Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009592.1 Corchorus olitorius cultivar O-4 contig09624, 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: 7676
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34


Found at i:778 original size:30 final size:30

Alignment explanation


    Indices: 742--830  Score: 117
    Period size: 30  Copynumber: 3.0  Consensus size: 30

        732 TACATACCAC

                            *          *  
        742 TAATAATTATTATTATTATAATAATAATTT
          1 TAATAATTATTATTATAATAATAATAAGTT

                        *   * *            
        772 TAATAATTA-TAATACCACTAATAATAAGTT
          1 TAATAATTATTATTA-TAATAATAATAAGTT

                                         
        802 TAATAATTATTATTATAATAATAATAAGT
          1 TAATAATTATTATTATAATAATAATAAGT

        831 CCAAATTAAC


Statistics
Matches: 49,  Mismatches: 8, Indels: 4
        0.80            0.13        0.07

Matches are distributed among these distances:
  29    4  0.08
  30   41  0.84
  31    4  0.08

ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45


Consensus pattern (30 bp):   
TAATAATTATTATTATAATAATAATAAGTT

Found at i:2614 original size:31 final size:30

Alignment explanation


    Indices: 2599--2656  Score: 98
    Period size: 31  Copynumber: 1.9  Consensus size: 30

       2589 TTACCTCTTG

                                   *       
       2599 AACTCTCAATTTTTGACATTTTTGCCCCATA
          1 AACTCTCAATTTTTGACA-TTTTACCCCATA

                                       
       2630 AACTCTCAATTTTTGACATTTTACCCC
          1 AACTCTCAATTTTTGACATTTTACCCC

       2657 CTCTCAAACA


Statistics
Matches: 26,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  30    8  0.31
  31   18  0.69

ACGTcount: A:0.26, C:0.28, G:0.05, T:0.41


Consensus pattern (30 bp):   
AACTCTCAATTTTTGACATTTTACCCCATA

Found at i:2754 original size:32 final size:32

Alignment explanation


    Indices: 2693--2773  Score: 90
    Period size: 32  Copynumber: 2.5  Consensus size: 32

       2683 CATCATACCA

                 *     * *   *              
       2693 ATGACGTGGCATTACCACGTCGGACCAAACCG
          1 ATGACATGGCAATGCCATGTCGGACCAAACCG

               *      *             *       
       2725 ATGGCATGGCCATGCCATGTCGGATCAAACCG
          1 ATGACATGGCAATGCCATGTCGGACCAAACCG

                 *           
       2757 ATGACGTGGCAATGCCA
          1 ATGACATGGCAATGCCA

       2774 CATCGGCGAC


Statistics
Matches: 39,  Mismatches: 10, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  32   39  1.00

ACGTcount: A:0.27, C:0.28, G:0.27, T:0.17


Consensus pattern (32 bp):   
ATGACATGGCAATGCCATGTCGGACCAAACCG
Done.