Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000333.1 Corchorus olitorius cultivar O-4 contig00333, 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, 838

Length: 1397
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32


Found at i:683 original size:31 final size:31

Alignment explanation


    Indices: 648--806  Score: 196
    Period size: 31  Copynumber: 5.2  Consensus size: 31

        638 GGTGTCCGAC

                  *                  *     
        648 GTGGCATGCCACATGTACCAAAAAGCGACAT
          1 GTGGCACGCCACATGTACCAAAAAGTGACAT

                        *            *     
        679 GTGGCACGCCACGTGTACCAAAAAGCGACAT
          1 GTGGCACGCCACATGTACCAAAAAGTGACAT

                   *  *                   *
        710 GTGGCACACCTCATGTACCAAAAAGTGACAC
          1 GTGGCACGCCACATGTACCAAAAAGTGACAT

            *      *                       
        741 ATGGCACACCACATGTACCAAAAAGTGACAT
          1 GTGGCACGCCACATGTACCAAAAAGTGACAT

                       **                 *
        772 GT--CACGCCATGTGTACCAAAAAGTGACAC
          1 GTGGCACGCCACATGTACCAAAAAGTGACAT

                  
        801 GTGGCA
          1 GTGGCA

        807 TGCCTCGTGC


Statistics
Matches: 111,  Mismatches: 15, Indels: 4
        0.85            0.12        0.03

Matches are distributed among these distances:
  29   25  0.23
  31   86  0.77

ACGTcount: A:0.35, C:0.27, G:0.22, T:0.16


Consensus pattern (31 bp):   
GTGGCACGCCACATGTACCAAAAAGTGACAT

Found at i:746 original size:62 final size:61

Alignment explanation


    Indices: 659--823  Score: 192
    Period size: 62  Copynumber: 2.7  Consensus size: 61

        649 TGGCATGCCA

                          *    *                                           
        659 CATGTACCAAAAAGCGACATGTGGCACGCCACGTGTACCAAAAAGCGACATGTGGCACACC-T
          1 CATGTACCAAAAAGTGACACGTGGCACGCCACGTGTACCAAAAAGCGACATGT--CACACCAT

                                *      *    *            *          *    
        721 CATGTACCAAAAAGTGACACATGGCACACCACATGTACCAAAAAGTGACATGTCACGCCAT
          1 CATGTACCAAAAAGTGACACGTGGCACGCCACGTGTACCAAAAAGCGACATGTCACACCAT

             *                        *   *    *        
        782 -GTGTACCAAAAAGTGACACGTGGCATGCCTCGTGCA-CAAAAA
          1 CATGTACCAAAAAGTGACACGTGGCACGCCACGTGTACCAAAAA

        824 TGACACGTGT


Statistics
Matches: 88,  Mismatches: 14, Indels: 5
        0.82            0.13        0.05

Matches are distributed among these distances:
  59    6  0.07
  60   34  0.39
  61    1  0.01
  62   47  0.53

ACGTcount: A:0.36, C:0.27, G:0.21, T:0.16


Consensus pattern (61 bp):   
CATGTACCAAAAAGTGACACGTGGCACGCCACGTGTACCAAAAAGCGACATGTCACACCAT

Done.