Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_36502

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, 781

Length: 1302
ACGTcount: A:0.35, C:0.14, G:0.31, T:0.20


Found at i:472 original size:21 final size:21

Alignment explanation


    Indices: 448--487  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        438 ACTCTTGGAA

                    *            
        448 GAGGAAGAGGAGGAGGAAGTG
          1 GAGGAAGAAGAGGAGGAAGTG

                               
        469 GAGGAAGAAGAGGAGGAAG
          1 GAGGAAGAAGAGGAGGAAG

        488 AGTCGGAGTA


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

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.42, C:0.00, G:0.55, T:0.03


Consensus pattern (21 bp):   
GAGGAAGAAGAGGAGGAAGTG

Found at i:486 original size:12 final size:12

Alignment explanation


    Indices: 451--488  Score: 58
    Period size: 12  Copynumber: 3.2  Consensus size: 12

        441 CTTGGAAGAG

                       *
        451 GAAGAGGAGGAG
          1 GAAGAGGAGGAA

                *       
        463 GAAGTGGAGGAA
          1 GAAGAGGAGGAA

                        
        475 GAAGAGGAGGAA
          1 GAAGAGGAGGAA

              
        487 GA
          1 GA

        489 GTCGGAGTAT


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  12   23  1.00

ACGTcount: A:0.45, C:0.00, G:0.53, T:0.03


Consensus pattern (12 bp):   
GAAGAGGAGGAA
Done.