Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010317.1 Corchorus capsularis cultivar CVL-1 contig10338, 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: 17134
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33


Found at i:3952 original size:2 final size:2

Alignment explanation


    Indices: 3945--3980  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       3935 CCATCTCTAA

                                                                 
       3945 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

       3981 CACAGAAAAG


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
TC

Found at i:11804 original size:12 final size:12

Alignment explanation


    Indices: 11787--11826  Score: 53
    Period size: 12  Copynumber: 3.1  Consensus size: 12

      11777 TCGCTTCCTG

                        
      11787 CGCCACCACCTC
          1 CGCCACCACCTC

                           
      11799 CGCCACCACCACCTC
          1 CG---CCACCACCTC

                        
      11814 CGCCACCACCTC
          1 CGCCACCACCTC

             
      11826 C
          1 C

      11827 TCCTCCTCCT


Statistics
Matches: 25,  Mismatches: 0, Indels: 6
        0.81            0.00        0.19

Matches are distributed among these distances:
  12   13  0.52
  15   12  0.48

ACGTcount: A:0.17, C:0.68, G:0.07, T:0.07


Consensus pattern (12 bp):   
CGCCACCACCTC

Found at i:11809 original size:15 final size:15

Alignment explanation


    Indices: 11789--11829  Score: 73
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      11779 GCTTCCTGCG

                           
      11789 CCACCACCTCCGCCA
          1 CCACCACCTCCGCCA

                           
      11804 CCACCACCTCCGCCA
          1 CCACCACCTCCGCCA

                 *     
      11819 CCACCTCCTCC
          1 CCACCACCTCC

      11830 TCCTCCTTCT


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  15   25  1.00

ACGTcount: A:0.17, C:0.68, G:0.05, T:0.10


Consensus pattern (15 bp):   
CCACCACCTCCGCCA
Done.