Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_14459

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, 410

Length: 684
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.22


Found at i:651 original size:6 final size:6

Alignment explanation


    Indices: 602--643  Score: 75
    Period size: 6  Copynumber: 7.0  Consensus size: 6

        592 GATGCGAAAC

                                      *                     
        602 CAGAAG CAGAAG CAGAAG CAGAAA CAGAAG CAGAAG CAGAAG
          1 CAGAAG CAGAAG CAGAAG CAGAAG CAGAAG CAGAAG CAGAAG

        644 AAACAGAAGA


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   6   34  1.00

ACGTcount: A:0.52, C:0.17, G:0.31, T:0.00


Consensus pattern (6 bp):   
CAGAAG

Found at i:654 original size:12 final size:12

Alignment explanation


    Indices: 597--643  Score: 67
    Period size: 12  Copynumber: 3.8  Consensus size: 12

        587 AAGATGATGC

                         
        597 GAAACCAGAAGCA
          1 GAAA-CAGAAGCA

               *        
        610 GAAGCAGAAGCA
          1 GAAACAGAAGCA

                        
        622 GAAACAGAAGCA
          1 GAAACAGAAGCA

               *      
        634 GAAGCAGAAG
          1 GAAACAGAAG

        644 AAACAGAAGA


Statistics
Matches: 31,  Mismatches: 3, Indels: 1
        0.89            0.09        0.03

Matches are distributed among these distances:
  12   28  0.90
  13    3  0.10

ACGTcount: A:0.53, C:0.17, G:0.30, T:0.00


Consensus pattern (12 bp):   
GAAACAGAAGCA

Found at i:664 original size:21 final size:21

Alignment explanation


    Indices: 621--666  Score: 56
    Period size: 21  Copynumber: 2.2  Consensus size: 21

        611 AAGCAGAAGC

                       * *       
        621 AGAAACAGAAGCAGAAGCAGA
          1 AGAAACAGAAGAAAAAGCAGA

                            * *  
        642 AGAAACAGAAGAAAAATCTGA
          1 AGAAACAGAAGAAAAAGCAGA

                
        663 AGAA
          1 AGAA

        667 GCTGGTGCAG


Statistics
Matches: 21,  Mismatches: 4, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.61, C:0.11, G:0.24, T:0.04


Consensus pattern (21 bp):   
AGAAACAGAAGAAAAAGCAGA
Done.