Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006030.1 Corchorus capsularis cultivar CVL-1 contig06048, 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, 1000

Length: 10915
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:97 original size:45 final size:45

Alignment explanation


    Indices: 47--136  Score: 153
    Period size: 45  Copynumber: 2.0  Consensus size: 45

         37 AGATTACTTC

                                                         
         47 TCCAGCTCATCATTAATCCGGGGTAGGGAACTTTTAGTAATTCCA
          1 TCCAGCTCATCATTAATCCGGGGTAGGGAACTTTTAGTAATTCCA

                   *         *           *               
         92 TCCAGCTTATCATTAATTCGGGGTAGGGATCTTTTAGTAATTCCA
          1 TCCAGCTCATCATTAATCCGGGGTAGGGAACTTTTAGTAATTCCA

        137 CTACTCTATT


Statistics
Matches: 42,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  45   42  1.00

ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34


Consensus pattern (45 bp):   
TCCAGCTCATCATTAATCCGGGGTAGGGAACTTTTAGTAATTCCA

Found at i:397 original size:24 final size:25

Alignment explanation


    Indices: 363--421  Score: 95
    Period size: 25  Copynumber: 2.4  Consensus size: 25

        353 AAATGAAGGA

                             *       
        363 AAATGAA-TTTGAAG-ATTTGTTAG
          1 AAATGAAGTTTGAAGAAGTTGTTAG

                                     
        386 AAATGAAGTTTGAAGAAGTTGTTAG
          1 AAATGAAGTTTGAAGAAGTTGTTAG

                       
        411 AAATGAAGTTT
          1 AAATGAAGTTT

        422 AGGGTTTGAA


Statistics
Matches: 33,  Mismatches: 1, Indels: 2
        0.92            0.03        0.06

Matches are distributed among these distances:
  23    7  0.21
  24    7  0.21
  25   19  0.58

ACGTcount: A:0.41, C:0.00, G:0.24, T:0.36


Consensus pattern (25 bp):   
AAATGAAGTTTGAAGAAGTTGTTAG

Found at i:5741 original size:41 final size:41

Alignment explanation


    Indices: 5696--5774  Score: 131
    Period size: 41  Copynumber: 1.9  Consensus size: 41

       5686 TGTCCCTCCT

                          *                          
       5696 AATAATTAAGGAAATAAATTAAATTCAGATTTAGCCCCCCA
          1 AATAATTAAGGAAAGAAATTAAATTCAGATTTAGCCCCCCA

                       *     *                    
       5737 AATAATTAAGGTAAGAATTTAAATTCAGATTTAGCCCC
          1 AATAATTAAGGAAAGAAATTAAATTCAGATTTAGCCCC

       5775 TAGTTATTGT


Statistics
Matches: 35,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  41   35  1.00

ACGTcount: A:0.44, C:0.15, G:0.11, T:0.29


Consensus pattern (41 bp):   
AATAATTAAGGAAAGAAATTAAATTCAGATTTAGCCCCCCA

Found at i:6909 original size:87 final size:87

Alignment explanation


    Indices: 6807--7035  Score: 404
    Period size: 87  Copynumber: 2.6  Consensus size: 87

       6797 ATTGTTAAAA

                                            *                                
       6807 TAATAATGAGAATATTTTCTAAATCTTGCCAACTTGTGGGAGATTTAGGAGATATTTTAAGAAAT
          1 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAT

                                  
       6872 AAATAAATTATAAAGATTGAGC
         66 AAATAAATTATAAAGATTGAGC

                 *                     *                                     
       6894 TAATAGTGAGAATATTTTCTAAATCTTCCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAT
          1 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAT

                                 *
       6959 AAATAAATTATAAAGATTGAGT
         66 AAATAAATTATAAAGATTGAGC

                  *                                         *      
       6981 TAATAAAGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATAT
          1 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATAT

       7036 AGAAAAGGAA


Statistics
Matches: 134,  Mismatches: 8, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  87  134  1.00

ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35


Consensus pattern (87 bp):   
TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAT
AAATAAATTATAAAGATTGAGC

Found at i:8346 original size:15 final size:13

Alignment explanation


    Indices: 8322--8355  Score: 59
    Period size: 13  Copynumber: 2.6  Consensus size: 13

       8312 GGCCGTAGTT

                         
       8322 TATATATATATAC
          1 TATATATATATAC

                   *     
       8335 TATATATCTATAC
          1 TATATATATATAC

                    
       8348 TATATATA
          1 TATATATA

       8356 AAAGTACGAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  13   19  1.00

ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47


Consensus pattern (13 bp):   
TATATATATATAC
Done.