Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_02216

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, 239

Length: 399
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.24


Found at i:38 original size:12 final size:12

Alignment explanation


    Indices: 23--72  Score: 50
    Period size: 12  Copynumber: 4.2  Consensus size: 12

         13 GAGCTGAAGC

                        
         23 CGAAGCCGGACT
          1 CGAAGCCGGACT

                   *    
         35 CGAAGCCAGACT
          1 CGAAGCCGGACT

                  *       
         47 C-AGAGTCGGAGC-
          1 CGA-AGCCGGA-CT

                        
         59 CGAAGCCGGACT
          1 CGAAGCCGGACT

              
         71 CG
          1 CG

         73 GAGTCAGAGC


Statistics
Matches: 30,  Mismatches: 4, Indels: 8
        0.71            0.10        0.19

Matches are distributed among these distances:
  11    2  0.07
  12   26  0.87
  13    2  0.07

ACGTcount: A:0.26, C:0.32, G:0.34, T:0.08


Consensus pattern (12 bp):   
CGAAGCCGGACT

Found at i:90 original size:24 final size:24

Alignment explanation


    Indices: 35--93  Score: 91
    Period size: 24  Copynumber: 2.5  Consensus size: 24

         25 AAGCCGGACT

                   *           *    
         35 CGAAGCCAGACTCAGAGTCGGAGC
          1 CGAAGCCGGACTCAGAGTCAGAGC

                         *          
         59 CGAAGCCGGACTCGGAGTCAGAGC
          1 CGAAGCCGGACTCAGAGTCAGAGC

                       
         83 CGAAGCCGGAC
          1 CGAAGCCGGAC

         94 GTGGATCCTC


Statistics
Matches: 32,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  24   32  1.00

ACGTcount: A:0.27, C:0.31, G:0.36, T:0.07


Consensus pattern (24 bp):   
CGAAGCCGGACTCAGAGTCAGAGC
Done.