Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008740.1 Corchorus olitorius cultivar O-4 contig08767, 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, 603

Length: 1005
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37


Found at i:453 original size:21 final size:19

Alignment explanation


    Indices: 417--458  Score: 57
    Period size: 21  Copynumber: 2.1  Consensus size: 19

        407 TATATAATGC

                 *             
        417 ATATTTTATTTATATATTA
          1 ATATTCTATTTATATATTA

                                 
        436 ATATTCTATATTATTATATTA
          1 ATATTCTAT-TTA-TATATTA

              
        457 AT
          1 AT

        459 TTATATAAAT


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  19    8  0.40
  20    3  0.15
  21    9  0.45

ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60


Consensus pattern (19 bp):   
ATATTCTATTTATATATTA

Found at i:471 original size:18 final size:18

Alignment explanation


    Indices: 450--487  Score: 58
    Period size: 18  Copynumber: 2.1  Consensus size: 18

        440 TCTATATTAT

                              
        450 TATATTAATTTATATAAA
          1 TATATTAATTTATATAAA

                  *        *  
        468 TATATTCATTTATATGAA
          1 TATATTAATTTATATAAA

              
        486 TA
          1 TA

        488 ATACTCTATT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50


Consensus pattern (18 bp):   
TATATTAATTTATATAAA

Found at i:540 original size:29 final size:28

Alignment explanation


    Indices: 502--558  Score: 96
    Period size: 29  Copynumber: 2.0  Consensus size: 28

        492 TCTATTATTA

                              *         
        502 TTAATACTATTACAATTATTACATATAT
          1 TTAATACTATTACAATTAGTACATATAT

                                         
        530 TTAATTACTATTACAATTAGTACATATAT
          1 TTAA-TACTATTACAATTAGTACATATAT

        559 ATTTAAATTT


Statistics
Matches: 27,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  28    4  0.15
  29   23  0.85

ACGTcount: A:0.42, C:0.11, G:0.02, T:0.46


Consensus pattern (28 bp):   
TTAATACTATTACAATTAGTACATATAT

Found at i:591 original size:21 final size:22

Alignment explanation


    Indices: 565--612  Score: 80
    Period size: 21  Copynumber: 2.2  Consensus size: 22

        555 ATATATTTAA

                                  
        565 ATTTATTATTCCATTTATAT-T
          1 ATTTATTATTCCATTTATATAT

                        *         
        586 ATTTATTATTCCGTTTATATAT
          1 ATTTATTATTCCATTTATATAT

                 
        608 ATTTA
          1 ATTTA

        613 AATAATAATA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  21   19  0.76
  22    6  0.24

ACGTcount: A:0.29, C:0.08, G:0.02, T:0.60


Consensus pattern (22 bp):   
ATTTATTATTCCATTTATATAT

Done.