Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024777.1 Corchorus olitorius cultivar O-4 contig24810, 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: 3539
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.37


Found at i:2668 original size:15 final size:15

Alignment explanation


    Indices: 2637--2678  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       2627 TTACTTTGCT

                      *     
       2637 TTGTTTTCTACTTTAA
          1 TTGTTTTCT-GTTTAA

                           
       2653 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
       2668 TTGCTTTCTGT
          1 TTGTTTTCTGT

       2679 CAATTTCTGT


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  15   15  0.62
  16    9  0.38

ACGTcount: A:0.12, C:0.12, G:0.12, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:2954 original size:29 final size:29

Alignment explanation


    Indices: 2851--2952  Score: 177
    Period size: 30  Copynumber: 3.4  Consensus size: 29

       2841 TTTGACGCCG

                                         
       2851 TTGCCGGGGAAGGGAACTTTTTCTGGTAT
          1 TTGCCGGGGAAGGGAACTTTTTCTGGTAT

                                          
       2880 TTGCCGGGGAAGGGTAACTTTTTCTGGTAT
          1 TTGCCGGGGAAGGG-AACTTTTTCTGGTAT

                                       * 
       2910 TTGCCGGGGAAGGGAACTTTTTCTGGTTT
          1 TTGCCGGGGAAGGGAACTTTTTCTGGTAT

                          
       2939 TTGCCAGGGGAAGG
          1 TTGCC-GGGGAAGG

       2953 AAAATAGACT


Statistics
Matches: 70,  Mismatches: 1, Indels: 3
        0.95            0.01        0.04

Matches are distributed among these distances:
  29   33  0.47
  30   37  0.53

ACGTcount: A:0.17, C:0.14, G:0.36, T:0.33


Consensus pattern (29 bp):   
TTGCCGGGGAAGGGAACTTTTTCTGGTAT
Done.