Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014211.1 Corchorus olitorius cultivar O-4 contig14244, 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: 7128
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34


Found at i:1656 original size:12 final size:12

Alignment explanation


    Indices: 1639--1683  Score: 72
    Period size: 12  Copynumber: 3.8  Consensus size: 12

       1629 AAGTCAGCGT

                        
       1639 CAAAAGCCATAA
          1 CAAAAGCCATAA

                       *
       1651 CAAAAGCCATAG
          1 CAAAAGCCATAA

                     *  
       1663 CAAAAGCCACAA
          1 CAAAAGCCATAA

                     
       1675 CAAAAGCCA
          1 CAAAAGCCA

       1684 CTATGATGGA


Statistics
Matches: 30,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  12   30  1.00

ACGTcount: A:0.56, C:0.29, G:0.11, T:0.04


Consensus pattern (12 bp):   
CAAAAGCCATAA

Found at i:1671 original size:24 final size:25

Alignment explanation


    Indices: 1620--1683  Score: 85
    Period size: 24  Copynumber: 2.6  Consensus size: 25

       1610 GGGAGGAAAT

                        *   *        
       1620 CCATAACAAAAGTCAGCGTCAAAAG
          1 CCATAACAAAAGCCAGAGTCAAAAG

                           *         
       1645 CCATAACAAAAGCCATAG-CAAAAG
          1 CCATAACAAAAGCCAGAGTCAAAAG

               *           
       1669 CCACAACAAAAGCCA
          1 CCATAACAAAAGCCA

       1684 CTATGATGGA


Statistics
Matches: 35,  Mismatches: 4, Indels: 1
        0.88            0.10        0.03

Matches are distributed among these distances:
  24   20  0.57
  25   15  0.43

ACGTcount: A:0.52, C:0.28, G:0.12, T:0.08


Consensus pattern (25 bp):   
CCATAACAAAAGCCAGAGTCAAAAG

Found at i:5055 original size:53 final size:53

Alignment explanation


    Indices: 4891--5053  Score: 308
    Period size: 53  Copynumber: 3.1  Consensus size: 53

       4881 TGTTTATTTA

                                                                 
       4891 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
          1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT

                                                      *          
       4944 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAAGGCAATGAACT
          1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT

                *                                                
       4997 ATTGGACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
          1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT

                
       5050 ATTG
          1 ATTG

       5054 GATTTAAAGA


Statistics
Matches: 107,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  53  107  1.00

ACGTcount: A:0.50, C:0.18, G:0.09, T:0.23


Consensus pattern (53 bp):   
ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
Done.