Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015798.1 Corchorus capsularis cultivar CVL-1 contig15819, 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: 6083
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29


Found at i:2694 original size:23 final size:23

Alignment explanation


    Indices: 2645--2698  Score: 74
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       2635 AAAGGATCAT

                                  *
       2645 GTGGCCGGGCATGGCCGAGTCAT
          1 GTGGCCGGGCATGGCCGAGTCAC

                                  * 
       2668 GTGGCCGGGCATGGCC-ATGTCGC
          1 GTGGCCGGGCATGGCCGA-GTCAC

                    
       2691 GTGGCCGG
          1 GTGGCCGG

       2699 TGATGGTCGA


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  22    1  0.04
  23   27  0.96

ACGTcount: A:0.09, C:0.28, G:0.46, T:0.17


Consensus pattern (23 bp):   
GTGGCCGGGCATGGCCGAGTCAC

Found at i:2724 original size:33 final size:32

Alignment explanation


    Indices: 2667--2798  Score: 165
    Period size: 33  Copynumber: 4.0  Consensus size: 32

       2657 GGCCGAGTCA

                 *       **   *             
       2667 TGTGGCCGGGCATGGCCATGTCGCGTGGCCGG
          1 TGTGGTCGGGCATCTCCAAGTCGCGTGGCCGG

                     *                       
       2699 TGATGGTCGAGCATCTCCAAGTCGCGTGGCCGG
          1 TG-TGGTCGGGCATCTCCAAGTCGCGTGGCCGG

                 **                          
       2732 TGTTGCACGGGCATCTCCAAGTCGCGTGGCCGG
          1 TG-TGGTCGGGCATCTCCAAGTCGCGTGGCCGG

               *                             
       2765 TGTTGTACGGGCATCTCCAAGTCGCGTGGCCGG
          1 TGTGGT-CGGGCATCTCCAAGTCGCGTGGCCGG

             
       2798 T
          1 T

       2799 CACAAGTGCT


Statistics
Matches: 86,  Mismatches: 12, Indels: 3
        0.85            0.12        0.03

Matches are distributed among these distances:
  32    3  0.03
  33   83  0.97

ACGTcount: A:0.11, C:0.28, G:0.39, T:0.22


Consensus pattern (32 bp):   
TGTGGTCGGGCATCTCCAAGTCGCGTGGCCGG
Done.