Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018618.1 Corchorus olitorius cultivar O-4 contig18651, 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: 3451
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31


Found at i:610 original size:27 final size:27

Alignment explanation


    Indices: 534--629  Score: 120
    Period size: 27  Copynumber: 3.5  Consensus size: 27

        524 AAAGTACTTG

                   *              *    
        534 AAATGACTAAAATGCCCCTGGACATGC
          1 AAATGACCAAAATGCCCCTGGATATGC

                           *       *   
        561 AAATGACCAAAATGCGCCTGGATGTGC
          1 AAATGACCAAAATGCCCCTGGATATGC

                                    *  *
        588 AAATGACCAAAATGCCCCTGGATTTTGA
          1 AAATGACCAAAATGCCCCTGGA-TATGC

                          
        616 AAATGACCCAAAAT
          1 AAATGA-CCAAAAT

        630 TCCCTTAGAT


Statistics
Matches: 60,  Mismatches: 7, Indels: 2
        0.87            0.10        0.03

Matches are distributed among these distances:
  27   44  0.73
  28    9  0.15
  29    7  0.12

ACGTcount: A:0.39, C:0.23, G:0.19, T:0.20


Consensus pattern (27 bp):   
AAATGACCAAAATGCCCCTGGATATGC

Found at i:2209 original size:35 final size:35

Alignment explanation


    Indices: 2165--2236  Score: 117
    Period size: 35  Copynumber: 2.1  Consensus size: 35

       2155 GAATAGGGAC

                *      *      *                
       2165 AGAGGCCAAAATGTTAAAGCCCAATGAAAATAATT
          1 AGAGCCCAAAAGGTTAAAACCCAATGAAAATAATT

                                               
       2200 AGAGCCCAAAAGGTTAAAACCCAATGAAAATAATT
          1 AGAGCCCAAAAGGTTAAAACCCAATGAAAATAATT

              
       2235 AG
          1 AG

       2237 GTTTTGTTAA


Statistics
Matches: 34,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  35   34  1.00

ACGTcount: A:0.50, C:0.15, G:0.17, T:0.18


Consensus pattern (35 bp):   
AGAGCCCAAAAGGTTAAAACCCAATGAAAATAATT
Done.