Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006974.1 Corchorus olitorius cultivar O-4 contig06999, 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, 768

Length: 1281
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36


Found at i:755 original size:22 final size:22

Alignment explanation


    Indices: 613--778  Score: 81
    Period size: 22  Copynumber: 7.6  Consensus size: 22

        603 TTAAATATTT

                *                  
        613 TTATAAAATTTTGATAACCACAC
          1 TTATGAAATTTTGATAACCAC-C

                        *  * **   
        636 -TATGAAATTTTAATCATTACC
          1 TTATGAAATTTTGATAACCACC

                    * *      ***  
        657 TTATGAAACTGTGATAAGTTCC
          1 TTATGAAATTTTGATAACCACC

              *     *            * 
        679 --CTGAAACTTTGATAACCTAGC
          1 TTATGAAATTTTGATAACC-ACC

                        *    *      
        700 -TATGAAATTTTAATAAACATTCC
          1 TTATGAAATTTTGATAACCA--CC

                  *            *  
        723 -TATGATATTTTGATAACCTCC
          1 TTATGAAATTTTGATAACCACC

                   *    *        *
        744 TTATGAATTTTTTATAACCACT
          1 TTATGAAATTTTGATAACCACC

                         
        766 TTATGAAATTTTG
          1 TTATGAAATTTTG

        779 TTAATATCCC


Statistics
Matches: 104,  Mismatches: 33, Indels: 13
        0.69            0.22        0.09

Matches are distributed among these distances:
  20   13  0.12
  21    5  0.05
  22   70  0.67
  23   16  0.15

ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40


Consensus pattern (22 bp):   
TTATGAAATTTTGATAACCACC

Found at i:777 original size:44 final size:43

Alignment explanation


    Indices: 680--837  Score: 131
    Period size: 45  Copynumber: 3.6  Consensus size: 43

        670 ATAAGTTCCC

                 *            *       *    *    *        
        680 TGAAACTTTGATAACCTAGCTATGAAATTTTAATAAACATTCCTA
          1 TGAAATTTTGATAACCT-CCTATGAATTTTTTATAACCATT-CTA

               *                                         
        725 TGATATTTTGATAACCTCCTTATGAATTTTTTATAACCACTT-TA
          1 TGAAATTTTGATAACCTCC-TATGAATTTTTTATAACCA-TTCTA

                      *   **       *                 *  
        769 TGAAATTTTGTTAATATCCCTATAAATTTTTTAT-ACCATTGTA
          1 TGAAATTTTGATAACCT-CCTATGAATTTTTTATAACCATTCTA

                  *       *           
        812 TGAAATCTTGATAATCTCTCTATGAA
          1 TGAAATTTTGATAACCTC-CTATGAA

        838 ATTATATATC


Statistics
Matches: 93,  Mismatches: 15, Indels: 12
        0.77            0.12        0.10

Matches are distributed among these distances:
  42    3  0.03
  43   26  0.28
  44   29  0.31
  45   33  0.35
  46    2  0.02

ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43


Consensus pattern (43 bp):   
TGAAATTTTGATAACCTCCTATGAATTTTTTATAACCATTCTA

Found at i:815 original size:43 final size:45

Alignment explanation


    Indices: 745--840  Score: 119
    Period size: 43  Copynumber: 2.2  Consensus size: 45

        735 ATAACCTCCT

                                           *   *         
        745 TATG-AATTTTTTATAACCACTTTATGAAATTTTGTTAATATCCC
          1 TATGAAATTTTTTATAACCACTTTATGAAATCTTGATAATATCCC

                                                     *  * 
        789 TAT-AAATTTTTTAT-ACCA-TTGTATGAAATCTTGATAATCTCTC
          1 TATGAAATTTTTTATAACCACTT-TATGAAATCTTGATAATATCCC

                     
        832 TATGAAATT
          1 TATGAAATT

        841 ATATATCATT


Statistics
Matches: 45,  Mismatches: 4, Indels: 6
        0.82            0.07        0.11

Matches are distributed among these distances:
  42    2  0.04
  43   25  0.56
  44   18  0.40

ACGTcount: A:0.33, C:0.12, G:0.07, T:0.47


Consensus pattern (45 bp):   
TATGAAATTTTTTATAACCACTTTATGAAATCTTGATAATATCCC

Found at i:840 original size:44 final size:44

Alignment explanation


    Indices: 680--840  Score: 127
    Period size: 44  Copynumber: 3.6  Consensus size: 44

        670 ATAAGTTCCC

                 *        *   *             *    *         
        680 TGAAACTTTGATAACCTAGCTATGAAA-TTTTAATAAACA-TTCCTA
          1 TGAAATTTTGATAATCT-CCTATGAAATTTTTTATAACCACTT--TA

               *          *                              
        725 TGATATTTTGATAACCTCCTTATG-AATTTTTTATAACCACTTTA
          1 TGAAATTTTGATAATCTCC-TATGAAATTTTTTATAACCACTTTA

                      *    *                              
        769 TGAAATTTTGTTAATATCCCTAT-AAATTTTTTAT-ACCA-TTGTA
          1 TGAAATTTTGATAATCT-CCTATGAAATTTTTTATAACCACTT-TA

                  *                      
        812 TGAAATCTTGATAATCTCTCTATGAAATT
          1 TGAAATTTTGATAATCTC-CTATGAAATT

        841 ATATATCATT


Statistics
Matches: 96,  Mismatches: 12, Indels: 17
        0.77            0.10        0.14

Matches are distributed among these distances:
  42    3  0.03
  43   24  0.25
  44   36  0.38
  45   31  0.32
  46    2  0.02

ACGTcount: A:0.34, C:0.14, G:0.08, T:0.43


Consensus pattern (44 bp):   
TGAAATTTTGATAATCTCCTATGAAATTTTTTATAACCACTTTA
Done.