Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000626.1 Corchorus capsularis cultivar CVL-1 contig00626, 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, 610

Length: 1017
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37


Found at i:258 original size:30 final size:30

Alignment explanation


    Indices: 222--299  Score: 90
    Period size: 29  Copynumber: 2.6  Consensus size: 30

        212 CATCAGAAAA

                                           
        222 GGGCTTATTTGGCCTTTTTAA-AGAGTTCAG
          1 GGGCTTATTTGGCC-TTTTAATAGAGTTCAG

                            **             
        252 GGGCTTATTTGG-C-TGCAATTAGAGTTCAG
          1 GGGCTTATTTGGCCTTTTAA-TAGAGTTCAG

                               
        281 GGGCTTATTTGGCCGTTTT
          1 GGGCTTATTTGGCC-TTTT

        300 GTGTAAGTTC


Statistics
Matches: 39,  Mismatches: 4, Indels: 8
        0.76            0.08        0.16

Matches are distributed among these distances:
  27    3  0.08
  29   22  0.56
  30   13  0.33
  32    1  0.03

ACGTcount: A:0.17, C:0.14, G:0.29, T:0.40


Consensus pattern (30 bp):   
GGGCTTATTTGGCCTTTTAATAGAGTTCAG

Found at i:391 original size:52 final size:52

Alignment explanation


    Indices: 334--492  Score: 189
    Period size: 52  Copynumber: 3.1  Consensus size: 52

        324 GCAATAAGCC

                          *                *                    
        334 TTTTATTTACTAATCACTCTAAAAAATTCAACCTTTTATCCAAAGATGACAT
          1 TTTTATTTACTAATTACTCTAAAAAATTCAATCTTTTATCCAAAGATGACAT

                      *                *            *     * *   *
        386 TTTTATTTACCAATTACT-TAAAAAAAATCAATCTTTTATTCAAAGGTTACAA
          1 TTTTATTTACTAATTACTCT-AAAAAATTCAATCTTTTATCCAAAGATGACAT

                                              *      *           
        438 TTTTATTTACTAATTACTCT-AAAAATTCAATCTCTTA-CTTAAAGATGACAT
          1 TTTTATTTACTAATTACTCTAAAAAATTCAATCTTTTATC-CAAAGATGACAT

                
        489 TTTT
          1 TTTT

        493 TACTTAAGTT


Statistics
Matches: 88,  Mismatches: 16, Indels: 7
        0.79            0.14        0.06

Matches are distributed among these distances:
  51   28  0.32
  52   59  0.67
  53    1  0.01

ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42


Consensus pattern (52 bp):   
TTTTATTTACTAATTACTCTAAAAAATTCAATCTTTTATCCAAAGATGACAT

Done.