Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga13g00515.F3

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: 4522
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31


Found at i:26 original size:17 final size:17

Alignment explanation


    Indices: 4--48  Score: 67
    Period size: 16  Copynumber: 2.8  Consensus size: 17

          1 AGC

                             
          4 AAAAGAG-AAAAAAAAA
          1 AAAAGAGAAAAAAAAAA

                             
         20 AAAA-AGAAAAAAAAAA
          1 AAAAGAGAAAAAAAAAA

            *            
         36 GAAAGAGAAAAAA
          1 AAAAGAGAAAAAA

         49 CCTCTCCTCA


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  15    2  0.08
  16   16  0.62
  17    8  0.31

ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00


Consensus pattern (17 bp):   
AAAAGAGAAAAAAAAAA

Found at i:27 original size:15 final size:15

Alignment explanation


    Indices: 4--48  Score: 63
    Period size: 15  Copynumber: 2.9  Consensus size: 15

          1 AGC

                *          
          4 AAAAGAGAAAAAAAA
          1 AAAAAAGAAAAAAAA

                           
         19 AAAAAAGAAAAAAAA
          1 AAAAAAGAAAAAAAA

                           
         34 AAGAAAGAGAAAAAA
          1 AA-AAA-AGAAAAAA

         49 CCTCTCCTCA


Statistics
Matches: 27,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  15   16  0.59
  16    3  0.11
  17    8  0.30

ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00


Consensus pattern (15 bp):   
AAAAAAGAAAAAAAA

Found at i:29 original size:11 final size:11

Alignment explanation


    Indices: 11--39  Score: 51
    Period size: 11  Copynumber: 2.7  Consensus size: 11

          1 AGCAAAAGAG

                       
         11 AAAA-AAAAAA
          1 AAAAGAAAAAA

                       
         21 AAAAGAAAAAA
          1 AAAAGAAAAAA

                    
         32 AAAAGAAA
          1 AAAAGAAA

         40 GAGAAAAAAC


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  10    4  0.22
  11   14  0.78

ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00


Consensus pattern (11 bp):   
AAAAGAAAAAA
Done.