Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000951.1 Corchorus capsularis cultivar CVL-1 contig00951, 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: 3920
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--57  Score: 114
    Period size: 2  Copynumber: 28.5  Consensus size: 2

                                                                          
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                                  
         43 TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC T

         58 GTGGAGATCC


Statistics
Matches: 55,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   55  1.00

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


Consensus pattern (2 bp):   
TC

Found at i:3629 original size:12 final size:13

Alignment explanation


    Indices: 3614--3658  Score: 74
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       3604 AATCTAAATC

                         
       3614 TAAAGCAGATT-A
          1 TAAAGCAGATTAA

                   *     
       3626 TAAAGCAAATTAA
          1 TAAAGCAGATTAA

                         
       3639 TAAAGCAGATTAA
          1 TAAAGCAGATTAA

                   
       3652 TAAAGCA
          1 TAAAGCA

       3659 AACAATAATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  12   10  0.33
  13   20  0.67

ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22


Consensus pattern (13 bp):   
TAAAGCAGATTAA

Found at i:3665 original size:25 final size:25

Alignment explanation


    Indices: 3614--3666  Score: 81
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       3604 AATCTAAATC

                                  *  
       3614 TAAAGCAGATTATAAAGCAAATTAA
          1 TAAAGCAGATTATAAAGCAAATCAA

                                      
       3639 TAAAGCAGATTAATAAAGCAAA-CAA
          1 TAAAGCAGATT-ATAAAGCAAATCAA

               
       3664 TAA
          1 TAA

       3667 TTATAAAGCA


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  25   16  0.62
  26   10  0.38

ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21


Consensus pattern (25 bp):   
TAAAGCAGATTATAAAGCAAATCAA
Done.