Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_24030

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, 734

Length: 1224
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26


Found at i:86 original size:6 final size:6

Alignment explanation


    Indices: 77--123  Score: 51
    Period size: 6  Copynumber: 7.8  Consensus size: 6

         67 GTGGTGGTGG

                                *                *          *      
         77 AAGAAA AAGAACA AA-AAG AAGAAA AAGAAA ATGAAA AAGAAG AAGAA
          1 AAGAAA AAGAA-A AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAA

        124 GAAGCACATC


Statistics
Matches: 34,  Mismatches: 5, Indels: 4
        0.79            0.12        0.09

Matches are distributed among these distances:
   5    2  0.06
   6   29  0.85
   7    3  0.09

ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02


Consensus pattern (6 bp):   
AAGAAA

Found at i:119 original size:24 final size:24

Alignment explanation


    Indices: 77--123  Score: 69
    Period size: 24  Copynumber: 2.0  Consensus size: 24

         67 GTGGTGGTGG

                                    
         77 AAGAAAAAGAACAAAAAGAAGAAA
          1 AAGAAAAAGAACAAAAAGAAGAAA

                   *                
        101 AAGAAAATGAA-AAAGAAGAAGAA
          1 AAGAAAAAGAACAAA-AAGAAGAA

        124 GAAGCACATC


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  23    3  0.14
  24   18  0.86

ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02


Consensus pattern (24 bp):   
AAGAAAAAGAACAAAAAGAAGAAA

Found at i:127 original size:9 final size:9

Alignment explanation


    Indices: 76--127  Score: 59
    Period size: 9  Copynumber: 5.4  Consensus size: 9

         66 GGTGGTGGTG

                     
         76 GAAGAAAAA
          1 GAAGAAAAA

               *     
         85 GAACAAAAA
          1 GAAGAAAAA

                     
         94 GAAGAAAAA
          1 GAAGAAAAA

                        
        103 GAAAATGAAAAA
          1 G--AA-GAAAAA

                  *  
        115 GAAGAAGAA
          1 GAAGAAAAA

                
        124 GAAG
          1 GAAG

        128 CACATCCATA


Statistics
Matches: 37,  Mismatches: 3, Indels: 6
        0.80            0.07        0.13

Matches are distributed among these distances:
   9   26  0.70
  10    2  0.05
  11    2  0.05
  12    7  0.19

ACGTcount: A:0.73, C:0.02, G:0.23, T:0.02


Consensus pattern (9 bp):   
GAAGAAAAA
Done.