Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002944.1 Corchorus olitorius cultivar O-4 contig02949, 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: 1974
ACGTcount: A:0.14, C:0.29, G:0.36, T:0.21


Found at i:876 original size:51 final size:50

Alignment explanation


    Indices: 821--1039  Score: 206
    Period size: 51  Copynumber: 4.3  Consensus size: 50

        811 GAAGCGCTTG

                       *                 *            *        
        821 TCGGTGCGGCCATCGTTGTCCAGGTCGCGGTCGGGGCCGCGGTGGGTCGCA
          1 TCGGTGCGGCCGTCGTTGTCCAGGTCGCGATCGGGGCCGCGGAGGGT-GCA

                                * *   *        *      *         
        872 TCGGTGCGGCCGTCGTTGTCGAAGTCTCGATCGGGACCGCCGAAGCGG-GCA
          1 TCGGTGCGGCCGTCGTTGTCCAGGTCGCGATCGGGGCCG-CGGAG-GGTGCA

                    *              *  *             *  *       
        923 TCGGTGCGTCCGTCGTTGTCCAGATCACGATCGGGGCCGCCGAAGGTGGCA
          1 TCGGTGCGGCCGTCGTTGTCCAGGTCGCGATCGGGGCCGCGGAGGGT-GCA

                    *                    *  *         * * *   *
        974 TCGGTGCGCCCGTCGTTGTCCAGGTCGCGGTCAGGGCCGCCGCACGTTGCG
          1 TCGGTGCGGCCGTCGTTGTCCAGGTCGCGATCGGGGCCG-CGGAGGGTGCA

                           
       1025 TCGGTGCGGCCGTCG
          1 TCGGTGCGGCCGTCG

       1040 CGGTCGACGT


Statistics
Matches: 135,  Mismatches: 28, Indels: 10
        0.78            0.16        0.06

Matches are distributed among these distances:
  49    2  0.01
  50    2  0.01
  51  122  0.90
  52    7  0.05
  53    2  0.01

ACGTcount: A:0.09, C:0.31, G:0.41, T:0.19


Consensus pattern (50 bp):   
TCGGTGCGGCCGTCGTTGTCCAGGTCGCGATCGGGGCCGCGGAGGGTGCA

Found at i:1029 original size:102 final size:102

Alignment explanation


    Indices: 806--1039  Score: 256
    Period size: 102  Copynumber: 2.3  Consensus size: 102

        796 ATCATCAGGG

                       ***            *           *  *  *          * **      
        806 CCGCCGAAGCGCTTGTCGGTGCGGCCATCGTTGTCCAGGTCGCGGTCGGGGCCGCGGTGGGTCGC
          1 CCGCCGAAGCGGGCGTCGGTGCGGCCGTCGTTGTCCAGATCACGATCGGGGCCGCCGAAGGTCGC

                     *           *     *         
        871 ATCGGTGCGGCCGTCGTTGTCGAAGTCTCGATCGGGA
         66 ATCGGTGCGCCCGTCGTTGTCCAAGTCGCGATCGGGA

                          *        *                                      *  
        908 CCGCCGAAGCGGGCATCGGTGCGTCCGTCGTTGTCCAGATCACGATCGGGGCCGCCGAAGGTGGC
          1 CCGCCGAAGCGGGCGTCGGTGCGGCCGTCGTTGTCCAGATCACGATCGGGGCCGCCGAAGGTCGC

                                   *      *       
        973 ATCGGTGCGCCCGTCGTTGTCCAGGTCGCGGTCAGGG-
         66 ATCGGTGCGCCCGTCGTTGTCCAAGTCGCGATC-GGGA

                  *     *                  
       1010 CCGCCGCA-CGTTGCGTCGGTGCGGCCGTCG
          1 CCGCCGAAGCG-GGCGTCGGTGCGGCCGTCG

       1040 CGGTCGACGT


Statistics
Matches: 108,  Mismatches: 22, Indels: 4
        0.81            0.16        0.03

Matches are distributed among these distances:
 101    2  0.02
 102  103  0.95
 103    3  0.03

ACGTcount: A:0.09, C:0.32, G:0.40, T:0.19


Consensus pattern (102 bp):   
CCGCCGAAGCGGGCGTCGGTGCGGCCGTCGTTGTCCAGATCACGATCGGGGCCGCCGAAGGTCGC
ATCGGTGCGCCCGTCGTTGTCCAAGTCGCGATCGGGA

Done.