Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_22901

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, 388

Length: 648
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.22


Found at i:549 original size:21 final size:21

Alignment explanation


    Indices: 502--553  Score: 68
    Period size: 21  Copynumber: 2.5  Consensus size: 21

        492 TAGAGAGGAG

                   *           **
        502 GCAGCAGAGAGGGAGGCAGCG
          1 GCAGCAGCGAGGGAGGCAGAA

             *                   
        523 GTAGCAGCGAGGGAGGCAGAA
          1 GCAGCAGCGAGGGAGGCAGAA

                      
        544 GCAGCAGCGA
          1 GCAGCAGCGA

        554 TGGCAGCAGA


Statistics
Matches: 26,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   26  1.00

ACGTcount: A:0.31, C:0.19, G:0.48, T:0.02


Consensus pattern (21 bp):   
GCAGCAGCGAGGGAGGCAGAA

Found at i:562 original size:21 final size:20

Alignment explanation


    Indices: 502--567  Score: 53
    Period size: 21  Copynumber: 3.2  Consensus size: 20

        492 TAGAGAGGAG

                   *    *       *
        502 GCAGCAGAGAGGGAGGCAGCG
          1 GCAGCAGCGAGGCAGGCAG-A

             *          *        
        523 GTAGCAGCGAGGGAGGCAGAA
          1 GCAGCAGCGAGGCAGGCAG-A

                                 
        544 GCAGCAGCGATGGCA-GCAGA
          1 GCAGCAGCGA-GGCAGGCAGA

                
        564 GCAG
          1 GCAG

        568 AGTAGAAAGT


Statistics
Matches: 38,  Mismatches: 6, Indels: 3
        0.81            0.13        0.06

Matches are distributed among these distances:
  20    5  0.13
  21   30  0.79
  22    3  0.08

ACGTcount: A:0.30, C:0.20, G:0.47, T:0.03


Consensus pattern (20 bp):   
GCAGCAGCGAGGCAGGCAGA
Done.