Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_15708

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: 3516
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29


Found at i:82 original size:12 final size:12

Alignment explanation


    Indices: 65--108  Score: 58
    Period size: 12  Copynumber: 3.9  Consensus size: 12

         55 CCAGGTTCTC

                        
         65 CTTCTTCTTCCT
          1 CTTCTTCTTCCT

                        
         77 CTTCTTCTTCCT
          1 CTTCTTCTTCCT

                   *    
         89 C--C-TCCTCCT
          1 CTTCTTCTTCCT

                       
         98 CTTCTTCTTCC
          1 CTTCTTCTTCC

        109 GATGATGATT


Statistics
Matches: 27,  Mismatches: 2, Indels: 6
        0.77            0.06        0.17

Matches are distributed among these distances:
   9    7  0.26
  10    1  0.04
  11    1  0.04
  12   18  0.67

ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52


Consensus pattern (12 bp):   
CTTCTTCTTCCT

Found at i:86 original size:18 final size:18

Alignment explanation


    Indices: 60--108  Score: 62
    Period size: 18  Copynumber: 2.7  Consensus size: 18

         50 CCACTCCAGG

                *       *     
         60 TTCTCCTTCTTCTTCCTC
          1 TTCTTCTTCTTCCTCCTC

                     *        
         78 TTCTTCTTCCTCCTCCTC
          1 TTCTTCTTCTTCCTCCTC

            *            
         96 CTCTTCTTCTTCC
          1 TTCTTCTTCTTCC

        109 GATGATGATT


Statistics
Matches: 26,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  18   26  1.00

ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53


Consensus pattern (18 bp):   
TTCTTCTTCTTCCTCCTC
Done.