Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga09g00483.N78

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, 348

Length: 580
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24


Found at i:284 original size:12 final size:12

Alignment explanation


    Indices: 269--315  Score: 51
    Period size: 12  Copynumber: 3.9  Consensus size: 12

        259 GAAAAAGGAA

                        
        269 GAAAAGAAAGAG
          1 GAAAAGAAAGAG

                       *
        281 GAAAAGAAAGAA
          1 GAAAAGAAAGAG

                     *   
        293 GAGAAA-AACGAG
          1 GA-AAAGAAAGAG

              *        
        305 GAGAAGAAAGA
          1 GAAAAGAAAGA

        316 AGTCAAGGAA


Statistics
Matches: 28,  Mismatches: 5, Indels: 4
        0.76            0.14        0.11

Matches are distributed among these distances:
  11    2  0.07
  12   23  0.82
  13    3  0.11

ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00


Consensus pattern (12 bp):   
GAAAAGAAAGAG

Found at i:285 original size:21 final size:21

Alignment explanation


    Indices: 250--298  Score: 64
    Period size: 21  Copynumber: 2.4  Consensus size: 21

        240 TAGGACCTGC

                             *   
        250 AAAAG-AAGAGAAAAAGGAAG
          1 AAAAGAAAGAGAAAAAGAAAG

                       *         
        270 AAAAGAAAGAGGAAAAGAAAG
          1 AAAAGAAAGAGAAAAAGAAAG

              *     
        291 AAGAGAAA
          1 AAAAGAAA

        299 AACGAGGAGA


Statistics
Matches: 25,  Mismatches: 3, Indels: 1
        0.86            0.10        0.03

Matches are distributed among these distances:
  20    5  0.20
  21   20  0.80

ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00


Consensus pattern (21 bp):   
AAAAGAAAGAGAAAAAGAAAG

Found at i:293 original size:24 final size:24

Alignment explanation


    Indices: 266--317  Score: 70
    Period size: 24  Copynumber: 2.2  Consensus size: 24

        256 AGAGAAAAAG

                                     
        266 GAAGA-AAAGAAAGAGGAAAAGAAA
          1 GAAGAGAAA-AAAGAGGAAAAGAAA

                       *     *      
        290 GAAGAGAAAAACGAGGAGAAGAAA
          1 GAAGAGAAAAAAGAGGAAAAGAAA

                
        314 GAAG
          1 GAAG

        318 TCAAGGAAGA


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  24   22  0.88
  25    3  0.12

ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00


Consensus pattern (24 bp):   
GAAGAGAAAAAAGAGGAAAAGAAA
Done.