Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_05855

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: 4214
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31


Found at i:77 original size:12 final size:12

Alignment explanation


    Indices: 60--90  Score: 53
    Period size: 12  Copynumber: 2.6  Consensus size: 12

         50 CTCAGGCAAG

                        
         60 AGAAGAAGACGA
          1 AGAAGAAGACGA

                        
         72 AGAAGAAGACGA
          1 AGAAGAAGACGA

            *      
         84 CGAAGAA
          1 AGAAGAA

         91 AAAAGCAGAA


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

Matches are distributed among these distances:
  12   18  1.00

ACGTcount: A:0.58, C:0.10, G:0.32, T:0.00


Consensus pattern (12 bp):   
AGAAGAAGACGA

Found at i:80 original size:15 final size:15

Alignment explanation


    Indices: 60--90  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

         50 CTCAGGCAAG

                           
         60 AGAAGAAGACGAAGA
          1 AGAAGAAGACGAAGA

                  *        
         75 AGAAGACGACGAAGA
          1 AGAAGAAGACGAAGA

             
         90 A
          1 A

         91 AAAAGCAGAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.58, C:0.10, G:0.32, T:0.00


Consensus pattern (15 bp):   
AGAAGAAGACGAAGA

Found at i:3734 original size:21 final size:21

Alignment explanation


    Indices: 3708--3752  Score: 90
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       3698 CCAAAAGAAG

                                 
       3708 CCAAACTTGAAAGAACGGACC
          1 CCAAACTTGAAAGAACGGACC

                                 
       3729 CCAAACTTGAAAGAACGGACC
          1 CCAAACTTGAAAGAACGGACC

               
       3750 CCA
          1 CCA

       3753 TTACAACTTC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.42, C:0.31, G:0.18, T:0.09


Consensus pattern (21 bp):   
CCAAACTTGAAAGAACGGACC
Done.