Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017309.1 Corchorus olitorius cultivar O-4 contig17342, 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: 4187
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:727 original size:22 final size:22

Alignment explanation


    Indices: 702--743  Score: 57
    Period size: 22  Copynumber: 1.9  Consensus size: 22

        692 GGCAAATTCG

                 *         *      
        702 TAACCTAAATGACCCGAGAAGT
          1 TAACCCAAATGACCCAAGAAGT

                  *             
        724 TAACCCGAATGACCCAAGAA
          1 TAACCCAAATGACCCAAGAA

        744 TATTATAAAC


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   17  1.00

ACGTcount: A:0.43, C:0.26, G:0.17, T:0.14


Consensus pattern (22 bp):   
TAACCCAAATGACCCAAGAAGT

Found at i:991 original size:11 final size:11

Alignment explanation


    Indices: 948--985  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

        938 TTCCTATATA

                *      
        948 AAATAAATTAT
          1 AAATTAATTAT

                        
        959 CAAA-TAATTAT
          1 -AAATTAATTAT

                       
        970 AAATTAATTAT
          1 AAATTAATTAT

                 
        981 AAATT
          1 AAATT

        986 TGTTATGAAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  10    3  0.12
  11   18  0.75
  12    3  0.12

ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39


Consensus pattern (11 bp):   
AAATTAATTAT

Found at i:1693 original size:17 final size:17

Alignment explanation


    Indices: 1671--1703  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       1661 TTTTATTGAT

                              
       1671 ATTTAT-ATTATTAATTA
          1 ATTTATAATT-TTAATTA

                            
       1688 ATTTATAATTTTAATT
          1 ATTTATAATTTTAATT

       1704 GATGTAATGA


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  17   12  0.80
  18    3  0.20

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (17 bp):   
ATTTATAATTTTAATTA

Found at i:2860 original size:24 final size:24

Alignment explanation


    Indices: 2833--2908  Score: 71
    Period size: 24  Copynumber: 3.1  Consensus size: 24

       2823 GGGCCAGCCA

                          *         
       2833 GGCGCGGCCCAAGCACCCAGGCCT
          1 GGCGCGGCCCAAGCGCCCAGGCCT

                     *   *    * *    *
       2857 GGCGCACGGGCCAGGCGCACGGGCCA
          1 GGCG--CGGCCCAAGCGCCCAGGCCT

               *                    
       2883 GGCACGGCCCAAGCGCCCAGGCCT
          1 GGCGCGGCCCAAGCGCCCAGGCCT

              
       2907 GG
          1 GG

       2909 TGCGCGGGCC


Statistics
Matches: 38,  Mismatches: 12, Indels: 4
        0.70            0.22        0.07

Matches are distributed among these distances:
  24   21  0.55
  26   17  0.45

ACGTcount: A:0.16, C:0.42, G:0.39, T:0.03


Consensus pattern (24 bp):   
GGCGCGGCCCAAGCGCCCAGGCCT

Found at i:2889 original size:11 final size:13

Alignment explanation


    Indices: 2852--2885  Score: 59
    Period size: 13  Copynumber: 2.6  Consensus size: 13

       2842 CAAGCACCCA

                *        
       2852 GGCCTGGCGCACG
          1 GGCCAGGCGCACG

                         
       2865 GGCCAGGCGCACG
          1 GGCCAGGCGCACG

                    
       2878 GGCCAGGC
          1 GGCCAGGC

       2886 ACGGCCCAAG


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   20  1.00

ACGTcount: A:0.12, C:0.38, G:0.47, T:0.03


Consensus pattern (13 bp):   
GGCCAGGCGCACG
Done.