Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018158.1 Corchorus olitorius cultivar O-4 contig18191, 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: 7748
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:611 original size:29 final size:30

Alignment explanation


    Indices: 567--683  Score: 96
    Period size: 29  Copynumber: 3.9  Consensus size: 30

        557 TCCTACAGGC

                                        *  
        567 CCCTCTACTTAAAAAAA-GGATCAATTTGGT
          1 CCCTCTACTTAAAAAAATGG-TCAATTTAGT

                       *      *           
        597 CCCTCTA-TTATAAAAATTGTCAATTTAGT
          1 CCCTCTACTTAAAAAAATGGTCAATTTAGT

                        *  **           *   
        626 CCCTCTACTT-ACAATTTGGTGTCAATTGAGT
          1 CCCTCTACTTAAAAAAAT-G-GTCAATTTAGT

                        *      *       
        657 CCCTCTACTTAACAAAATCCGTCAATT
          1 CCCTCTACTTAAAAAAAT-GGTCAATT

        684 GATTATATAT


Statistics
Matches: 69,  Mismatches: 13, Indels: 9
        0.76            0.14        0.10

Matches are distributed among these distances:
  29   27  0.39
  30   10  0.14
  31   27  0.39
  32    5  0.07

ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35


Consensus pattern (30 bp):   
CCCTCTACTTAAAAAAATGGTCAATTTAGT

Found at i:681 original size:31 final size:30

Alignment explanation


    Indices: 567--685  Score: 95
    Period size: 31  Copynumber: 3.9  Consensus size: 30

        557 TCCTACAGGC

                             **             
        567 CCCTCTACTTAA-AAAAAGGATCAATTTG-GT
          1 CCCTCTACTTAACAAAATTG-TCAA-TTGAGT

                                       *   
        597 CCCTCTA-TTATA-AAAATTGTCAATTTAGT
          1 CCCTCTACTTA-ACAAAATTGTCAATTGAGT

                           **               
        626 CCCTCTACTT-ACAATTTGGTGTCAATTGAGT
          1 CCCTCTACTTAACAAAAT--TGTCAATTGAGT

                               *         
        657 CCCTCTACTTAACAAAATCCGTCAATTGA
          1 CCCTCTACTTAACAAAAT-TGTCAATTGA

        686 TTATATATTT


Statistics
Matches: 72,  Mismatches: 10, Indels: 13
        0.76            0.11        0.14

Matches are distributed among these distances:
  28    3  0.04
  29   19  0.26
  30   15  0.21
  31   30  0.42
  32    5  0.07

ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34


Consensus pattern (30 bp):   
CCCTCTACTTAACAAAATTGTCAATTGAGT
Done.