Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001409.1 Corchorus capsularis cultivar CVL-1 contig01409, 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, 862

Length: 1438
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36


Found at i:226 original size:23 final size:23

Alignment explanation


    Indices: 180--226  Score: 60
    Period size: 23  Copynumber: 2.0  Consensus size: 23

        170 TTTTCATTTG

                               *   
        180 TAAATTATAATTTTATAATGAAA
          1 TAAATTATAATTTTATAATAAAA

                             *      
        203 TAAATTATAAATTTT-TTATAAAA
          1 TAAATTAT-AATTTTATAATAAAA

             
        226 T
          1 T

        227 TTTTATGCTT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  23   15  0.71
  24    6  0.29

ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47


Consensus pattern (23 bp):   
TAAATTATAATTTTATAATAAAA

Found at i:645 original size:16 final size:16

Alignment explanation


    Indices: 611--667  Score: 89
    Period size: 16  Copynumber: 3.6  Consensus size: 16

        601 GTCAATTGGG

                         *  
        611 CGGGTTCGGGTA-CTT
          1 CGGGTTCGGGTATTTT

                            
        626 CGGGTTCGGGTATTTT
          1 CGGGTTCGGGTATTTT

                       *    
        642 CGGGTTCGGGTTTTTT
          1 CGGGTTCGGGTATTTT

                      
        658 CGGGTTCGGG
          1 CGGGTTCGGG

        668 CTCGGACTGG


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  15   12  0.31
  16   27  0.69

ACGTcount: A:0.04, C:0.16, G:0.42, T:0.39


Consensus pattern (16 bp):   
CGGGTTCGGGTATTTT

Found at i:696 original size:17 final size:16

Alignment explanation


    Indices: 657--701  Score: 54
    Period size: 17  Copynumber: 2.7  Consensus size: 16

        647 TCGGGTTTTT

                        *   
        657 TCGGGTTCGGGCTCGG
          1 TCGGGTTCGGGCCCGG

            *                 
        673 ACTGGGTTCGGGCCCGGG
          1 TC-GGGTTCGGGCCC-GG

                       
        691 TCGGGTTCGGG
          1 TCGGGTTCGGG

        702 TTCACTTTCG


Statistics
Matches: 24,  Mismatches: 3, Indels: 3
        0.80            0.10        0.10

Matches are distributed among these distances:
  16    1  0.04
  17   20  0.83
  18    3  0.12

ACGTcount: A:0.02, C:0.24, G:0.51, T:0.22


Consensus pattern (16 bp):   
TCGGGTTCGGGCCCGG
Done.