Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g00100.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: 2041
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29


Found at i:644 original size:15 final size:15

Alignment explanation


    Indices: 619--671  Score: 54
    Period size: 15  Copynumber: 3.5  Consensus size: 15

        609 AGACTATGGA

                  *        
        619 AGAAGAGGTGGA-GT
          1 AGAAGAAGTGGAGGT

                            
        633 ATGAAGAAGTGGAGGT
          1 A-GAAGAAGTGGAGGT

                    **    *
        649 AGAAGAAGAAGAGGA
          1 AGAAGAAGTGGAGGT

                    
        664 AGAAGAAG
          1 AGAAGAAG

        672 AAGAGGAGGA


Statistics
Matches: 33,  Mismatches: 4, Indels: 3
        0.82            0.10        0.08

Matches are distributed among these distances:
  14    1  0.03
  15   29  0.88
  16    3  0.09

ACGTcount: A:0.47, C:0.00, G:0.43, T:0.09


Consensus pattern (15 bp):   
AGAAGAAGTGGAGGT

Found at i:680 original size:18 final size:18

Alignment explanation


    Indices: 617--684  Score: 66
    Period size: 18  Copynumber: 3.8  Consensus size: 18

        607 GGAGACTATG

                      *       *
        617 GAAGAAGAGGTGG-AGTAT
          1 GAAGAAGAGGAGGAAG-AA

                   *     *    
        635 GAAGAAGTGGAGGTAGAA
          1 GAAGAAGAGGAGGAAGAA

                       *      
        653 GAAGAAGAGGAAGAAGAA
          1 GAAGAAGAGGAGGAAGAA

                 *        
        671 GAAGAGGAGGAGGA
          1 GAAGAAGAGGAGGA

        685 GGAGGAGGAA


Statistics
Matches: 41,  Mismatches: 8, Indels: 2
        0.80            0.16        0.04

Matches are distributed among these distances:
  18   39  0.95
  19    2  0.05

ACGTcount: A:0.47, C:0.00, G:0.46, T:0.07


Consensus pattern (18 bp):   
GAAGAAGAGGAGGAAGAA
Done.