Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020283.1 Corchorus olitorius cultivar O-4 contig20316, 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: 3727
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.39


Found at i:1470 original size:31 final size:29

Alignment explanation


    Indices: 1435--1508  Score: 80
    Period size: 31  Copynumber: 2.6  Consensus size: 29

       1425 TTAATGCCCT

                                      *    
       1435 TTTTGCCCCCTGAACTTTTACGATTTTGACG
          1 TTTTGCCCCCTGAACTTTTA--ATTTGGACG

                    *  *               * 
       1466 TTTTGCCCTCTAAAC-TTTAATTTGGATG
          1 TTTTGCCCCCTGAACTTTTAATTTGGACG

                            
       1494 -TTTGCCCCCTGAACT
          1 TTTTGCCCCCTGAACT

       1509 CGCAATTTGG


Statistics
Matches: 36,  Mismatches: 6, Indels: 5
        0.77            0.13        0.11

Matches are distributed among these distances:
  27   12  0.33
  28    7  0.19
  30    4  0.11
  31   13  0.36

ACGTcount: A:0.18, C:0.26, G:0.15, T:0.42


Consensus pattern (29 bp):   
TTTTGCCCCCTGAACTTTTAATTTGGACG

Found at i:3087 original size:22 final size:22

Alignment explanation


    Indices: 3042--3088  Score: 58
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       3032 TTTTTAAACA

                  *           **  
       3042 TTTTTAGTAACCTTATAAGTTT
          1 TTTTTAATAACCTTATAAAATT

                      *           
       3064 TTTTTAATAATCTTATAAAATT
          1 TTTTTAATAACCTTATAAAATT

               
       3086 TTT
          1 TTT

       3089 AACACTTTTT


Statistics
Matches: 21,  Mismatches: 4, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.32, C:0.06, G:0.04, T:0.57


Consensus pattern (22 bp):   
TTTTTAATAACCTTATAAAATT

Found at i:3550 original size:23 final size:23

Alignment explanation


    Indices: 3505--3550  Score: 56
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       3495 ATAATAACTC

                              *    
       3505 TTTTAGTAATCTTAAAAGTTTTT
          1 TTTTAGTAATCTTAAAAGGTTTT

                 *    *   *        
       3528 TTTTATTAATTTTATAAGGTTTT
          1 TTTTAGTAATCTTAAAAGGTTTT

       3551 AGAAAGCATA


Statistics
Matches: 19,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  23   19  1.00

ACGTcount: A:0.28, C:0.02, G:0.09, T:0.61


Consensus pattern (23 bp):   
TTTTAGTAATCTTAAAAGGTTTT
Done.