Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017441.1 Corchorus olitorius cultivar O-4 contig17474, 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: 9178
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32


Found at i:1901 original size:34 final size:34

Alignment explanation


    Indices: 1862--2000  Score: 94
    Period size: 34  Copynumber: 4.2  Consensus size: 34

       1852 CGCTACCTTG

                                  *            
       1862 TGCGCGGGCTGAGGCAGCAGCATCGGCCTGCTG-T
          1 TGCGCGGGCT-AGGCAGCAGCAGCGGCCTGCTGCT

                  *        * *     *     *   *
       1896 TGCGCGCGC-A-GCATCGGC--CTG-CTGTTGCG
          1 TGCGCGGGCTAGGCAGCAGCAGCGGCCTGCTGCT

            *            *          *         
       1925 CGCGCGGGCTAGGTAGCAGCAGCGCCCTGCTGCT
          1 TGCGCGGGCTAGGCAGCAGCAGCGGCCTGCTGCT

                   *                   *       
       1959 TG-GCGGACTGAGGCAGCAGCAGCGGCTTGCTGCT
          1 TGCGCGGGCT-AGGCAGCAGCAGCGGCCTGCTGCT

                    
       1993 TGGCGCGG
          1 T-GCGCGG

       2001 ATAGCCTGCC


Statistics
Matches: 76,  Mismatches: 20, Indels: 16
        0.68            0.18        0.14

Matches are distributed among these distances:
  28    5  0.07
  29    9  0.12
  30    1  0.01
  31   11  0.14
  32    1  0.01
  33    7  0.09
  34   37  0.49
  35    1  0.01
  36    4  0.05

ACGTcount: A:0.11, C:0.31, G:0.41, T:0.17


Consensus pattern (34 bp):   
TGCGCGGGCTAGGCAGCAGCAGCGGCCTGCTGCT

Found at i:1906 original size:25 final size:25

Alignment explanation


    Indices: 1878--1929  Score: 104
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       1868 GGCTGAGGCA

                                     
       1878 GCAGCATCGGCCTGCTGTTGCGCGC
          1 GCAGCATCGGCCTGCTGTTGCGCGC

                                     
       1903 GCAGCATCGGCCTGCTGTTGCGCGC
          1 GCAGCATCGGCCTGCTGTTGCGCGC

              
       1928 GC
          1 GC

       1930 GGGCTAGGTA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   27  1.00

ACGTcount: A:0.08, C:0.37, G:0.37, T:0.19


Consensus pattern (25 bp):   
GCAGCATCGGCCTGCTGTTGCGCGC
Done.