Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000542.1 Corchorus capsularis cultivar CVL-1 contig00542, 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, 810

Length: 1351
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:529 original size:17 final size:17

Alignment explanation


    Indices: 507--566  Score: 74
    Period size: 15  Copynumber: 3.8  Consensus size: 17

        497 TTCAGCAATT

                             
        507 TATATATATTTTTATTA
          1 TATATATATTTTTATTA

                   *         
        524 TATATATTTTTTTATT-
          1 TATATATATTTTTATTA

               *             
        540 TATTTAT-TTTTTATTA
          1 TATATATATTTTTATTA

                         
        556 T-TAT-TATTTTT
          1 TATATATATTTTT

        567 TTTTGGAAAA


Statistics
Matches: 38,  Mismatches: 3, Indels: 6
        0.81            0.06        0.13

Matches are distributed among these distances:
  14    1  0.03
  15   15  0.39
  16    7  0.18
  17   15  0.39

ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73


Consensus pattern (17 bp):   
TATATATATTTTTATTA

Found at i:567 original size:17 final size:17

Alignment explanation


    Indices: 515--568  Score: 62
    Period size: 17  Copynumber: 3.3  Consensus size: 17

        505 TTTATATATA

                              
        515 TTTTTATTA-TATATATT
          1 TTTTTATTATTAT-TATT

                              
        532 TTTTTA-T-TTATT-TAT
          1 TTTTTATTATTATTAT-T

                             
        547 TTTTTATTATTATTATT
          1 TTTTTATTATTATTATT

                 
        564 TTTTT
          1 TTTTT

        569 TTGGAAAATT


Statistics
Matches: 32,  Mismatches: 0, Indels: 10
        0.76            0.00        0.24

Matches are distributed among these distances:
  14    1  0.03
  15    8  0.25
  16    5  0.16
  17   17  0.53
  18    1  0.03

ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78


Consensus pattern (17 bp):   
TTTTTATTATTATTATT

Found at i:569 original size:33 final size:33

Alignment explanation


    Indices: 504--568  Score: 98
    Period size: 32  Copynumber: 2.0  Consensus size: 33

        494 GTTTTCAGCA

                                             
        504 ATTTATATATATTTTTATTATATATATTTTTTT
          1 ATTTATATATATTTTTATTATATATATTTTTTT

                  *                           
        537 ATTTATTTAT-TTTTTATTAT-TATTATTTTTTT
          1 ATTTATATATATTTTTATTATATA-TATTTTTTT

        569 TTGGAAAATT


Statistics
Matches: 30,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  31    2  0.07
  32   19  0.63
  33    9  0.30

ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74


Consensus pattern (33 bp):   
ATTTATATATATTTTTATTATATATATTTTTTT

Found at i:694 original size:27 final size:27

Alignment explanation


    Indices: 636--715  Score: 88
    Period size: 27  Copynumber: 3.0  Consensus size: 27

        626 AAGTGAACTT

                     *          * * * *
        636 AAAAATGACTAAAATGCCCCCGAGTGT
          1 AAAAATGACCAAAATGCCCCTGGGCGC

                                       
        663 AAAAATGACCAAAATGCCCCTGGGCGC
          1 AAAAATGACCAAAATGCCCCTGGGCGC

            *              *   *      
        690 GAAAATGACCAAAATACCCTTGGGCG
          1 AAAAATGACCAAAATGCCCCTGGGCG

        716 ACCCCAATGC


Statistics
Matches: 45,  Mismatches: 8, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  27   45  1.00

ACGTcount: A:0.39, C:0.25, G:0.21, T:0.15


Consensus pattern (27 bp):   
AAAAATGACCAAAATGCCCCTGGGCGC
Done.