Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024758.1 Corchorus olitorius cultivar O-4 contig24791, 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: 15236
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:5482 original size:11 final size:11

Alignment explanation


    Indices: 5439--5476  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       5429 TTCCTATATA

                *      
       5439 AAATAAATTAT
          1 AAATTAATTAT

                        
       5450 CAAA-TAATTAT
          1 -AAATTAATTAT

                       
       5461 AAATTAATTAT
          1 AAATTAATTAT

                 
       5472 AAATT
          1 AAATT

       5477 TGTTATTAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  10    3  0.12
  11   18  0.75
  12    3  0.12

ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39


Consensus pattern (11 bp):   
AAATTAATTAT

Found at i:9675 original size:30 final size:29

Alignment explanation


    Indices: 9621--9677  Score: 78
    Period size: 29  Copynumber: 1.9  Consensus size: 29

       9611 CATCAAATTT

                             *           
       9621 TATTTTATTTTGATCACTTTGCACCCTAA
          1 TATTTTATTTTGATCACATTGCACCCTAA

                       **               
       9650 TATTTTATTTTTTTCCACATTGCACCCT
          1 TATTTTATTTTGAT-CACATTGCACCCT

       9678 GTGTTACGGT


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  29   12  0.50
  30   12  0.50

ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51


Consensus pattern (29 bp):   
TATTTTATTTTGATCACATTGCACCCTAA

Found at i:10213 original size:29 final size:30

Alignment explanation


    Indices: 10180--10241  Score: 81
    Period size: 29  Copynumber: 2.1  Consensus size: 30

      10170 AATTTGTATG

                    *    *                
      10180 TTTTGGACGTTTTGCCCCATGAACT-TCAA
          1 TTTTGGACATTTTCCCCCATGAACTCTCAA

                   *          *           
      10209 TTTTGGATATTTTCCCCCTTGAACTCTCAA
          1 TTTTGGACATTTTCCCCCATGAACTCTCAA

               
      10239 TTT
          1 TTT

      10242 GAAGCCCCGT


Statistics
Matches: 28,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  29   21  0.75
  30    7  0.25

ACGTcount: A:0.19, C:0.24, G:0.13, T:0.44


Consensus pattern (30 bp):   
TTTTGGACATTTTCCCCCATGAACTCTCAA

Done.