Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001067.1 Corchorus olitorius cultivar O-4 contig01067, 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, 969

Length: 1615
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38


Found at i:233 original size:14 final size:13

Alignment explanation


    Indices: 216--254  Score: 51
    Period size: 14  Copynumber: 2.9  Consensus size: 13

        206 AAAATGTAAA

                         
        216 ATTTAAAAAATTT
          1 ATTTAAAAAATTT

                   *    * 
        229 CATTTAAGAAATAT
          1 -ATTTAAAAAATTT

                        
        243 ATTTAAAAAATT
          1 ATTTAAAAAATT

        255 CTAATATATA


Statistics
Matches: 21,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  13   10  0.48
  14   11  0.52

ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41


Consensus pattern (13 bp):   
ATTTAAAAAATTT

Found at i:453 original size:123 final size:129

Alignment explanation


    Indices: 240--497  Score: 411
    Period size: 123  Copynumber: 2.0  Consensus size: 129

        230 ATTTAAGAAA

                                                                             
        240 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTTAATTTAAAATAGTAAAATGGTAAAAATA
          1 TATATTTAAAAAATTCTAATATATATAAG-TTTTTTTAATTTAAAATAGTAAAATGGTAAAAAT-

                                                                          *  
        305 AAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTA
         64 --ATA-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATA

                
        370 AAAG
        126 AAAG

                                                                             
        374 TATATTTAAAAAATTCTAATATATATAAG-TTTTTTAA-TTAAAATAGTAAAATGGTAAAAAT-T
          1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTTAAAATAGTAAAATGGTAAAAATAT

                           *                                                
        436 A-TA-AA-GATATTATATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
         66 AGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG

             
        497 T
          1 T

        498 TTAAACAATG


Statistics
Matches: 122,  Mismatches: 2, Indels: 11
        0.90            0.01        0.08

Matches are distributed among these distances:
 123   55  0.45
 124    2  0.02
 125    2  0.02
 127    2  0.02
 131   24  0.20
 132    8  0.07
 134   29  0.24

ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39


Consensus pattern (129 bp):   
TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTTAAAATAGTAAAATGGTAAAAATAT
AGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG

Done.