Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009084.1 Corchorus olitorius cultivar O-4 contig09112, 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, 633

Length: 1056
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.37


Found at i:96 original size:21 final size:19

Alignment explanation


    Indices: 60--101  Score: 57
    Period size: 21  Copynumber: 2.1  Consensus size: 19

         50 TATATAATGC

                 *             
         60 ATATTTTATTTATATATTA
          1 ATATTCTATTTATATATTA

                                 
         79 ATATTCTATATTATTATATTA
          1 ATATTCTAT-TTA-TATATTA

              
        100 AT
          1 AT

        102 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:114 original size:18 final size:18

Alignment explanation


    Indices: 93--130  Score: 58
    Period size: 18  Copynumber: 2.1  Consensus size: 18

         83 TCTATATTAT

                              
         93 TATATTAATTTATATAAA
          1 TATATTAATTTATATAAA

                  *        *  
        111 TATATTCATTTATATGAA
          1 TATATTAATTTATATAAA

              
        129 TA
          1 TA

        131 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:183 original size:29 final size:28

Alignment explanation


    Indices: 145--201  Score: 96
    Period size: 29  Copynumber: 2.0  Consensus size: 28

        135 TCTATTATTA

                              *         
        145 TTAATACTATTACAATTATTACATATAT
          1 TTAATACTATTACAATTAGTACATATAT

                                         
        173 TTAATTACTATTACAATTAGTACATATAT
          1 TTAA-TACTATTACAATTAGTACATATAT

        202 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:234 original size:21 final size:22

Alignment explanation


    Indices: 208--255  Score: 80
    Period size: 21  Copynumber: 2.2  Consensus size: 22

        198 ATATATTTAA

                                  
        208 ATTTATTATTCCATTTATAT-T
          1 ATTTATTATTCCATTTATATAT

                        *         
        229 ATTTATTATTCCGTTTATATAT
          1 ATTTATTATTCCATTTATATAT

                 
        251 ATTTA
          1 ATTTA

        256 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

Found at i:774 original size:21 final size:21

Alignment explanation


    Indices: 746--808  Score: 117
    Period size: 21  Copynumber: 3.0  Consensus size: 21

        736 TAGAACTACT

                                 
        746 ACTCTTAGAACCAGAAATAAA
          1 ACTCTTAGAACCAGAAATAAA

               *                 
        767 ACTTTTAGAACCAGAAATAAA
          1 ACTCTTAGAACCAGAAATAAA

                                 
        788 ACTCTTAGAACCAGAAATAAA
          1 ACTCTTAGAACCAGAAATAAA

        809 TAGGCTTACC


Statistics
Matches: 40,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   40  1.00

ACGTcount: A:0.52, C:0.17, G:0.10, T:0.21


Consensus pattern (21 bp):   
ACTCTTAGAACCAGAAATAAA
Done.