Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019220.1 Corchorus olitorius cultivar O-4 contig19253, 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: 14190
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31


Found at i:706 original size:94 final size:88

Alignment explanation


    Indices: 511--695  Score: 262
    Period size: 94  Copynumber: 2.0  Consensus size: 88

        501 AACTTTTTTT

                          *                                **                
        511 CAAGAAAATTTTTATTATTTTCGAAAAAAAGTTAATATGTTACAAAATTTTTAAAAGGTCATAAA
          1 CAAGAAAATTTTTAGTATTTTCGAAAAAAAGTTAATATGTTACAAAAAATTTAAAAGGTCATAAA

                                   
        576 TGACTTGATTAGAGTATTAATTA
         66 TGACTTGATTAGAGTATTAATTA

                                                                      *      
        599 CAAGAAAATTTTTAGTATTTTCGAAATAAAAGTTAATACTATGTTACAAAAAAAATTTCAAAGGT
          1 CAAGAAAATTTTTAGTATTTTCGAAA-AAAAGTT-A-A-TATGTTAC--AAAAAATTTAAAAGGT

                     *              *    
        664 CATAAATGATTTGATTAGAGTATTGATTA
         60 CATAAATGACTTGATTAGAGTATTAATTA

               
        693 CAA
          1 CAA

        696 TTAGAATTTT


Statistics
Matches: 85,  Mismatches: 6, Indels: 6
        0.88            0.06        0.06

Matches are distributed among these distances:
  88   25  0.29
  89    7  0.08
  90    1  0.01
  91    1  0.01
  92    8  0.09
  94   43  0.51

ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37


Consensus pattern (88 bp):   
CAAGAAAATTTTTAGTATTTTCGAAAAAAAGTTAATATGTTACAAAAAATTTAAAAGGTCATAAA
TGACTTGATTAGAGTATTAATTA

Found at i:3641 original size:18 final size:19

Alignment explanation


    Indices: 3602--3641  Score: 55
    Period size: 21  Copynumber: 2.1  Consensus size: 19

       3592 GTGCTTCCGT

                                 
       3602 TGTGATGCTCCCACTTTTCAA
          1 TGTGATGCTCCCA--TTTCAA

                               
       3623 TGTGATGCTCCCA-TTCAA
          1 TGTGATGCTCCCATTTCAA

             
       3641 T
          1 T

       3642 TCTGACCATT


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  18    6  0.32
  21   13  0.68

ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38


Consensus pattern (19 bp):   
TGTGATGCTCCCATTTCAA

Found at i:9410 original size:2 final size:2

Alignment explanation


    Indices: 9403--9433  Score: 55
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       9393 ATGAAGTTGC

                                                           
       9403 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       9434 AAAGCCATAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   27  0.96

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
TA

Done.