Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013009.1 Corchorus capsularis cultivar CVL-1 contig13030, 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: 9696
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:83 original size:2 final size:2

Alignment explanation


    Indices: 76--109  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

         66 CAACTTGCTA

                                                              
         76 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        110 TTATGGATTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:860 original size:17 final size:17

Alignment explanation


    Indices: 835--867  Score: 50
    Period size: 16  Copynumber: 1.9  Consensus size: 17

        825 TAATTATAAA

                              
        835 ACTAGTATAGTAAAAAAT
          1 ACTAGTATAG-AAAAAAT

                            
        853 ACTA-TATAGAAAAAA
          1 ACTAGTATAGAAAAAA

        868 CAACTTAGAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    6  0.40
  17    5  0.33
  18    4  0.27

ACGTcount: A:0.61, C:0.06, G:0.09, T:0.24


Consensus pattern (17 bp):   
ACTAGTATAGAAAAAAT

Found at i:6582 original size:8 final size:8

Alignment explanation


    Indices: 6565--6608  Score: 56
    Period size: 8  Copynumber: 5.8  Consensus size: 8

       6555 TAAGTTCCTC

                 *  
       6565 TCTTTCTT
          1 TCTTTTTT

                    
       6573 TCTTTTTT
          1 TCTTTTTT

                    
       6581 TC-TTTTT
          1 TCTTTTTT

                    
       6588 TC-TTTTT
          1 TCTTTTTT

                    
       6595 TCTTTTTT
          1 TCTTTTTT

            *     
       6603 CCTTTT
          1 TCTTTT

       6609 CCCTTTTATT


Statistics
Matches: 33,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
   7   14  0.42
   8   19  0.58

ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82


Consensus pattern (8 bp):   
TCTTTTTT

Found at i:6588 original size:7 final size:7

Alignment explanation


    Indices: 6565--6608  Score: 61
    Period size: 7  Copynumber: 5.9  Consensus size: 7

       6555 TAAGTTCCTC

                    
       6565 TCTTTCTT
          1 TCTTT-TT

                    
       6573 TCTTTTTT
          1 TC-TTTTT

                   
       6581 TCTTTTT
          1 TCTTTTT

                   
       6588 TCTTTTT
          1 TCTTTTT

                   
       6595 TCTTTTT
          1 TCTTTTT

                   
       6602 TCCTTTT
          1 T-CTTTT

       6609 CCCTTTTATT


Statistics
Matches: 34,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   7   20  0.59
   8   11  0.32
   9    3  0.09

ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82


Consensus pattern (7 bp):   
TCTTTTT

Found at i:9573 original size:2 final size:2

Alignment explanation


    Indices: 9566--9604  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       9556 TAACATTTAG

                                                                      
       9566 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       9605 CCATGTACAT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Done.