Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_12161

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: 2337
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24


Found at i:183 original size:12 final size:12

Alignment explanation


    Indices: 168--196  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

        158 ACGAAGACTT

                        
        168 CGAGGAAGAAGA
          1 CGAGGAAGAAGA

                        
        180 CGAGGAAGAAGA
          1 CGAGGAAGAAGA

                  
        192 -GAGGA
          1 CGAGGA

        197 GGAGAGAGAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  11    5  0.29
  12   12  0.71

ACGTcount: A:0.48, C:0.07, G:0.45, T:0.00


Consensus pattern (12 bp):   
CGAGGAAGAAGA

Found at i:379 original size:15 final size:15

Alignment explanation


    Indices: 349--393  Score: 54
    Period size: 15  Copynumber: 3.0  Consensus size: 15

        339 GGAGGAAGTG

                 *     *   
        349 GAGGAGGAAGAAGAA
          1 GAGGAAGAAGAGGAA

              *     *      
        364 GATGAAGATGAGGAA
          1 GAGGAAGAAGAGGAA

                           
        379 GAGGAAGAAGAGGAA
          1 GAGGAAGAAGAGGAA

        394 AGTGAGAGAA


Statistics
Matches: 24,  Mismatches: 6, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  15   24  1.00

ACGTcount: A:0.51, C:0.00, G:0.44, T:0.04


Consensus pattern (15 bp):   
GAGGAAGAAGAGGAA

Found at i:399 original size:24 final size:23

Alignment explanation


    Indices: 340--409  Score: 68
    Period size: 24  Copynumber: 2.8  Consensus size: 23

        330 AACGGCGAAG

                          *         
        340 GAGGAAGTGGAGGAGGAAGAAGAA
          1 GAGGAAGT-GAGGAAGAAGAAGAA

              *              *      
        364 GATGAAGATGAGGAAGAGGAAGAA
          1 GAGGAAG-TGAGGAAGAAGAAGAA

                                  
        388 GAGGAAAGTGAGAGAAGGAAGA
          1 GAGG-AAGTGAG-GAA-GAAGA

        410 GAAAGATTAA


Statistics
Matches: 37,  Mismatches: 5, Indels: 6
        0.77            0.10        0.12

Matches are distributed among these distances:
  24   26  0.70
  25    7  0.19
  26    4  0.11

ACGTcount: A:0.49, C:0.00, G:0.46, T:0.06


Consensus pattern (23 bp):   
GAGGAAGTGAGGAAGAAGAAGAA
Done.