Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000001.1 Corchorus olitorius cultivar O-4 contig00001, 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, 985

Length: 1642
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36


Found at i:334 original size:53 final size:53

Alignment explanation


    Indices: 251--359  Score: 123
    Period size: 53  Copynumber: 2.1  Consensus size: 53

        241 AAAAAGCTCT

                             *       *     ***                    
        251 TAAGATTACTAAAAGAGTTATTAAGTAGTTTTCTAAAGTTATTAAAA-AAATTA
          1 TAAGATTACTAAAAGAGCTATTAAGAAGTTTAAGAAA-TTATTAAAATAAATTA

                    *              *                              
        304 TAAGATTAGTAAGAAG-GCTATTTAGAAGTTTAAGAAATTATTAAAATAAATTA
          1 TAAGATTACTAA-AAGAGCTATTAAGAAGTTTAAGAAATTATTAAAATAAATTA

               
        357 TAA
          1 TAA

        360 AGCTAGTAAA


Statistics
Matches: 47,  Mismatches: 7, Indels: 4
        0.81            0.12        0.07

Matches are distributed among these distances:
  52    9  0.19
  53   35  0.74
  54    3  0.06

ACGTcount: A:0.49, C:0.03, G:0.13, T:0.36


Consensus pattern (53 bp):   
TAAGATTACTAAAAGAGCTATTAAGAAGTTTAAGAAATTATTAAAATAAATTA

Found at i:529 original size:21 final size:20

Alignment explanation


    Indices: 471--535  Score: 60
    Period size: 21  Copynumber: 3.1  Consensus size: 20

        461 TTAAAAAAAT

                    *            
        471 TTAAAAAAACTTATAATGTTA
          1 TTAAAAAATCTTATAA-GTTA

            *                     
        492 CTAAAAAATC-TACTAAGCTTA
          1 TTAAAAAATCTTA-TAAG-TTA

                  *              
        513 TTAAAAGATCTTATAAGATTA
          1 TTAAAAAATCTTATAAG-TTA

              
        534 TT
          1 TT

        536 TTTAAAAAGA


Statistics
Matches: 36,  Mismatches: 5, Indels: 6
        0.77            0.11        0.13

Matches are distributed among these distances:
  20    3  0.08
  21   31  0.86
  22    2  0.06

ACGTcount: A:0.48, C:0.09, G:0.06, T:0.37


Consensus pattern (20 bp):   
TTAAAAAATCTTATAAGTTA

Found at i:587 original size:23 final size:23

Alignment explanation


    Indices: 561--608  Score: 69
    Period size: 23  Copynumber: 2.1  Consensus size: 23

        551 AAAAGGTGTT

                  *           *    
        561 AAAAAATTTATAAGATTATTAAA
          1 AAAAAACTTATAAGATTACTAAA

                          *        
        584 AAAAAACTTATAAGGTTACTAAA
          1 AAAAAACTTATAAGATTACTAAA

              
        607 AA
          1 AA

        609 TGCTTAAAAA


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  23   22  1.00

ACGTcount: A:0.60, C:0.04, G:0.06, T:0.29


Consensus pattern (23 bp):   
AAAAAACTTATAAGATTACTAAA

Found at i:1032 original size:20 final size:20

Alignment explanation


    Indices: 999--1038  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 20

        989 TACTTTGTAC

                  *              
        999 TAAAAATACTTATATAGTTTA
          1 TAAAAAAACTTATATA-TTTA

                                
       1020 TAAAAAAAC-TATATATTTA
          1 TAAAAAAACTTATATATTTA

       1039 CAGACAAATT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  19    4  0.22
  20    6  0.33
  21    8  0.44

ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40


Consensus pattern (20 bp):   
TAAAAAAACTTATATATTTA
Done.