Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016802.1 Corchorus olitorius cultivar O-4 contig16835, 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: 5422
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33


Found at i:4842 original size:28 final size:27

Alignment explanation


    Indices: 4811--4910  Score: 128
    Period size: 27  Copynumber: 3.7  Consensus size: 27

       4801 AGGGTCATCT

                                **      
       4811 AGGGGCATTTTGGTCATTTTTAAAATCC
          1 AGGGGCATTTTGGTCA-TTTGCAAATCC

                              *   *    
       4839 AGGGGCATTTTGGTCATTCGCACATCC
          1 AGGGGCATTTTGGTCATTTGCAAATCC

                                  ** * 
       4866 AGGGGCATTTTGGTCATTTGCATGTTC
          1 AGGGGCATTTTGGTCATTTGCAAATCC

                              
       4893 AGGGGCATTTTGGTCATT
          1 AGGGGCATTTTGGTCATT

       4911 CTAGGATCAC


Statistics
Matches: 64,  Mismatches: 8, Indels: 1
        0.88            0.11        0.01

Matches are distributed among these distances:
  27   48  0.75
  28   16  0.25

ACGTcount: A:0.19, C:0.17, G:0.27, T:0.37


Consensus pattern (27 bp):   
AGGGGCATTTTGGTCATTTGCAAATCC

Found at i:4871 original size:55 final size:54

Alignment explanation


    Indices: 4806--4911  Score: 149
    Period size: 54  Copynumber: 1.9  Consensus size: 54

       4796 GCATTAGGGT

                *                    *                             
       4806 CATCTAGGGGCATTTTGGTCATTTTTAAAATCCAGGGGCATTTTGGTCATTCGCA
          1 CATCCAGGGGCATTTTGGTCA-TTTGAAAATCCAGGGGCATTTTGGTCATTCGCA

                                     * ** *                    
       4861 CATCCAGGGGCATTTTGGTCATTTGCATGTTCAGGGGCATTTTGGTCATTC
          1 CATCCAGGGGCATTTTGGTCATTTGAAAATCCAGGGGCATTTTGGTCATTC

       4912 TAGGATCACC


Statistics
Matches: 45,  Mismatches: 6, Indels: 1
        0.87            0.12        0.02

Matches are distributed among these distances:
  54   25  0.56
  55   20  0.44

ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37


Consensus pattern (54 bp):   
CATCCAGGGGCATTTTGGTCATTTGAAAATCCAGGGGCATTTTGGTCATTCGCA

Done.