Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014666.1 Corchorus olitorius cultivar O-4 contig14699, 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: 10316
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Found at i:1775 original size:51 final size:51

Alignment explanation


    Indices: 1713--1820  Score: 207
    Period size: 51  Copynumber: 2.1  Consensus size: 51

       1703 CATTTATAAA

                              *                                
       1713 TTAATTAGACACAAATTTGTATGAATGTAAAGTAAGGGTATGTTGGTCTTT
          1 TTAATTAGACACAAATTTATATGAATGTAAAGTAAGGGTATGTTGGTCTTT

                                                               
       1764 TTAATTAGACACAAATTTATATGAATGTAAAGTAAGGGTATGTTGGTCTTT
          1 TTAATTAGACACAAATTTATATGAATGTAAAGTAAGGGTATGTTGGTCTTT

                  
       1815 TTAATT
          1 TTAATT

       1821 GTTATTCCTT


Statistics
Matches: 56,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  51   56  1.00

ACGTcount: A:0.34, C:0.06, G:0.19, T:0.41


Consensus pattern (51 bp):   
TTAATTAGACACAAATTTATATGAATGTAAAGTAAGGGTATGTTGGTCTTT

Found at i:6441 original size:3 final size:3

Alignment explanation


    Indices: 6433--6497  Score: 94
    Period size: 3  Copynumber: 21.7  Consensus size: 3

       6423 TAGTTCTGCC

                                                                        *  
       6433 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT CCT
          1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT

             **         *         
       6481 TGG TCT TCT CCT TCT TC
          1 TCT TCT TCT TCT TCT TC

       6498 GACTTTCTCT


Statistics
Matches: 54,  Mismatches: 8, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
   3   54  1.00

ACGTcount: A:0.00, C:0.35, G:0.03, T:0.62


Consensus pattern (3 bp):   
TCT

Found at i:9376 original size:19 final size:19

Alignment explanation


    Indices: 9343--9379  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       9333 GCTGCTCTAA

                     **        
       9343 TAATCTCATTTGTACAGTG
          1 TAATCTCATCCGTACAGTG

                              
       9362 TAATCTCATCCGTACAGT
          1 TAATCTCATCCGTACAGT

       9380 TACCAAACAG


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  19   16  1.00

ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38


Consensus pattern (19 bp):   
TAATCTCATCCGTACAGTG

Found at i:9984 original size:5 final size:5

Alignment explanation


    Indices: 9973--10004  Score: 55
    Period size: 5  Copynumber: 6.4  Consensus size: 5

       9963 ATATAATATA

                    *                             
       9973 CTCTG CTTTG CTCTG CTCTG CTCTG CTCTG CT
          1 CTCTG CTCTG CTCTG CTCTG CTCTG CTCTG CT

      10005 TGCCATCATC


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   5   25  1.00

ACGTcount: A:0.00, C:0.38, G:0.19, T:0.44


Consensus pattern (5 bp):   
CTCTG

Done.