Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007315.1 Corchorus olitorius cultivar O-4 contig07340, 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: 13960
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:4728 original size:3 final size:3

Alignment explanation


    Indices: 4720--4745  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

       4710 TTATATTACA

                                              
       4720 TTC TTC TTC TTC TTC TTC TTC TTC TT
          1 TTC TTC TTC TTC TTC TTC TTC TTC TT

       4746 TTTTTTTTTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69


Consensus pattern (3 bp):   
TTC

Found at i:9576 original size:32 final size:32

Alignment explanation


    Indices: 9535--9599  Score: 130
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       9525 TTTACCACCA

                                            
       9535 GGAAGCGCCTTTTTCTATAAAGCAAACAATAG
          1 GGAAGCGCCTTTTTCTATAAAGCAAACAATAG

                                            
       9567 GGAAGCGCCTTTTTCTATAAAGCAAACAATAG
          1 GGAAGCGCCTTTTTCTATAAAGCAAACAATAG

             
       9599 G
          1 G

       9600 CGGGCGTTTG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   33  1.00

ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25


Consensus pattern (32 bp):   
GGAAGCGCCTTTTTCTATAAAGCAAACAATAG

Found at i:13727 original size:29 final size:30

Alignment explanation


    Indices: 13693--13771  Score: 99
    Period size: 29  Copynumber: 2.7  Consensus size: 30

      13683 GCTAAATACC

                                      *    
      13693 CAAAA-AATCCCTTATGTTTTGTTTTTGGGA
          1 CAAAATAATCCCTTATGTTTT-TTTTCGGGA

                       *                  
      13723 CAAAATAATCCTTTATG-TTTTTTTCGGGA
          1 CAAAATAATCCCTTATGTTTTTTTTCGGGA

                *          *    
      13752 CAAATTAATCCCTTACGTTT
          1 CAAAATAATCCCTTATGTTT

      13772 CAAAAATGAG


Statistics
Matches: 42,  Mismatches: 5, Indels: 4
        0.82            0.10        0.08

Matches are distributed among these distances:
  29   22  0.52
  30   10  0.24
  31   10  0.24

ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43


Consensus pattern (30 bp):   
CAAAATAATCCCTTATGTTTTTTTTCGGGA

Done.