Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_04626

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, 412

Length: 687
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.18


Found at i:502 original size:15 final size:15

Alignment explanation


    Indices: 484--540  Score: 55
    Period size: 15  Copynumber: 3.9  Consensus size: 15

        474 GGAAAACAAG

                           
        484 GAAGAAGAGAAGAAA
          1 GAAGAAGAGAAGAAA

                *          
        499 GAAGCAGAGAAGAAA
          1 GAAGAAGAGAAGAAA

            *    *    *  * 
        514 CAAGATGA-AGGAGA
          1 GAAGAAGAGAAGAAA

                          
        528 GAAGAA-AGAAGAA
          1 GAAGAAGAGAAGAA

        541 GATCAAGGCA


Statistics
Matches: 31,  Mismatches: 10, Indels: 3
        0.70            0.23        0.07

Matches are distributed among these distances:
  13    1  0.03
  14   11  0.35
  15   19  0.61

ACGTcount: A:0.61, C:0.04, G:0.33, T:0.02


Consensus pattern (15 bp):   
GAAGAAGAGAAGAAA

Found at i:528 original size:21 final size:21

Alignment explanation


    Indices: 499--539  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        489 AGAGAAGAAA

                                 
        499 GAAGCAGAGAAGAAACAAGAT
          1 GAAGCAGAGAAGAAACAAGAT

                *          *    
        520 GAAGGAGAGAAGAAAGAAGA
          1 GAAGCAGAGAAGAAACAAGA

        540 AGATCAAGGC


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

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.59, C:0.05, G:0.34, T:0.02


Consensus pattern (21 bp):   
GAAGCAGAGAAGAAACAAGAT
Done.