Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013586.1 Corchorus capsularis cultivar CVL-1 contig13607, 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: 30699
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:7418 original size:22 final size:23

Alignment explanation


    Indices: 7388--7432  Score: 65
    Period size: 22  Copynumber: 2.0  Consensus size: 23

       7378 TTATTAGTTA

                                   
       7388 TTTAGTTTATG-CTTTAATTTTC
          1 TTTAGTTTATGTCTTTAATTTTC

                *            *     
       7410 TTTATTTTATGTCTTTATTTTTC
          1 TTTAGTTTATGTCTTTAATTTTC

       7433 AAGTTTAATT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  22   10  0.50
  23   10  0.50

ACGTcount: A:0.16, C:0.09, G:0.07, T:0.69


Consensus pattern (23 bp):   
TTTAGTTTATGTCTTTAATTTTC

Found at i:16730 original size:30 final size:28

Alignment explanation


    Indices: 16659--16736  Score: 86
    Period size: 29  Copynumber: 2.7  Consensus size: 28

      16649 GAACTTACAC

                *                       
      16659 AAAACGGCCAAATAAGCCCCTGAACTCT
          1 AAAAAGGCCAAATAAGCCCCTGAACTCT

               **                           
      16687 -AATTGCAGCCAAATAAGCCCCTGAACTCTTT
          1 AAAAAG--GCCAAATAAGCCCCTGAACTC--T

                               
      16718 AAAAAGGCCAAATAAGCCC
          1 AAAAAGGCCAAATAAGCCC

      16737 TTTTTTTATG


Statistics
Matches: 41,  Mismatches: 4, Indels: 8
        0.77            0.08        0.15

Matches are distributed among these distances:
  27    3  0.07
  29   21  0.51
  30   13  0.32
  31    1  0.02
  32    3  0.07

ACGTcount: A:0.40, C:0.29, G:0.14, T:0.17


Consensus pattern (28 bp):   
AAAAAGGCCAAATAAGCCCCTGAACTCT

Found at i:17203 original size:30 final size:30

Alignment explanation


    Indices: 17167--17244  Score: 90
    Period size: 29  Copynumber: 2.6  Consensus size: 30

      17157 TATCAGAAAA

                                           
      17167 GGGCTTATTTGGCCTTTTTAA-AGAGTTCAG
          1 GGGCTTATTTGGCC-TTTTAATAGAGTTCAG

                            **             
      17197 GGGCTTATTTGG-C-TGCAATTAGAGTTCAG
          1 GGGCTTATTTGGCCTTTTAA-TAGAGTTCAG

                               
      17226 GGGCTTATTTGGCCGTTTT
          1 GGGCTTATTTGGCC-TTTT

      17245 GTGTAAGTTC


Statistics
Matches: 39,  Mismatches: 4, Indels: 8
        0.76            0.08        0.16

Matches are distributed among these distances:
  27    3  0.08
  29   22  0.56
  30   13  0.33
  32    1  0.03

ACGTcount: A:0.17, C:0.14, G:0.29, T:0.40


Consensus pattern (30 bp):   
GGGCTTATTTGGCCTTTTAATAGAGTTCAG
Done.