Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_32497

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, 399

Length: 665
ACGTcount: A:0.38, C:0.16, G:0.28, T:0.18


Found at i:325 original size:17 final size:17

Alignment explanation


    Indices: 303--338  Score: 56
    Period size: 17  Copynumber: 2.1  Consensus size: 17

        293 AGAAGAACCG

                              
        303 AGGAAAGAAGAAA-AGAA
          1 AGGAAAG-AGAAAGAGAA

                             
        320 AGGAAAGAGAAAGAGAA
          1 AGGAAAGAGAAAGAGAA

              
        337 AG
          1 AG

        339 AGAGGGAAGA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  16    5  0.28
  17   13  0.72

ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00


Consensus pattern (17 bp):   
AGGAAAGAGAAAGAGAA

Found at i:333 original size:6 final size:6

Alignment explanation


    Indices: 305--341  Score: 51
    Period size: 6  Copynumber: 6.3  Consensus size: 6

        295 AAGAACCGAG

                                                         
        305 GAAAGAA GAAA-A GAAAG- GAAAGA GAAAGA GAAAGA GA
          1 GAAAG-A GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA GA

        342 GGGAAGAAGA


Statistics
Matches: 28,  Mismatches: 0, Indels: 5
        0.85            0.00        0.15

Matches are distributed among these distances:
   5   10  0.36
   6   14  0.50
   7    4  0.14

ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00


Consensus pattern (6 bp):   
GAAAGA

Done.