Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015347.1 Corchorus capsularis cultivar CVL-1 contig15368, 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, 759

Length: 1265
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33


Found at i:662 original size:14 final size:15

Alignment explanation


    Indices: 645--677  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

        635 GAAAACAGGG

                      *    
        645 ATTATGAA-ATAACA
          1 ATTATGAAGAAAACA

                           
        659 ATTATGAAGAAAACA
          1 ATTATGAAGAAAACA

                
        674 ATTA
          1 ATTA

        678 AACTACAAAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  14    8  0.47
  15    9  0.53

ACGTcount: A:0.58, C:0.06, G:0.09, T:0.27


Consensus pattern (15 bp):   
ATTATGAAGAAAACA

Found at i:709 original size:6 final size:6

Alignment explanation


    Indices: 693--724  Score: 57
    Period size: 6  Copynumber: 5.5  Consensus size: 6

        683 CAAATAAAGC

                                                  
        693 AAATC- AAATCT AAATCT AAATCT AAATCT AAA
          1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA

        725 GCAGATTATA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   5    5  0.19
   6   21  0.81

ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28


Consensus pattern (6 bp):   
AAATCT

Found at i:736 original size:12 final size:13

Alignment explanation


    Indices: 721--765  Score: 74
    Period size: 13  Copynumber: 3.5  Consensus size: 13

        711 AATCTAAATC

                         
        721 TAAAGCAGATT-A
          1 TAAAGCAGATTAA

                   *     
        733 TAAAGCAAATTAA
          1 TAAAGCAGATTAA

                         
        746 TAAAGCAGATTAA
          1 TAAAGCAGATTAA

                   
        759 TAAAGCA
          1 TAAAGCA

        766 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:772 original size:25 final size:25

Alignment explanation


    Indices: 721--773  Score: 81
    Period size: 25  Copynumber: 2.1  Consensus size: 25

        711 AATCTAAATC

                                  *  
        721 TAAAGCAGATTATAAAGCAAATTAA
          1 TAAAGCAGATTATAAAGCAAATCAA

                                      
        746 TAAAGCAGATTAATAAAGCAAA-CAA
          1 TAAAGCAGATT-ATAAAGCAAATCAA

               
        771 TAA
          1 TAA

        774 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.