Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016224.1 Corchorus olitorius cultivar O-4 contig16257, 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: 23812
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:2688 original size:31 final size:32

Alignment explanation


    Indices: 2633--2692  Score: 86
    Period size: 31  Copynumber: 1.9  Consensus size: 32

       2623 CTACATCTGC

                      *        *            
       2633 GGCGTTTTTTTTGAAAAACGCCATTGATTCAT
          1 GGCGTTTTTTATGAAAAACACCATTGATTCAT

                          *              
       2665 GGCGTTTTTTATG-TAAACACCATTGATT
          1 GGCGTTTTTTATGAAAAACACCATTGATT

       2693 GTTGAAATTA


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

Matches are distributed among these distances:
  31   13  0.52
  32   12  0.48

ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42


Consensus pattern (32 bp):   
GGCGTTTTTTATGAAAAACACCATTGATTCAT

Found at i:8947 original size:2 final size:2

Alignment explanation


    Indices: 8940--8973  Score: 52
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       8930 AAATTTATTG

                                                               
       8940 TA TA TA TA TGA TA TA TA -A TA TA TA TA TA TA TA TA
          1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA

       8974 GTAACTTATA


Statistics
Matches: 30,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   1    1  0.03
   2   27  0.90
   3    2  0.07

ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:15394 original size:3 final size:3

Alignment explanation


    Indices: 15379--15413  Score: 61
    Period size: 3  Copynumber: 11.7  Consensus size: 3

      15369 GATATCTTAT

                    *                                     
      15379 TTG TTG GTG TTG TTG TTG TTG TTG TTG TTG TTG TT
          1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT

      15414 TGTGTCTCGC


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   3   30  1.00

ACGTcount: A:0.00, C:0.00, G:0.34, T:0.66


Consensus pattern (3 bp):   
TTG

Done.