Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_10180

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, 855

Length: 1425
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.24


Found at i:127 original size:15 final size:15

Alignment explanation


    Indices: 109--160  Score: 59
    Period size: 15  Copynumber: 3.5  Consensus size: 15

         99 AGAGGAAGAG

                          *
        109 GAGGAAGTGGAAGTT
          1 GAGGAAGTGGAAGTA

                   *  *  * 
        124 GAGGAAGAGGTAGAA
          1 GAGGAAGTGGAAGTA

                           
        139 GAGGAAGTGGAAGTA
          1 GAGGAAGTGGAAGTA

              *    
        154 GAAGAAG
          1 GAGGAAG

        161 AAGAGGACGA


Statistics
Matches: 29,  Mismatches: 8, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
  15   29  1.00

ACGTcount: A:0.42, C:0.00, G:0.46, T:0.12


Consensus pattern (15 bp):   
GAGGAAGTGGAAGTA

Found at i:132 original size:24 final size:24

Alignment explanation


    Indices: 100--146  Score: 69
    Period size: 24  Copynumber: 2.0  Consensus size: 24

         90 TGAAGAAATA

                             *       
        100 GAGGAAGAGG-AGGAAGTGGAAGTT
          1 GAGGAAGAGGTA-GAAGAGGAAGTT

                                   
        124 GAGGAAGAGGTAGAAGAGGAAGT
          1 GAGGAAGAGGTAGAAGAGGAAGT

        147 GGAAGTAGAA


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

Matches are distributed among these distances:
  24   20  0.95
  25    1  0.05

ACGTcount: A:0.40, C:0.00, G:0.49, T:0.11


Consensus pattern (24 bp):   
GAGGAAGAGGTAGAAGAGGAAGTT

Found at i:143 original size:30 final size:30

Alignment explanation


    Indices: 99--161  Score: 90
    Period size: 30  Copynumber: 2.1  Consensus size: 30

         89 ATGAAGAAAT

                     *              *  *  
         99 AGAGGAAGAGGAGGAAGTGGAAGTTGAGGA
          1 AGAGGAAGAAGAGGAAGTGGAAGTAGAAGA

                 *                        
        129 AGAGGTAGAAGAGGAAGTGGAAGTAGAAGA
          1 AGAGGAAGAAGAGGAAGTGGAAGTAGAAGA

               
        159 AGA
          1 AGA

        162 AGAGGACGAG


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  30   29  1.00

ACGTcount: A:0.44, C:0.00, G:0.46, T:0.10


Consensus pattern (30 bp):   
AGAGGAAGAAGAGGAAGTGGAAGTAGAAGA

Done.