Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_20097

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, 282

Length: 471
ACGTcount: A:0.38, C:0.17, G:0.29, T:0.15


Found at i:143 original size:27 final size:27

Alignment explanation


    Indices: 100--161  Score: 72
    Period size: 27  Copynumber: 2.3  Consensus size: 27

         90 CCGTACTTTT

                               *   *    
        100 AAGAAGGAACAGGCTGAAGTGGAGGAAG
          1 AAGAA-GAACAGGCTGAAGAGGAAGAAG

                                     *  
        128 AAGAAGAAC-GGTCTGAAGAGGAAGTAG
          1 AAGAAGAACAGG-CTGAAGAGGAAGAAG

                   
        155 AAGAAGA
          1 AAGAAGA

        162 GCCTGAGAAA


Statistics
Matches: 30,  Mismatches: 3, Indels: 3
        0.83            0.08        0.08

Matches are distributed among these distances:
  26    2  0.07
  27   23  0.77
  28    5  0.17

ACGTcount: A:0.47, C:0.06, G:0.39, T:0.08


Consensus pattern (27 bp):   
AAGAAGAACAGGCTGAAGAGGAAGAAG

Found at i:167 original size:24 final size:24

Alignment explanation


    Indices: 121--167  Score: 60
    Period size: 24  Copynumber: 2.0  Consensus size: 24

        111 GGCTGAAGTG

                              *     
        121 GAGGAAGAAGAAGAACGGTCTGAA
          1 GAGGAAGAAGAAGAACGGCCTGAA

                   *                
        145 GAGGAAGTAGAAGAA-GAGCCTGA
          1 GAGGAAGAAGAAGAACG-GCCTGA

        168 GAAACGAAAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  23    1  0.05
  24   19  0.95

ACGTcount: A:0.45, C:0.09, G:0.38, T:0.09


Consensus pattern (24 bp):   
GAGGAAGAAGAAGAACGGCCTGAA
Done.