Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015019.1 Corchorus olitorius cultivar O-4 contig15052, 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: 2602
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33


Found at i:772 original size:69 final size:70

Alignment explanation


    Indices: 661--821  Score: 252
    Period size: 69  Copynumber: 2.3  Consensus size: 70

        651 ATTTCCCGCA

                                                                     *   *   
        661 ACAAGTCCGGGACAGGACTTGGGTAACTCCCGCCCAGGTCTTGTCCTGTA-ATTTGCGCTCTTCA
          1 ACAAGTCCGGGACAGGACTTGGGTAACTCCCGCCCAGGTCTTGTCCTGTATATTTGCACTCCTCA

                 
        725 ACAGC
         66 ACAGC

                                          *                    *      *      
        730 ACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTTTGCATTCCTCA
          1 ACAAGTCCGGGACAGGACTTGGGTAACTCCCGCCCAGGTCTTGTCCTGTATATTTGCACTCCTCA

                 
        795 ACAGC
         66 ACAGC

            *       *             
        800 CCAAGTCCTGGACAGGACTTGG
          1 ACAAGTCCGGGACAGGACTTGG

        822 CCAAGATCTG


Statistics
Matches: 84,  Mismatches: 7, Indels: 1
        0.91            0.08        0.01

Matches are distributed among these distances:
  69   49  0.58
  70   35  0.42

ACGTcount: A:0.20, C:0.29, G:0.25, T:0.25


Consensus pattern (70 bp):   
ACAAGTCCGGGACAGGACTTGGGTAACTCCCGCCCAGGTCTTGTCCTGTATATTTGCACTCCTCA
ACAGC

Found at i:853 original size:70 final size:70

Alignment explanation


    Indices: 661--853  Score: 167
    Period size: 70  Copynumber: 2.8  Consensus size: 70

        651 ATTTCCCGCA

                                  **  *   *  *    *         *  *     **  *   
        661 ACAAGTCCGGGACAGGACTTGGGTAACTCCCGCCCAGGTCTTGTCCTGTA-ATTTGCGCTCTTCA
          1 ACAAGTCCGGGACAGGACTTGGCCAAATCCTGCACAGGACTTGTCCTGCATTTTTGCATTCCTCA

                 
        725 ACAGC
         66 ACAGC

                                  **  *      *    *         *                
        730 ACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTTTGCATTCCTCA
          1 ACAAGTCCGGGACAGGACTTGGCCAAATCCTGCACAGGACTTGTCCTGCATTTTTGCATTCCTCA

                 
        795 ACAGC
         66 ACAGC

            *       *                        *                      
        800 CCAAGTCCTGGACAGGACTTGGCCAAGAT-CTGGACAGGACTTG-CTCTGCATTTT
          1 ACAAGTCCGGGACAGGACTTGGCCAA-ATCCTGCACAGGACTTGTC-CTGCATTTT

        854 CATTTTTCTT


Statistics
Matches: 107,  Mismatches: 14, Indels: 5
        0.85            0.11        0.04

Matches are distributed among these distances:
  69   50  0.47
  70   56  0.52
  71    1  0.01

ACGTcount: A:0.21, C:0.28, G:0.24, T:0.26


Consensus pattern (70 bp):   
ACAAGTCCGGGACAGGACTTGGCCAAATCCTGCACAGGACTTGTCCTGCATTTTTGCATTCCTCA
ACAGC

Found at i:1167 original size:21 final size:19

Alignment explanation


    Indices: 1110--1167  Score: 71
    Period size: 19  Copynumber: 2.9  Consensus size: 19

       1100 CTGTTTAGCA

                               
       1110 ACTGTACAGATGAGATTAC
          1 ACTGTACAGATGAGATTAC

                       * *      *
       1129 ACTGTACAGATTAAATTAGGT
          1 ACTGTACAGATGAGATTA--C

                              
       1150 ACTGTACAGATGAGATTA
          1 ACTGTACAGATGAGATTA

       1168 TTAGAGCAGC


Statistics
Matches: 32,  Mismatches: 5, Indels: 2
        0.82            0.13        0.05

Matches are distributed among these distances:
  19   16  0.50
  21   16  0.50

ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29


Consensus pattern (19 bp):   
ACTGTACAGATGAGATTAC
Done.