Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001205.1 Corchorus olitorius cultivar O-4 contig01205, 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, 600

Length: 1000
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.39


Found at i:217 original size:39 final size:40

Alignment explanation


    Indices: 171--251  Score: 137
    Period size: 39  Copynumber: 2.0  Consensus size: 40

        161 ATATCTAAGA

                                                    
        171 ATTTAATTAATGTAAGTATTTCAGTTATTA-TAATATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTACTAATATTAC

                                 *          *       
        210 ATTTAATTAATGTAAGTATTTTAGTTATTACTTATATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTACTAATATTAC

              
        250 AT
          1 AT

        252 AGGAATTAAA


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  39   29  0.74
  40   10  0.26

ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51


Consensus pattern (40 bp):   
ATTTAATTAATGTAAGTATTTCAGTTATTACTAATATTAC

Found at i:239 original size:21 final size:21

Alignment explanation


    Indices: 176--239  Score: 64
    Period size: 21  Copynumber: 3.2  Consensus size: 21

        166 TAAGAATTTA

                                 
        176 ATTAATGTAAGTATTTCAGTT
          1 ATTAATGTAAGTATTTCAGTT

                           *  *  
        197 ATT-A--TAA-TATTACATTT
          1 ATTAATGTAAGTATTTCAGTT

                             *    
        214 AATTAATGTAAGTATTTTAGTT
          1 -ATTAATGTAAGTATTTCAGTT

                
        236 ATTA
          1 ATTA

        240 CTTATATTAC


Statistics
Matches: 33,  Mismatches: 5, Indels: 10
        0.69            0.10        0.21

Matches are distributed among these distances:
  17    8  0.24
  18    6  0.18
  19    1  0.03
  20    1  0.03
  21   10  0.30
  22    7  0.21

ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50


Consensus pattern (21 bp):   
ATTAATGTAAGTATTTCAGTT
Done.