Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008083.1 Corchorus capsularis cultivar CVL-1 contig08104, 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: 17049
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34


Found at i:6300 original size:33 final size:33

Alignment explanation


    Indices: 6209--6301  Score: 134
    Period size: 33  Copynumber: 2.8  Consensus size: 33

       6199 TACACTGAGT

                                    *        
       6209 CTCCCCACTAGGACGGCTCAGCCACGGCGGAGC
          1 CTCCCCACTAGGACGGCTCAGCCATGGCGGAGC

                           *                 
       6242 CTCCCCACTAGGACGACTCAGCCATGGCGGAGC
          1 CTCCCCACTAGGACGGCTCAGCCATGGCGGAGC

                     *  *               
       6275 CTCCCCACTGGGGCGGCTTCA-CCATGG
          1 CTCCCCACTAGGACGGC-TCAGCCATGG

       6302 GCAGGCCGTC


Statistics
Matches: 54,  Mismatches: 5, Indels: 2
        0.89            0.08        0.03

Matches are distributed among these distances:
  33   51  0.94
  34    3  0.06

ACGTcount: A:0.17, C:0.41, G:0.29, T:0.13


Consensus pattern (33 bp):   
CTCCCCACTAGGACGGCTCAGCCATGGCGGAGC

Found at i:6355 original size:32 final size:33

Alignment explanation


    Indices: 6278--6341  Score: 94
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       6268 GCGGAGCCTC

                                  *          
       6278 CCCACTGGGGCGGCTTCACCATGGGCAGGCCGT
          1 CCCACTGGGGCGGCTTCACCATCGGCAGGCCGT

                  *          *              
       6311 CCCACTAGGGCGGCTTCGCCA-CGGCAGGCCG
          1 CCCACTGGGGCGGCTTCACCATCGGCAGGCCG

       6342 CCTCGGTGGG


Statistics
Matches: 28,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  32    9  0.32
  33   19  0.68

ACGTcount: A:0.12, C:0.39, G:0.36, T:0.12


Consensus pattern (33 bp):   
CCCACTGGGGCGGCTTCACCATCGGCAGGCCGT

Found at i:9390 original size:15 final size:14

Alignment explanation


    Indices: 9366--9412  Score: 85
    Period size: 14  Copynumber: 3.3  Consensus size: 14

       9356 ACTATTATTT

                          
       9366 AAAAAGTTGGGAGG
          1 AAAAAGTTGGGAGG

                           
       9380 AAAAAGTTTGGGAGG
          1 AAAAAG-TTGGGAGG

                          
       9395 AAAAAGTTGGGAGG
          1 AAAAAGTTGGGAGG

                
       9409 AAAA
          1 AAAA

       9413 TGTTTAAAAG


Statistics
Matches: 32,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  14   18  0.56
  15   14  0.44

ACGTcount: A:0.47, C:0.00, G:0.38, T:0.15


Consensus pattern (14 bp):   
AAAAAGTTGGGAGG

Found at i:9427 original size:24 final size:23

Alignment explanation


    Indices: 9363--9444  Score: 92
    Period size: 24  Copynumber: 3.3  Consensus size: 23

       9353 ACTACTATTA

                                 * 
       9363 TTTAAAAAGTTGGGAGGAAAAAG
          1 TTTAAAAAGTTGGGAGGAAAATG

                                         
       9386 TTTGGGAGGAAAAAGTTGGGAGGAAAATG
          1 TTT------AAAAAGTTGGGAGGAAAATG

                                    
       9415 TTTAAAAGAGTTGGGAGGAAAATG
          1 TTTAAAA-AGTTGGGAGGAAAATG

                  
       9439 TTTAAA
          1 TTTAAA

       9445 GCAAGGGAAT


Statistics
Matches: 51,  Mismatches: 1, Indels: 13
        0.78            0.02        0.20

Matches are distributed among these distances:
  23    7  0.14
  24   22  0.43
  29   22  0.43

ACGTcount: A:0.43, C:0.00, G:0.33, T:0.24


Consensus pattern (23 bp):   
TTTAAAAAGTTGGGAGGAAAATG
Done.