Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002145.1 Corchorus olitorius cultivar O-4 contig02145, 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, 660

Length: 1100
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28


Found at i:310 original size:3 final size:3

Alignment explanation


    Indices: 302--360  Score: 118
    Period size: 3  Copynumber: 19.7  Consensus size: 3

        292 AATTTTACAT

                                                                           
        302 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

                          
        350 TTA TTA TTA TT
          1 TTA TTA TTA TT

        361 TTTACACTAA


Statistics
Matches: 56,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   56  1.00

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (3 bp):   
TTA

Found at i:612 original size:13 final size:13

Alignment explanation


    Indices: 594--625  Score: 55
    Period size: 13  Copynumber: 2.5  Consensus size: 13

        584 GAAGCAGCAA

                         
        594 CAAGGCTGCTCAG
          1 CAAGGCTGCTCAG

                       * 
        607 CAAGGCTGCTCCG
          1 CAAGGCTGCTCAG

                  
        620 CAAGGC
          1 CAAGGC

        626 CGCCACAGCA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   18  1.00

ACGTcount: A:0.22, C:0.34, G:0.31, T:0.12


Consensus pattern (13 bp):   
CAAGGCTGCTCAG

Found at i:648 original size:27 final size:27

Alignment explanation


    Indices: 617--682  Score: 87
    Period size: 27  Copynumber: 2.4  Consensus size: 27

        607 CAAGGCTGCT

                                      *
        617 CCGCAAGGCCGCCACAGCACCAGCAGT
          1 CCGCAAGGCCGCCACAGCACCAGCAGC

            *        *   *    *        
        644 TCGCAAGGCTGCCCCAGCTCCAGCAGC
          1 CCGCAAGGCCGCCACAGCACCAGCAGC

                        
        671 CCGCAAGGCCGC
          1 CCGCAAGGCCGC

        683 TAACAGCAGC


Statistics
Matches: 32,  Mismatches: 7, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  27   32  1.00

ACGTcount: A:0.21, C:0.45, G:0.27, T:0.06


Consensus pattern (27 bp):   
CCGCAAGGCCGCCACAGCACCAGCAGC
Done.