Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009578.1 Corchorus capsularis cultivar CVL-1 contig09599, 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: 6875
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31


Found at i:2687 original size:19 final size:18

Alignment explanation


    Indices: 2654--2689  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       2644 TTGAAATAAT

                              
       2654 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       2672 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       2690 GAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:6555 original size:12 final size:13

Alignment explanation


    Indices: 6538--6582  Score: 74
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       6528 CTAATAAATC

                         
       6538 TAAAGCAGATT-A
          1 TAAAGCAGATTAA

                   *     
       6550 TAAAGCAAATTAA
          1 TAAAGCAGATTAA

                         
       6563 TAAAGCAGATTAA
          1 TAAAGCAGATTAA

                   
       6576 TAAAGCA
          1 TAAAGCA

       6583 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:6589 original size:25 final size:25

Alignment explanation


    Indices: 6538--6590  Score: 81
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       6528 CTAATAAATC

                                  *  
       6538 TAAAGCAGATTATAAAGCAAATTAA
          1 TAAAGCAGATTATAAAGCAAATCAA

                                      
       6563 TAAAGCAGATTAATAAAGCAAA-CAA
          1 TAAAGCAGATT-ATAAAGCAAATCAA

               
       6588 TAA
          1 TAA

       6591 TTAAAAAGCA


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.