Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_18394

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, 1000

Length: 6510
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27


Found at i:2800 original size:27 final size:27

Alignment explanation


    Indices: 2762--2813  Score: 86
    Period size: 27  Copynumber: 1.9  Consensus size: 27

       2752 GTACGTGGTC

                         *      *      
       2762 GCTCCAAAGGGACGTCTGAGGGTAGTG
          1 GCTCCAAAGGGACCTCTGAGCGTAGTG

                                     
       2789 GCTCCAAAGGGACCTCTGAGCGTAG
          1 GCTCCAAAGGGACCTCTGAGCGTAG

       2814 AGCAAGGCGA


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   23  1.00

ACGTcount: A:0.23, C:0.23, G:0.37, T:0.17


Consensus pattern (27 bp):   
GCTCCAAAGGGACCTCTGAGCGTAGTG

Found at i:4267 original size:24 final size:24

Alignment explanation


    Indices: 4235--4280  Score: 58
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       4225 ACTTCCACTG

                                     
       4235 CTGTGGCAATA-GCAGCAGCTGCTT
          1 CTGTGGCAA-AGGCAGCAGCTGCTT

                *        *        
       4259 CTGTTGCAAAGGCTGCAGCTGC
          1 CTGTGGCAAAGGCAGCAGCTGC

       4281 AGCTGCCAAG


Statistics
Matches: 19,  Mismatches: 2, Indels: 2
        0.83            0.09        0.09

Matches are distributed among these distances:
  23    1  0.05
  24   18  0.95

ACGTcount: A:0.20, C:0.26, G:0.30, T:0.24


Consensus pattern (24 bp):   
CTGTGGCAAAGGCAGCAGCTGCTT
Done.