Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006855.1 Corchorus capsularis cultivar CVL-1 contig06876, 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: 7309
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31


Found at i:4144 original size:22 final size:21

Alignment explanation


    Indices: 4105--4148  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 21

       4095 AAAAAGAATC

                   *     *       
       4105 TTTATTATTTATCGTTTTATT
          1 TTTATTAATTATCCTTTTATT

                                  
       4126 TTTATTTAATTATCCTTTTATT
          1 TTTA-TTAATTATCCTTTTATT

             
       4148 T
          1 T

       4149 AATTATTTCG


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

Matches are distributed among these distances:
  21    4  0.20
  22   16  0.80

ACGTcount: A:0.20, C:0.07, G:0.02, T:0.70


Consensus pattern (21 bp):   
TTTATTAATTATCCTTTTATT

Found at i:5654 original size:15 final size:15

Alignment explanation


    Indices: 5616--5688  Score: 74
    Period size: 16  Copynumber: 4.7  Consensus size: 15

       5606 GGCAATTGGG

                      *  *  
       5616 CGGGTTCGGGCAGGTT
          1 CGGGTTCGGGTA-CTT

                           
       5632 CGGGTTCGGGTACTT
          1 CGGGTTCGGGTACTT

             *         *    
       5647 CAGGTTCGGGTTCTTT
          1 CGGGTTCGGGTAC-TT

                         *  
       5663 CGGGTTCGGGTATTTT
          1 CGGGTTCGGGTA-CTT

                      
       5679 CGGGTTCGGG
          1 CGGGTTCGGG

       5689 CCCGGATCAG


Statistics
Matches: 48,  Mismatches: 7, Indels: 4
        0.81            0.12        0.07

Matches are distributed among these distances:
  15   13  0.27
  16   35  0.73

ACGTcount: A:0.05, C:0.18, G:0.42, T:0.34


Consensus pattern (15 bp):   
CGGGTTCGGGTACTT

Found at i:5656 original size:31 final size:32

Alignment explanation


    Indices: 5618--5689  Score: 83
    Period size: 31  Copynumber: 2.3  Consensus size: 32

       5608 CAATTGGGCG

                      *                     
       5618 GGTTCGGGCAGGTTCGGGTTCGGGTA-CTTCA
          1 GGTTCGGGCACGTTCGGGTTCGGGTATCTTCA

                    ** *               *   *
       5649 GGTTCGGGTTCTTTCGGGTTCGGGTATTTTCG
          1 GGTTCGGGCACGTTCGGGTTCGGGTATCTTCA

                     
       5681 GGTTCGGGC
          1 GGTTCGGGC

       5690 CCGGATCAGG


Statistics
Matches: 33,  Mismatches: 7, Indels: 1
        0.80            0.17        0.02

Matches are distributed among these distances:
  31   22  0.67
  32   11  0.33

ACGTcount: A:0.06, C:0.18, G:0.42, T:0.35


Consensus pattern (32 bp):   
GGTTCGGGCACGTTCGGGTTCGGGTATCTTCA

Found at i:5670 original size:16 final size:16

Alignment explanation


    Indices: 5630--5688  Score: 77
    Period size: 16  Copynumber: 3.8  Consensus size: 16

       5620 TTCGGGCAGG

                         *  
       5630 TTCGGGTTCGGGTAC-
          1 TTCGGGTTCGGGTTCT

               *            
       5645 TTCAGGTTCGGGTTCT
          1 TTCGGGTTCGGGTTCT

                             
       5661 TTCGGGTTCGGGTAT-T
          1 TTCGGGTTCGGGT-TCT

                        
       5677 TTCGGGTTCGGG
          1 TTCGGGTTCGGG

       5689 CCCGGATCAG


Statistics
Matches: 39,  Mismatches: 3, Indels: 3
        0.87            0.07        0.07

Matches are distributed among these distances:
  15   13  0.33
  16   25  0.64
  17    1  0.03

ACGTcount: A:0.05, C:0.17, G:0.39, T:0.39


Consensus pattern (16 bp):   
TTCGGGTTCGGGTTCT

Found at i:6153 original size:31 final size:33

Alignment explanation


    Indices: 6118--6189  Score: 80
    Period size: 31  Copynumber: 2.3  Consensus size: 33

       6108 TAAATTGTAG

                             *               
       6118 CAAATTAAAACA-AAT-TAAGTATTAAATTAAA
          1 CAAATTAAAACAGAATGCAAGTATTAAATTAAA

                   * *            *          
       6149 CAAA-T-CATCAGAATGCAAGTCTTAAATTAAA
          1 CAAATTAAAACAGAATGCAAGTATTAAATTAAA

                      
       6180 CAAATTAAAA
          1 CAAATTAAAA

       6190 GCTAATGGAC


Statistics
Matches: 31,  Mismatches: 6, Indels: 6
        0.72            0.14        0.14

Matches are distributed among these distances:
  29    3  0.10
  30    4  0.13
  31   22  0.71
  32    1  0.03
  33    1  0.03

ACGTcount: A:0.57, C:0.11, G:0.06, T:0.26


Consensus pattern (33 bp):   
CAAATTAAAACAGAATGCAAGTATTAAATTAAA

Found at i:6430 original size:16 final size:16

Alignment explanation


    Indices: 6411--6451  Score: 64
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       6401 GATTGTCTCG

                      *  *  
       6411 GGTTCGGGTATTTTCA
          1 GGTTCGGGTAATTCCA

                            
       6427 GGTTCGGGTAATTCCA
          1 GGTTCGGGTAATTCCA

                     
       6443 GGTTCGGGT
          1 GGTTCGGGT

       6452 TCGGGTTCAG


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  16   23  1.00

ACGTcount: A:0.12, C:0.15, G:0.37, T:0.37


Consensus pattern (16 bp):   
GGTTCGGGTAATTCCA
Done.