Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold4375

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, 325

Length: 543
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.25


Found at i:185 original size:12 final size:12

Alignment explanation


    Indices: 170--239  Score: 68
    Period size: 12  Copynumber: 5.7  Consensus size: 12

        160 AAAAGAAAAA

                        
        170 GAAAAAGAAGTT
          1 GAAAAAGAAGTT

                        
        182 GAAAAAGAAGTT
          1 GAAAAAGAAGTT

            *        *  
        194 AAAAAAGAAATT
          1 GAAAAAGAAGTT

            *          ***
        206 AAAAAAGAAAAAAA
          1 GAAAAAG--AAGTT

                        
        220 GAAAAAGAAGTT
          1 GAAAAAGAAGTT

                    
        232 GAAAAAGA
          1 GAAAAAGA

        240 GACTGAATTT


Statistics
Matches: 48,  Mismatches: 8, Indels: 4
        0.80            0.13        0.07

Matches are distributed among these distances:
  12   39  0.81
  14    9  0.19

ACGTcount: A:0.70, C:0.00, G:0.19, T:0.11


Consensus pattern (12 bp):   
GAAAAAGAAGTT

Found at i:348 original size:21 final size:21

Alignment explanation


    Indices: 307--349  Score: 52
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        297 CGAAAGTGTG

                           **    
        307 AGGAAAAAGAGAAGATTGAAA
          1 AGGAAAAAGAGAAGAGAGAAA

                                  
        328 AGGAAAAAGA-AATGAGAGAAA
          1 AGGAAAAAGAGAA-GAGAGAAA

             
        349 A
          1 A

        350 AGAGGCAAGT


Statistics
Matches: 19,  Mismatches: 2, Indels: 2
        0.83            0.09        0.09

Matches are distributed among these distances:
  20    2  0.11
  21   17  0.89

ACGTcount: A:0.65, C:0.00, G:0.28, T:0.07


Consensus pattern (21 bp):   
AGGAAAAAGAGAAGAGAGAAA
Done.