Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003649.1 Corchorus capsularis cultivar CVL-1 contig03657, 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, 618

Length: 1031
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29


Found at i:117 original size:19 final size:20

Alignment explanation


    Indices: 71--118  Score: 62
    Period size: 22  Copynumber: 2.4  Consensus size: 20

         61 TGTGGCACGC

                                 *
         71 CACATGTACCAAAAAGTCGTGC
          1 CACATGTACCAAAAA--CGTGA

                                
         93 CACATGTACCAAAAA-GTGA
          1 CACATGTACCAAAAACGTGA

                   
        112 CACATGT
          1 CACATGT

        119 CACGCCACGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  19   10  0.40
  22   15  0.60

ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19


Consensus pattern (20 bp):   
CACATGTACCAAAAACGTGA

Found at i:123 original size:53 final size:53

Alignment explanation


    Indices: 38--140  Score: 161
    Period size: 53  Copynumber: 1.9  Consensus size: 53

         28 GACGTGGCAC

                 *                 **                            
         38 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTCGT
          1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT

                                       *        *             
         91 GCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAAAGT
          1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGT

        141 GACATATGGC


Statistics
Matches: 45,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  53   45  1.00

ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17


Consensus pattern (53 bp):   
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT

Found at i:157 original size:31 final size:31

Alignment explanation


    Indices: 90--188  Score: 117
    Period size: 31  Copynumber: 3.2  Consensus size: 31

         80 CAAAAAGTCG

                                        *  
         90 TGCCACATGTACCAAAAAGTGACACATGTCA
          1 TGCCACATGTACCAAAAAGTGACACATGGCA

            *     *                 *      
        121 CGCCACGTGTACCAAAAAGTGACATATGGCA
          1 TGCCACATGTACCAAAAAGTGACACATGGCA

                      **      *  *   *     
        152 TGCCACATGTTTCAAAAAATGGCACGTGGCA
          1 TGCCACATGTACCAAAAAGTGACACATGGCA

                  
        183 TGCCAC
          1 TGCCAC

        189 GTGCACAAAA


Statistics
Matches: 56,  Mismatches: 12, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  31   56  1.00

ACGTcount: A:0.34, C:0.26, G:0.20, T:0.19


Consensus pattern (31 bp):   
TGCCACATGTACCAAAAAGTGACACATGGCA
Done.