Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013324.1 Corchorus capsularis cultivar CVL-1 contig13345, 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: 21429
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29


Found at i:2287 original size:7 final size:7

Alignment explanation


    Indices: 2277--2303  Score: 54
    Period size: 7  Copynumber: 3.9  Consensus size: 7

       2267 GGCTACTGGC

                   
       2277 TTGTGAA
          1 TTGTGAA

                   
       2284 TTGTGAA
          1 TTGTGAA

                   
       2291 TTGTGAA
          1 TTGTGAA

                  
       2298 TTGTGA
          1 TTGTGA

       2304 TTTTGAATGA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   20  1.00

ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44


Consensus pattern (7 bp):   
TTGTGAA

Found at i:2780 original size:16 final size:16

Alignment explanation


    Indices: 2742--2780  Score: 55
    Period size: 16  Copynumber: 2.5  Consensus size: 16

       2732 ATCTTCAATG

                            
       2742 TGATTAA-AATAAATA
          1 TGATTAATAATAAATA

                             
       2757 TAGA-TAATAATAAATA
          1 T-GATTAATAATAAATA

                    
       2773 TGATTAAT
          1 TGATTAAT

       2781 TATGCTCAAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 5
        0.81            0.00        0.19

Matches are distributed among these distances:
  15    6  0.29
  16   15  0.71

ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36


Consensus pattern (16 bp):   
TGATTAATAATAAATA

Found at i:6970 original size:44 final size:44

Alignment explanation


    Indices: 6907--6991  Score: 161
    Period size: 44  Copynumber: 1.9  Consensus size: 44

       6897 AGCCACCAAG

                                                        
       6907 TCCAAAACAAAGGATGCAAGGCAACTACATATATATATATATAC
          1 TCCAAAACAAAGGATGCAAGGCAACTACATATATATATATATAC

                                       *             
       6951 TCCAAAACAAAGGATGCAAGGCAACTATATATATATATATA
          1 TCCAAAACAAAGGATGCAAGGCAACTACATATATATATATA

       6992 CATATATATT


Statistics
Matches: 40,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  44   40  1.00

ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24


Consensus pattern (44 bp):   
TCCAAAACAAAGGATGCAAGGCAACTACATATATATATATATAC

Found at i:16688 original size:19 final size:19

Alignment explanation


    Indices: 16664--16703  Score: 80
    Period size: 19  Copynumber: 2.1  Consensus size: 19

      16654 AAAAAAAAAA

                               
      16664 AAAGTAATCTTTCTATAGT
          1 AAAGTAATCTTTCTATAGT

                               
      16683 AAAGTAATCTTTCTATAGT
          1 AAAGTAATCTTTCTATAGT

              
      16702 AA
          1 AA

      16704 TTTCCACTAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   21  1.00

ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40


Consensus pattern (19 bp):   
AAAGTAATCTTTCTATAGT
Done.