32 final size:32

Alignment explanation


    Indices: 8610--8673  Score: 110
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       8600 ATCCCGATTA

                *                           
       8610 AACCGGAACCAAGGCACGTCAAACCTCAGATG
          1 AACCAGAACCAAGGCACGTCAAACCTCAGATG

                                *           
       8642 AACCAGAACCAAGGCACGTCGAACCTCAGATG
          1 AACCAGAACCAAGGCACGTCAAACCTCAGATG

       8674 GGAAAAACTC


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  32   30  1.00

ACGTcount: A:0.38, C:0.31, G:0.22, T:0.09


Consensus pattern (32 bp):   
AACCAGAACCAAGGCACGTCAAACCTCAGATG

Found at i:12130 original size:108 final size:109

Alignment explanation


    Indices: 11936--12209  Score: 437
    Period size: 108  Copynumber: 2.5  Consensus size: 109

      11926 ACTATTATAG

                         *                     *                             
      11936 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
          1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT

                                                             
      12001 TATTTTTACCAAAAAATTTGGATATACT-AAATTTTTTCTAATATACAA
         61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA

                                                                             
      12049 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
          1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT

                                 *                      
      12114 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
         66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA

                           *                                      
      12158 TTTTATTCTACTAAACACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTATA
          1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATA

      12210 TATTTTTTTT


Statistics
Matches: 155,  Mismatches: 4, Indels: 9
        0.92            0.02        0.05

Matches are distributed among these distances:
 108   66  0.43
 109   66  0.43
 110    2  0.01
 113   21  0.14

ACGTcount: A:0.38, C:0.12, G:0.02, T:0.49


Consensus pattern (109 bp):   
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA

Done.