Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g01761.F1

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: 3218
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36


Found at i:584 original size:12 final size:12

Alignment explanation


    Indices: 564--619  Score: 78
    Period size: 12  Copynumber: 4.7  Consensus size: 12

        554 GAAAAAGAAC

                        
        564 AAAAAGAGAATG
          1 AAAAAGAGAATG

                *    *  
        576 AAAATGAGATTG
          1 AAAAAGAGAATG

                         
        588 AAAAAG-GAATTG
          1 AAAAAGAGAA-TG

                        
        600 AAAAAGAGAATG
          1 AAAAAGAGAATG

                    
        612 AAAAAGAG
          1 AAAAAGAG

        620 TTTGAGAGAG


Statistics
Matches: 38,  Mismatches: 4, Indels: 4
        0.83            0.09        0.09

Matches are distributed among these distances:
  11    2  0.05
  12   33  0.87
  13    3  0.08

ACGTcount: A:0.62, C:0.00, G:0.25, T:0.12


Consensus pattern (12 bp):   
AAAAAGAGAATG

Found at i:2069 original size:44 final size:44

Alignment explanation


    Indices: 2006--2093  Score: 176
    Period size: 44  Copynumber: 2.0  Consensus size: 44

       1996 GCAAGAAGGA

                                                        
       2006 ACATTTTCAAAGGGACAAATGGCTCGACTTGACAACAAGTCAAT
          1 ACATTTTCAAAGGGACAAATGGCTCGACTTGACAACAAGTCAAT

                                                        
       2050 ACATTTTCAAAGGGACAAATGGCTCGACTTGACAACAAGTCAAT
          1 ACATTTTCAAAGGGACAAATGGCTCGACTTGACAACAAGTCAAT

       2094 TTCAAGAGGG


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  44   44  1.00

ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23


Consensus pattern (44 bp):   
ACATTTTCAAAGGGACAAATGGCTCGACTTGACAACAAGTCAAT
Done.