Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021580.1 Corchorus olitorius cultivar O-4 contig21613, 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: 16116
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35


Found at i:9203 original size:2 final size:2

Alignment explanation


    Indices: 9196--9236  Score: 75
    Period size: 2  Copynumber: 21.0  Consensus size: 2

       9186 ATTGATTAGA

                                                                          
       9196 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       9237 GTCTCAAATC


Statistics
Matches: 38,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   37  0.97

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
AT

Found at i:9587 original size:22 final size:22

Alignment explanation


    Indices: 9536--9721  Score: 103
    Period size: 22  Copynumber: 8.5  Consensus size: 22

       9526 TGAATATTTT

                             *    
       9536 TATGAAATTTTGATAACTACCC
          1 TATGAAATTTTGATAACCACCC

                               *** 
       9558 TACT-AAATTTTGATAACCGGGC
          1 TA-TGAAATTTTGATAACCACCC

                       *    **  * 
       9580 TATGAAATTTTAATAATTA-TC
          1 TATGAAATTTTGATAACCACCC

                     *      * *  *
       9601 TATGAAATTGTGATAAACTCCA
          1 TATGAAATTTTGATAACCACCC

                   *             * 
       9623 TATGAAACTTTGATAACCTA-AC
          1 TATGAAATTTTGATAACC-ACCC

                       *       **  
       9645 TATGAAATTTTAATAAACCTTCC
          1 TATGAAATTTTGAT-AACCACCC

                              ** *
       9668 TATGAAATTTT-ATAACCTTCA
          1 TATGAAATTTTGATAACCACCC

                  *           *   
       9689 TATG-ATTTTTGATAACCTCCC
          1 TATGAAATTTTGATAACCACCC

                 *      
       9710 TATGAGATTTTG
          1 TATGAAATTTTG

       9722 TTAATGTCCC


Statistics
Matches: 124,  Mismatches: 32, Indels: 16
        0.72            0.19        0.09

Matches are distributed among these distances:
  20    5  0.04
  21   39  0.31
  22   63  0.51
  23   17  0.14

ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39


Consensus pattern (22 bp):   
TATGAAATTTTGATAACCACCC

Found at i:9693 original size:44 final size:44

Alignment explanation


    Indices: 9562--9720  Score: 118
    Period size: 44  Copynumber: 3.7  Consensus size: 44

       9552 CTACCCTACT

                           ***                  *         
       9562 AAATTTTGAT-AACCGGGCTATGAAATTTTAATAA-TTATC-TATG
          1 AAATTTTGATAAACCTTCCTATGAAATTTT-ATAACCT-TCATATG

                 *                         *        *      
       9605 AAATTGTGATAAA-C-TCCATATGAAACTTTGATAACC-TAACTATG
          1 AAATTTTGATAAACCTTCC-TATGAAA-TTTTATAACCTTCA-TATG

                   *                                    
       9649 AAATTTTAATAAACCTTCCTATGAAATTTTATAACCTTCATATG
          1 AAATTTTGATAAACCTTCCTATGAAATTTTATAACCTTCATATG

              *             *       *     
       9693 -ATTTTTGAT-AACCTCCCTATGAGATTTT
          1 AAATTTTGATAAACCTTCCTATGAAATTTT

       9721 GTTAATGTCC


Statistics
Matches: 93,  Mismatches: 14, Indels: 19
        0.74            0.11        0.15

Matches are distributed among these distances:
  42   19  0.20
  43   28  0.30
  44   33  0.35
  45   10  0.11
  46    3  0.03

ACGTcount: A:0.36, C:0.14, G:0.10, T:0.39


Consensus pattern (44 bp):   
AAATTTTGATAAACCTTCCTATGAAATTTTATAACCTTCATATG

Found at i:9700 original size:65 final size:65

Alignment explanation


    Indices: 9536--9720  Score: 164
    Period size: 65  Copynumber: 2.8  Consensus size: 65

       9526 TGAATATTTT

                     *            *                   ***                    
       9536 TATGAAATTTTGAT-AACTACCCTACT-AAATTTTGATAACCGGGCTATGAAATTTTAATAATTA
          1 TATGAAATTGTGATAAACT-CCATA-TGAAATTTTGATAACCTAACTATGAAATTTTAATAATTA

            * 
       9599 TC
         64 CC

                                         *                                   
       9601 TATGAAATTGTGATAAACTCCATATGAAACTTTGATAACCTAACTATGAAATTTTAATAAACCTT
          1 TATGAAATTGTGATAAACTCCATATGAAATTTTGATAACCTAACTATGAAATTTTAAT-AA--TT

               
       9666 -CC
         63 ACC

                       *    *  *        *            **      *     
       9668 TATGAAATT-TTATAACCTTCATATG-ATTTTTGATAACCTCCCTATGAGATTTT
          1 TATGAAATTGTGATAAACTCCATATGAAATTTTGATAACCTAACTATGAAATTTT

       9721 GTTAATGTCC


Statistics
Matches: 100,  Mismatches: 15, Indels: 10
        0.80            0.12        0.08

Matches are distributed among these distances:
  64    1  0.01
  65   68  0.68
  66   19  0.19
  67   10  0.10
  68    2  0.02

ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39


Consensus pattern (65 bp):   
TATGAAATTGTGATAAACTCCATATGAAATTTTGATAACCTAACTATGAAATTTTAATAATTACC
Done.