Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014347.1 Corchorus olitorius cultivar O-4 contig14380, 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: 3359
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34


Found at i:253 original size:30 final size:29

Alignment explanation


    Indices: 187--259  Score: 87
    Period size: 29  Copynumber: 2.5  Consensus size: 29

        177 TACACAAAAC

                            *           * 
        187 GGCCAAATAAGCCCCTGAACTCTAATTGCA
          1 GGCCAAATAAGCCCCTCAACTCTAA-TGAA

                                           
        217 -GCCAAATAAGCCCCTCAACTCTTAA-GAAA
          1 GGCCAAATAAGCCCCTCAACTC-TAATG-AA

                          
        246 GGCCAAATAAGCCC
          1 GGCCAAATAAGCCC

        260 TTTTCATATG


Statistics
Matches: 38,  Mismatches: 2, Indels: 6
        0.83            0.04        0.13

Matches are distributed among these distances:
  28    1  0.03
  29   21  0.55
  30   16  0.42

ACGTcount: A:0.37, C:0.32, G:0.15, T:0.16


Consensus pattern (29 bp):   
GGCCAAATAAGCCCCTCAACTCTAATGAA

Found at i:735 original size:34 final size:35

Alignment explanation


    Indices: 691--756  Score: 107
    Period size: 34  Copynumber: 1.9  Consensus size: 35

        681 CGGTCAGAAA

                           *                   
        691 AGGGTTTATTTGGCTTAAATTAGAGTTGAGGGTTT
          1 AGGGTTTATTTGGCTGAAATTAGAGTTGAGGGTTT

                            *               
        726 AGGG-TTATTTGGCTGCAATTAGAGTTGAGGG
          1 AGGGTTTATTTGGCTGAAATTAGAGTTGAGGG

        757 GCTTATTTGG


Statistics
Matches: 29,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  34   25  0.86
  35    4  0.14

ACGTcount: A:0.23, C:0.05, G:0.35, T:0.38


Consensus pattern (35 bp):   
AGGGTTTATTTGGCTGAAATTAGAGTTGAGGGTTT
Done.