Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_05114

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, 871

Length: 1452
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22


Found at i:157 original size:12 final size:12

Alignment explanation


    Indices: 140--205  Score: 69
    Period size: 12  Copynumber: 5.5  Consensus size: 12

        130 CTGCAACTAC

                   *    
        140 AGGAAGTGGAAG
          1 AGGAAGTAGAAG

                        
        152 AGGAAGTAGAAG
          1 AGGAAGTAGAAG

            *     *     
        164 TGGAAGAAGAAG
          1 AGGAAGTAGAAG

            **          
        176 TTGAAGTAGAAG
          1 AGGAAGTAGAAG

                   *    
        188 AGGAAGTTGAAG
          1 AGGAAGTAGAAG

             *    
        200 AAGAAG
          1 AGGAAG

        206 ACGACGATGA


Statistics
Matches: 45,  Mismatches: 9, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  12   45  1.00

ACGTcount: A:0.47, C:0.00, G:0.41, T:0.12


Consensus pattern (12 bp):   
AGGAAGTAGAAG

Found at i:165 original size:18 final size:18

Alignment explanation


    Indices: 142--199  Score: 89
    Period size: 18  Copynumber: 3.2  Consensus size: 18

        132 GCAACTACAG

                             *
        142 GAAGTGGAAGAGGAAGTA
          1 GAAGTGGAAGAGGAAGTT

                       *      
        160 GAAGTGGAAGAAGAAGTT
          1 GAAGTGGAAGAGGAAGTT

                 *            
        178 GAAGTAGAAGAGGAAGTT
          1 GAAGTGGAAGAGGAAGTT

                
        196 GAAG
          1 GAAG

        200 AAGAAGACGA


Statistics
Matches: 36,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  18   36  1.00

ACGTcount: A:0.45, C:0.00, G:0.41, T:0.14


Consensus pattern (18 bp):   
GAAGTGGAAGAGGAAGTT

Found at i:204 original size:18 final size:18

Alignment explanation


    Indices: 142--206  Score: 85
    Period size: 18  Copynumber: 3.6  Consensus size: 18

        132 GCAACTACAG

                 *           *
        142 GAAGTGGAAGAGGAAGTA
          1 GAAGTAGAAGAGGAAGTT

                 *     *      
        160 GAAGTGGAAGAAGAAGTT
          1 GAAGTAGAAGAGGAAGTT

                              
        178 GAAGTAGAAGAGGAAGTT
          1 GAAGTAGAAGAGGAAGTT

                *      
        196 GAAGAAGAAGA
          1 GAAGTAGAAGA

        207 CGACGATGAC


Statistics
Matches: 42,  Mismatches: 5, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   42  1.00

ACGTcount: A:0.48, C:0.00, G:0.40, T:0.12


Consensus pattern (18 bp):   
GAAGTAGAAGAGGAAGTT
Done.