Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_34343

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, 244

Length: 408
ACGTcount: A:0.32, C:0.21, G:0.34, T:0.13


Found at i:126 original size:51 final size:51

Alignment explanation


    Indices: 68--226  Score: 246
    Period size: 51  Copynumber: 3.0  Consensus size: 51

         58 GAAGAAGAGA

                           *                              *    
         68 AGCACAAGGGAGAAGCTCATCACGAAGGCGGCCATGGCTATGGCGCTGCTG
          1 AGCACAAGGGAGAAGTTCATCACGAAGGCGGCCATGGCTATGGCGCCGCTG

                                                                     
        119 AGCACAAGGGAGAAGTTCATCACGAAGGCGGCCATGGCTATGGTTATGGCGCCGCTG
          1 AGCACAAGGGAGAAGTTCATCACGAAGGCGGCCATGGC------TATGGCGCCGCTG

                                                               
        176 AGCACAAGGGAGAAGTTCATCACGAAGGCGGCCATGGCTATGGCGCCGCTG
          1 AGCACAAGGGAGAAGTTCATCACGAAGGCGGCCATGGCTATGGCGCCGCTG

        227 CGGTCGCCGG


Statistics
Matches: 100,  Mismatches: 2, Indels: 12
        0.88            0.02        0.11

Matches are distributed among these distances:
  51   50  0.50
  57   50  0.50

ACGTcount: A:0.25, C:0.25, G:0.35, T:0.15


Consensus pattern (51 bp):   
AGCACAAGGGAGAAGTTCATCACGAAGGCGGCCATGGCTATGGCGCCGCTG

Found at i:194 original size:57 final size:56

Alignment explanation


    Indices: 68--218  Score: 240
    Period size: 57  Copynumber: 2.8  Consensus size: 56

         58 GAAGAAGAGA

                           *                                   *    
         68 AGCACAAGGGAGAAGCTCATCACGAAGGCGGCCATGGC-----TATGGCGCTGCTG
          1 AGCACAAGGGAGAAGTTCATCACGAAGGCGGCCATGGCTATGGTATGGCGCCGCTG

                                                                     
        119 AGCACAAGGGAGAAGTTCATCACGAAGGCGGCCATGGCTATGGTTATGGCGCCGCTG
          1 AGCACAAGGGAGAAGTTCATCACGAAGGCGGCCATGGCTATGG-TATGGCGCCGCTG

                                                       
        176 AGCACAAGGGAGAAGTTCATCACGAAGGCGGCCATGGCTATGG
          1 AGCACAAGGGAGAAGTTCATCACGAAGGCGGCCATGGCTATGG

        219 CGCCGCTGCG


Statistics
Matches: 92,  Mismatches: 2, Indels: 6
        0.92            0.02        0.06

Matches are distributed among these distances:
  51   37  0.40
  57   55  0.60

ACGTcount: A:0.26, C:0.23, G:0.35, T:0.15


Consensus pattern (56 bp):   
AGCACAAGGGAGAAGTTCATCACGAAGGCGGCCATGGCTATGGTATGGCGCCGCTG
Done.