Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003098.1 Corchorus capsularis cultivar CVL-1 contig03106, 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, 751

Length: 1253
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39


Found at i:557 original size:6 final size:6

Alignment explanation


    Indices: 546--596  Score: 86
    Period size: 6  Copynumber: 8.7  Consensus size: 6

        536 ATTAATTTGC

                            *                                      
        546 TTTAGA TTTAGA TTCAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA

                
        593 TTTA
          1 TTTA

        597 CTTTGCTTAG


Statistics
Matches: 43,  Mismatches: 2, Indels: 1
        0.93            0.04        0.02

Matches are distributed among these distances:
   5    5  0.12
   6   38  0.88

ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51


Consensus pattern (6 bp):   
TTTAGA

Found at i:634 original size:15 final size:15

Alignment explanation


    Indices: 614--643  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

        604 TAGTATTTAG

                    *      
        614 TTTAATTGTTTTCTT
          1 TTTAATTGCTTTCTT

                           
        629 TTTAATTGCTTTCTT
          1 TTTAATTGCTTTCTT

        644 AAAATCCCCT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70


Consensus pattern (15 bp):   
TTTAATTGCTTTCTT

Found at i:915 original size:20 final size:19

Alignment explanation


    Indices: 890--931  Score: 66
    Period size: 20  Copynumber: 2.2  Consensus size: 19

        880 GTTTTTTCTT

                                
        890 AAAAAAAAAAATTTGCGTCG
          1 AAAAAAAAAAA-TTGCGTCG

                          *    
        910 AAAAAAAAAAATTGTGTCG
          1 AAAAAAAAAAATTGCGTCG

               
        929 AAA
          1 AAA

        932 TAAATTTAGG


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  19   10  0.48
  20   11  0.52

ACGTcount: A:0.60, C:0.07, G:0.14, T:0.19


Consensus pattern (19 bp):   
AAAAAAAAAAATTGCGTCG
Done.