Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000669.1 Corchorus capsularis cultivar CVL-1 contig00669, 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, 702

Length: 1171
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39


Found at i:532 original size:12 final size:13

Alignment explanation


    Indices: 492--538  Score: 78
    Period size: 13  Copynumber: 3.7  Consensus size: 13

        482 TTAATTATTG

                         
        492 TTTGCTTTATTAA
          1 TTTGCTTTATTAA

             *           
        505 TCTGCTTTATTAA
          1 TTTGCTTTATTAA

                         
        518 TTTGCTTTA-TAA
          1 TTTGCTTTATTAA

                     
        530 TTTGCTTTA
          1 TTTGCTTTA

        539 GATTTAGATT


Statistics
Matches: 32,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  12   12  0.38
  13   20  0.62

ACGTcount: A:0.21, C:0.11, G:0.09, T:0.60


Consensus pattern (13 bp):   
TTTGCTTTATTAA

Found at i:546 original size:6 final size:6

Alignment explanation


    Indices: 535--561  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

        525 TATAATTTGC

                                           
        535 TTTAGA TTTAGA TTTAGA TTTAGA TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTT

        562 GCTTTGCTTT


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

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56


Consensus pattern (6 bp):   
TTTAGA

Found at i:968 original size:37 final size:36

Alignment explanation


    Indices: 900--974  Score: 91
    Period size: 37  Copynumber: 2.1  Consensus size: 36

        890 AAAATTAGGG

                                    *        *  
        900 TTTCCGATTTTTCTTTAAAAAAAATTAATTTTTCTT
          1 TTTCCGATTTTTCTTTAAAAAAAAATAATTTTTATT

                                                   
        936 TTTCCG-TTTTTCCTTTTAAAAAAAAA-ATATTTTTATT
          1 TTTCCGATTTTT-C-TTTAAAAAAAAATA-ATTTTTATT

              
        973 TT
          1 TT

        975 CTGTTTCTGC


Statistics
Matches: 34,  Mismatches: 2, Indels: 5
        0.83            0.05        0.12

Matches are distributed among these distances:
  35    5  0.15
  36    8  0.24
  37   21  0.62

ACGTcount: A:0.31, C:0.11, G:0.03, T:0.56


Consensus pattern (36 bp):   
TTTCCGATTTTTCTTTAAAAAAAAATAATTTTTATT

Found at i:975 original size:36 final size:35

Alignment explanation


    Indices: 900--990  Score: 89
    Period size: 36  Copynumber: 2.5  Consensus size: 35

        890 AAAATTAGGG

                                                 
        900 TTTCCGATTTTTC-TTTAAAAAAAATTAATTTTTCTT
          1 TTTCCG-TTTTTCTTTTAAAAAAAA-TAATTTTTCTT

                                                  
        936 TTTCCGTTTTTCCTTTTAAAAAAAA-AATATTTT-TAT
          1 TTTCCGTTTTT-CTTTTAAAAAAAATAAT-TTTTCT-T

                *      *       
        972 TTTCTGTTTCTGCTTTTAA
          1 TTTCCGTTT-TTCTTTTAA

        991 TTTTATTTAA


Statistics
Matches: 48,  Mismatches: 2, Indels: 10
        0.80            0.03        0.17

Matches are distributed among these distances:
  35    9  0.19
  36   27  0.56
  37   12  0.25

ACGTcount: A:0.27, C:0.12, G:0.04, T:0.56


Consensus pattern (35 bp):   
TTTCCGTTTTTCTTTTAAAAAAAATAATTTTTCTT
Done.