Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021821.1 Corchorus olitorius cultivar O-4 contig21854, 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: 14372
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32


Found at i:31 original size:13 final size:12

Alignment explanation


    Indices: 5--38  Score: 50
    Period size: 13  Copynumber: 2.8  Consensus size: 12

          1 TTGT

                        
          5 TTTTTTCTTTTC
          1 TTTTTTCTTTTC

                *        
         17 TTTTCTCTTTCTC
          1 TTTTTTCTTT-TC

                     
         30 TTTTTTCTT
          1 TTTTTTCTT

         39 CAATGTAATG


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  12    9  0.47
  13   10  0.53

ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79


Consensus pattern (12 bp):   
TTTTTTCTTTTC

Found at i:660 original size:27 final size:27

Alignment explanation


    Indices: 585--662  Score: 102
    Period size: 27  Copynumber: 2.9  Consensus size: 27

        575 AGTGGACTTA

                   *            *  *   
        585 AAATGACCAAAATGCCCCTGAATATGC
          1 AAATGACAAAAATGCCCCTGGATGTGC

               *             *         
        612 AAACGACAAAAATGCCCATGGATGTGC
          1 AAATGACAAAAATGCCCCTGGATGTGC

                   *                
        639 AAATGACTAAAATGCCCCTGGATG
          1 AAATGACAAAAATGCCCCTGGATG

        663 ACTTACGTGC


Statistics
Matches: 43,  Mismatches: 8, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  27   43  1.00

ACGTcount: A:0.40, C:0.23, G:0.19, T:0.18


Consensus pattern (27 bp):   
AAATGACAAAAATGCCCCTGGATGTGC

Found at i:9901 original size:21 final size:21

Alignment explanation


    Indices: 9877--9923  Score: 60
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       9867 CCGCTGGGCG

                                  
       9877 CCCAGGCGA-AATGCCTCAGCA
          1 CCCAGGCGACAA-GCCTCAGCA

                         *      *
       9898 CCCAGGCGACAAGGCTCAGCG
          1 CCCAGGCGACAAGCCTCAGCA

                 
       9919 CCCAG
          1 CCCAG

       9924 CTCGATCCCT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  21   21  0.91
  22    2  0.09

ACGTcount: A:0.26, C:0.40, G:0.28, T:0.06


Consensus pattern (21 bp):   
CCCAGGCGACAAGCCTCAGCA
Done.