Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012904.1 Corchorus capsularis cultivar CVL-1 contig12925, 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: 61947
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:2315 original size:13 final size:13

Alignment explanation


    Indices: 2293--2325  Score: 57
    Period size: 13  Copynumber: 2.5  Consensus size: 13

       2283 ATCTAAATCT

                 *       
       2293 AAGCAGATTAATA
          1 AAGCAAATTAATA

                         
       2306 AAGCAAATTAATA
          1 AAGCAAATTAATA

                   
       2319 AAGCAAA
          1 AAGCAAA

       2326 CAATAATTAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   19  1.00

ACGTcount: A:0.61, C:0.09, G:0.12, T:0.18


Consensus pattern (13 bp):   
AAGCAAATTAATA

Found at i:3852 original size:20 final size:20

Alignment explanation


    Indices: 3829--3867  Score: 51
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       3819 AAAATAGGGT

                                
       3829 AAAAACACATAAAAATAGCA
          1 AAAAACACATAAAAATAGCA

                ** *           
       3849 AAAAGTATATAAAAATAGC
          1 AAAAACACATAAAAATAGC

       3868 TATAAAAATA


Statistics
Matches: 16,  Mismatches: 3, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.67, C:0.10, G:0.08, T:0.15


Consensus pattern (20 bp):   
AAAAACACATAAAAATAGCA

Found at i:8535 original size:15 final size:15

Alignment explanation


    Indices: 8515--8548  Score: 68
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       8505 CAATCATGGT

                           
       8515 ACTGTATAAACTATA
          1 ACTGTATAAACTATA

                           
       8530 ACTGTATAAACTATA
          1 ACTGTATAAACTATA

                
       8545 ACTG
          1 ACTG

       8549 AGCTTTGATA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   19  1.00

ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32


Consensus pattern (15 bp):   
ACTGTATAAACTATA

Found at i:57641 original size:12 final size:12

Alignment explanation


    Indices: 57624--57656  Score: 57
    Period size: 12  Copynumber: 2.8  Consensus size: 12

      57614 ACTCGCGATA

                        
      57624 CATATCAAAAGG
          1 CATATCAAAAGG

                        
      57636 CATATCAAAAGG
          1 CATATCAAAAGG

              *      
      57648 CAAATCAAA
          1 CATATCAAA

      57657 GTACTCTACA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   20  1.00

ACGTcount: A:0.55, C:0.18, G:0.12, T:0.15


Consensus pattern (12 bp):   
CATATCAAAAGG
Done.