Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_34605

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, 200

Length: 318
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.19


Found at i:70 original size:18 final size:18

Alignment explanation


    Indices: 49--91  Score: 61
    Period size: 18  Copynumber: 2.4  Consensus size: 18

         39 GAAGGAAGTT

                           *   
         49 GTTGCTGC-AGAAGAGGAA
          1 GTTGCTGCTA-AAGAAGAA

                              
         67 GTTGCTGCTAAAGAAGAA
          1 GTTGCTGCTAAAGAAGAA

                   
         85 GTTGCTG
          1 GTTGCTG

         92 AAAATGAGAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  18   22  0.96
  19    1  0.04

ACGTcount: A:0.30, C:0.12, G:0.35, T:0.23


Consensus pattern (18 bp):   
GTTGCTGCTAAAGAAGAA

Found at i:81 original size:21 final size:21

Alignment explanation


    Indices: 41--83  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

         31 GTTGTTGAGA

                     *    **     
         41 AGGAAGTTGTTGCTGCAGAAG
          1 AGGAAGTTGCTGCTAAAGAAG

                                 
         62 AGGAAGTTGCTGCTAAAGAAG
          1 AGGAAGTTGCTGCTAAAGAAG

             
         83 A
          1 A

         84 AGTTGCTGAA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.35, C:0.09, G:0.35, T:0.21


Consensus pattern (21 bp):   
AGGAAGTTGCTGCTAAAGAAG
Done.