Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016156.1 Corchorus olitorius cultivar O-4 contig16189, 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: 2375
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32


Found at i:599 original size:24 final size:24

Alignment explanation


    Indices: 572--632  Score: 77
    Period size: 24  Copynumber: 2.5  Consensus size: 24

        562 CGCGGCCCAA

                    *               
        572 GCGCGTGGCCCAGCGCCAGGCCAG
          1 GCGCGTGGGCCAGCGCCAGGCCAG

                 *           *    * 
        596 GCGCGCGGGCCAGCGCCTGGCCCG
          1 GCGCGTGGGCCAGCGCCAGGCCAG

                *        
        620 GCGCCTGGGCCAG
          1 GCGCGTGGGCCAG

        633 GCTTCGGCCC


Statistics
Matches: 31,  Mismatches: 6, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  24   31  1.00

ACGTcount: A:0.08, C:0.43, G:0.44, T:0.05


Consensus pattern (24 bp):   
GCGCGTGGGCCAGCGCCAGGCCAG

Found at i:603 original size:37 final size:37

Alignment explanation


    Indices: 561--634  Score: 96
    Period size: 36  Copynumber: 2.0  Consensus size: 37

        551 GGCCAGAAGG

                           *                      
        561 GCGCGGCCCAAGCGCGTGGCCCAGCGCC-AGGCCAGGC
          1 GCGCGGCCC-AGCGCCTGGCCCAGCGCCTAGGCCAGGC

                  *              *      *        
        598 GCGCGGGCCAGCGCCTGGCCCGGCGCCTGGGCCAGGC
          1 GCGCGGCCCAGCGCCTGGCCCAGCGCCTAGGCCAGGC

        635 TTCGGCCCTA


Statistics
Matches: 32,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  36   16  0.50
  37   16  0.50

ACGTcount: A:0.09, C:0.43, G:0.43, T:0.04


Consensus pattern (37 bp):   
GCGCGGCCCAGCGCCTGGCCCAGCGCCTAGGCCAGGC

Found at i:625 original size:12 final size:12

Alignment explanation


    Indices: 565--632  Score: 50
    Period size: 12  Copynumber: 5.6  Consensus size: 12

        555 AGAAGGGCGC

                       * 
        565 GGCCCAAGCGCGT
          1 GGCCC-AGCGCCT

                       *
        578 GGCCCAGCGCCA
          1 GGCCCAGCGCCT

                          
        590 GG-CCAGGCGCGC-
          1 GGCCCA-GCGC-CT

              *         
        602 GGGCCAGCGCCT
          1 GGCCCAGCGCCT

                 *      
        614 GGCCCGGCGCCT
          1 GGCCCAGCGCCT

              *    
        626 GGGCCAG
          1 GGCCCAG

        633 GCTTCGGCCC


Statistics
Matches: 45,  Mismatches: 6, Indels: 9
        0.75            0.10        0.15

Matches are distributed among these distances:
  11    4  0.09
  12   32  0.71
  13    9  0.20

ACGTcount: A:0.10, C:0.43, G:0.43, T:0.04


Consensus pattern (12 bp):   
GGCCCAGCGCCT
Done.