Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023666.1 Corchorus olitorius cultivar O-4 contig23699, 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: 18255
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Found at i:13156 original size:6 final size:6

Alignment explanation


    Indices: 13147--13229  Score: 53
    Period size: 6  Copynumber: 13.3  Consensus size: 6

      13137 AGAGAATGTT

                        *              *                    *       *
      13147 GAAGAA GAAGAG GAAG-A GAAAGAG GAAGAA -ATAGAA GAAGCA GAAGAG
          1 GAAGAA GAAGAA GAAGAA G-AAGAA GAAGAA GA-AGAA GAAGAA GAAGAA

                 *                    *             
      13195 GAAGAG GAAGAA GATATTGAA GATGAA GAAGAA GA
          1 GAAGAA GAAGAA GA-A--GAA GAAGAA GAAGAA GA

      13230 GAATGTATCT


Statistics
Matches: 60,  Mismatches: 10, Indels: 14
        0.71            0.12        0.17

Matches are distributed among these distances:
   5    2  0.03
   6   50  0.83
   7    3  0.05
   9    5  0.08

ACGTcount: A:0.57, C:0.01, G:0.36, T:0.06


Consensus pattern (6 bp):   
GAAGAA

Found at i:13162 original size:12 final size:12

Alignment explanation


    Indices: 13147--13205  Score: 59
    Period size: 12  Copynumber: 4.9  Consensus size: 12

      13137 AGAGAATGTT

                        
      13147 GAAGAAGAAGAG
          1 GAAGAAGAAGAG

                         
      13159 GAAG-AGAAAGAG
          1 GAAGAAG-AAGAG

                        *
      13171 GAAGAA-ATAGAA
          1 GAAGAAGA-AGAG

                *       
      13183 GAAGCAGAAGAG
          1 GAAGAAGAAGAG

                 *     
      13195 GAAGAGGAAGA
          1 GAAGAAGAAGA

      13206 AGATATTGAA


Statistics
Matches: 38,  Mismatches: 5, Indels: 8
        0.75            0.10        0.16

Matches are distributed among these distances:
  11    3  0.08
  12   33  0.87
  13    2  0.05

ACGTcount: A:0.58, C:0.02, G:0.39, T:0.02


Consensus pattern (12 bp):   
GAAGAAGAAGAG

Found at i:13183 original size:30 final size:30

Alignment explanation


    Indices: 13149--13206  Score: 91
    Period size: 30  Copynumber: 1.9  Consensus size: 30

      13139 AGAATGTTGA

                                           
      13149 AGAAGAAG-AGGAAGAGAAAGAGGAAGAAAT
          1 AGAAGAAGCA-GAAGAGAAAGAGGAAGAAAT

                            *           
      13179 AGAAGAAGCAGAAGAGGAAGAGGAAGAA
          1 AGAAGAAGCAGAAGAGAAAGAGGAAGAA

      13207 GATATTGAAG


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  30   25  0.96
  31    1  0.04

ACGTcount: A:0.59, C:0.02, G:0.38, T:0.02


Consensus pattern (30 bp):   
AGAAGAAGCAGAAGAGAAAGAGGAAGAAAT

Done.