Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010980.1 Corchorus capsularis cultivar CVL-1 contig11001, 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: 6830
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29


Found at i:411 original size:40 final size:42

Alignment explanation


    Indices: 336--413  Score: 133
    Period size: 40  Copynumber: 1.9  Consensus size: 42

        326 GTAGTTTTAG

                             *                        
        336 GAGTCCTTAAAACCCAACAAGTTTTGAAGTGATGTAAAATAC
          1 GAGTCCTTAAAACCCAAAAAGTTTTGAAGTGATGTAAAATAC

                                                  
        378 GAGTCCTT-AAACCCAAAAAG-TTTGAAGTGATGTAAA
          1 GAGTCCTTAAAACCCAAAAAGTTTTGAAGTGATGTAAA

        414 TATATCTGGG


Statistics
Matches: 35,  Mismatches: 1, Indels: 2
        0.92            0.03        0.05

Matches are distributed among these distances:
  40   16  0.46
  41   11  0.31
  42    8  0.23

ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26


Consensus pattern (42 bp):   
GAGTCCTTAAAACCCAAAAAGTTTTGAAGTGATGTAAAATAC

Found at i:2361 original size:15 final size:15

Alignment explanation


    Indices: 2341--2372  Score: 57
    Period size: 14  Copynumber: 2.2  Consensus size: 15

       2331 AAATAAAAAT

                           
       2341 CGAAAAAACCGA-AC
          1 CGAAAAAACCGACAC

                           
       2355 CGAAAAAACCGACAC
          1 CGAAAAAACCGACAC

               
       2370 CGA
          1 CGA

       2373 CTGATGAGCA


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14   12  0.71
  15    5  0.29

ACGTcount: A:0.53, C:0.31, G:0.16, T:0.00


Consensus pattern (15 bp):   
CGAAAAAACCGACAC
Done.