Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_14706

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, 777

Length: 1296
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28


Found at i:36 original size:15 final size:15

Alignment explanation


    Indices: 16--50  Score: 61
    Period size: 15  Copynumber: 2.3  Consensus size: 15

          6 CTGCCACCAC

                           
         16 CACCACCACCAGCAG
          1 CACCACCACCAGCAG

                    *      
         31 CACCACCAGCAGCAG
          1 CACCACCACCAGCAG

                 
         46 CACCA
          1 CACCA

         51 TACCTCCGCC


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

Matches are distributed among these distances:
  15   19  1.00

ACGTcount: A:0.34, C:0.51, G:0.14, T:0.00


Consensus pattern (15 bp):   
CACCACCACCAGCAG

Found at i:39 original size:12 final size:12

Alignment explanation


    Indices: 9--50  Score: 57
    Period size: 12  Copynumber: 3.5  Consensus size: 12

          1 ATGGCCTG

                  *  *  
          9 CCACCACCACCA
          1 CCACCAGCAGCA

                        
         21 CCACCAGCAGCA
          1 CCACCAGCAGCA

                        
         33 CCACCAGCAGCA
          1 CCACCAGCAGCA

            *     
         45 GCACCA
          1 CCACCA

         51 TACCTCCGCC


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  12   27  1.00

ACGTcount: A:0.33, C:0.55, G:0.12, T:0.00


Consensus pattern (12 bp):   
CCACCAGCAGCA

Found at i:907 original size:5 final size:6

Alignment explanation


    Indices: 889--915  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

        879 TGAAGCAGAG

                                           
        889 AATAAA AATAAA AATAAA AATAAA AAT
          1 AATAAA AATAAA AATAAA AATAAA AAT

        916 GGTGAGCTTT


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

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19


Consensus pattern (6 bp):   
AATAAA
Done.