Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005996.1 Corchorus olitorius cultivar O-4 contig06021, 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, 648

Length: 1080
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.39


Found at i:554 original size:2 final size:2

Alignment explanation


    Indices: 547--586  Score: 71
    Period size: 2  Copynumber: 20.0  Consensus size: 2

        537 ATATTATTAG

                                          *                            
        547 TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

        587 CTAGTTTTAA


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:717 original size:22 final size:22

Alignment explanation


    Indices: 692--1080  Score: 167
    Period size: 22  Copynumber: 17.6  Consensus size: 22

        682 ATTACACTAT

                   *              
        692 TTTTGATGACCTCCTTATGAAA
          1 TTTTGATAACCTCCTTATGAAA

                      * **        
        714 TTTTGATAACATTTTTATGAAA
          1 TTTTGATAACCTCCTTATGAAA

                *      * *         
        736 TTTTAATAACGATAC-TATGAAA
          1 TTTTGATAAC-CTCCTTATGAAA

               *  *     **       *
        758 TTTCGAGAACCTTTTTAT-AAT
          1 TTTTGATAACCTCCTTATGAAA

                **      *         
        779 TTTTTTTAACCTTCTTATGAAA
          1 TTTTGATAACCTCCTTATGAAA

                 *            * *  
        801 TTTTGTTAACCTTCC-TAAGGAA
          1 TTTTGATAACC-TCCTTATGAAA

                                    
        823 TTTTGA-AGACCTCAC-TATGAAA
          1 TTTTGATA-ACCTC-CTTATGAAA

                      *   **      
        845 TTTTGATAACTTCCCAATGAAA
          1 TTTTGATAACCTCCTTATGAAA

                        *         * 
        867 TTTTGATAACCAACAC-TATGAGA
          1 TTTTGATAACC-TC-CTTATGAAA

            **                   * 
        890 CGTTGATAACCT-CTATATGATA
          1 TTTTGATAACCTCCT-TATGAAA

             *         * *   *     
        912 TATTGATAACCACGTTACGAAAA
          1 TTTTGATAACCTCCTTATG-AAA

                  *       *       
        935 TTTT-AAAACCTCCATATG-AA
          1 TTTTGATAACCTCCTTATGAAA

                       * *     *     
        955 TTGTT-AGTAATCACAC-TCTGAAA
          1 TT-TTGA-TAACCTC-CTTATGAAA

                     * *           
        978 TTTTGATAATCACAC-TATGAAA
          1 TTTTGATAACCTC-CTTATGAAA

              *                    
       1000 TTGTGATAACCTCGC-TATGAAA
          1 TTTTGATAACCTC-CTTATGAAA

                                *   
       1022 TTTTGATAAACCTTCC-TATAAAA
          1 TTTTGAT-AACC-TCCTTATGAAA

                           *   *   
       1045 TTTTGATAAACCTCCCTATAAAA
          1 TTTTGAT-AACCTCCTTATGAAA

                         
       1068 TTTTGATAACCTC
          1 TTTTGATAACCTC


Statistics
Matches: 285,  Mismatches: 60, Indels: 44
        0.73            0.15        0.11

Matches are distributed among these distances:
  20    5  0.02
  21   23  0.08
  22  185  0.65
  23   69  0.24
  24    3  0.01

ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38


Consensus pattern (22 bp):   
TTTTGATAACCTCCTTATGAAA

Found at i:1040 original size:23 final size:23

Alignment explanation


    Indices: 992--1076  Score: 111
    Period size: 23  Copynumber: 3.7  Consensus size: 23

        982 GATAATCACA

                *     *            
        992 CTATGAAATTGTGAT-AACC-TC
          1 CTATAAAATTTTGATAAACCTTC

                 *                  
       1013 GCTATGAAATTTTGATAAACCTTC
          1 -CTATAAAATTTTGATAAACCTTC

                                 * 
       1037 CTATAAAATTTTGATAAACCTCC
          1 CTATAAAATTTTGATAAACCTTC

                             
       1060 CTATAAAATTTTGATAA
          1 CTATAAAATTTTGATAA

       1077 CCTC


Statistics
Matches: 58,  Mismatches: 3, Indels: 3
        0.91            0.05        0.05

Matches are distributed among these distances:
  22   14  0.24
  23   42  0.72
  24    2  0.03

ACGTcount: A:0.38, C:0.16, G:0.09, T:0.36


Consensus pattern (23 bp):   
CTATAAAATTTTGATAAACCTTC

Found at i:1079 original size:45 final size:45

Alignment explanation


    Indices: 975--1079  Score: 124
    Period size: 45  Copynumber: 2.3  Consensus size: 45

        965 TCACACTCTG

                        *         *                *    *
        975 AAATTTTGATAATC-ACACTATGAAATTGTGATAACCTCGCTATG
          1 AAATTTTGATAACCTACACTATAAAATTGTGATAACCTCCCTATA

                            *            *                 
       1019 AAATTTTGATAAACCTTC-CTATAAAATTTTGATAAACCTCCCTATA
          1 AAATTTTGAT-AACCTACACTATAAAATTGTGAT-AACCTCCCTATA

                           
       1065 AAATTTTGATAACCT
          1 AAATTTTGATAACCT

       1080 C


Statistics
Matches: 52,  Mismatches: 6, Indels: 5
        0.83            0.10        0.08

Matches are distributed among these distances:
  44   10  0.19
  45   21  0.40
  46   21  0.40

ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36


Consensus pattern (45 bp):   
AAATTTTGATAACCTACACTATAAAATTGTGATAACCTCCCTATA
Done.