Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010253.1 Corchorus olitorius cultivar O-4 contig10285, 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: 4662
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33


Found at i:1078 original size:60 final size:59

Alignment explanation


    Indices: 996--1161  Score: 215
    Period size: 60  Copynumber: 2.8  Consensus size: 59

        986 GGCTAATTGC

                             *                 * *     *                
        996 TCAAATAGGCCCTTAACATATGCGAAAATGCTCAATTTAGGCCTCATGCTTTTAATTTGG
          1 TCAAATAGGCCC-TAACGTATGCGAAAATGCTCAAATAAGGCCACATGCTTTTAATTTGG

             **                                      *                  
       1056 TTGAATAGAGCCCTAACGTATGCGAAAATGCTCAAATAAGGGCACATGCTTTTAATTTGG
          1 TCAAATAG-GCCCTAACGTATGCGAAAATGCTCAAATAAGGCCACATGCTTTTAATTTGG

                      **       *                          
       1116 TCAAATAGGGTTCTAACGTTTGCGAAAATGCTCAAATAAGGCCACA
          1 TCAAATA-GGCCCTAACGTATGCGAAAATGCTCAAATAAGGCCACA

       1162 GTATCAATTG


Statistics
Matches: 91,  Mismatches: 13, Indels: 4
        0.84            0.12        0.04

Matches are distributed among these distances:
  60   86  0.95
  61    5  0.05

ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29


Consensus pattern (59 bp):   
TCAAATAGGCCCTAACGTATGCGAAAATGCTCAAATAAGGCCACATGCTTTTAATTTGG

Found at i:3817 original size:20 final size:20

Alignment explanation


    Indices: 3788--3827  Score: 71
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       3778 TTCAATGAGA

                                
       3788 AGAAACAAAGTTGGTTGGAT
          1 AGAAACAAAGTTGGTTGGAT

                 *              
       3808 AGAAATAAAGTTGGTTGGAT
          1 AGAAACAAAGTTGGTTGGAT

       3828 TTCGGAACTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.40, C:0.03, G:0.30, T:0.28


Consensus pattern (20 bp):   
AGAAACAAAGTTGGTTGGAT
Done.