Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_23560

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: 1731
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.25


Found at i:430 original size:17 final size:18

Alignment explanation


    Indices: 405--444  Score: 57
    Period size: 17  Copynumber: 2.3  Consensus size: 18

        395 TAAGAGAGAA

                *             
        405 AGAAAGAAC-TGAAAAGG
          1 AGAAGGAACGTGAAAAGG

                              
        422 AGAAGGAACGTGAAAAGG
          1 AGAAGGAACGTGAAAAGG

                  
        440 A-AAGG
          1 AGAAGG

        445 GAGAAGGAAC


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

Matches are distributed among these distances:
  17   12  0.57
  18    9  0.43

ACGTcount: A:0.55, C:0.05, G:0.35, T:0.05


Consensus pattern (18 bp):   
AGAAGGAACGTGAAAAGG

Found at i:441 original size:12 final size:12

Alignment explanation


    Indices: 421--475  Score: 56
    Period size: 12  Copynumber: 4.6  Consensus size: 12

        411 AACTGAAAAG

                       *
        421 GAGAAGGAACGT
          1 GAGAAGGAACGC

              *      * *
        433 GAAAAGGAAAGG
          1 GAGAAGGAACGC

                        
        445 GAGAAGGAACGC
          1 GAGAAGGAACGC

                     * *
        457 GAGAAGGAAAGG
          1 GAGAAGGAACGC

                   
        469 GAGAAGG
          1 GAGAAGG

        476 CTGAAAGCAA


Statistics
Matches: 35,  Mismatches: 8, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  12   35  1.00

ACGTcount: A:0.47, C:0.05, G:0.45, T:0.02


Consensus pattern (12 bp):   
GAGAAGGAACGC

Found at i:447 original size:24 final size:24

Alignment explanation


    Indices: 415--475  Score: 95
    Period size: 24  Copynumber: 2.5  Consensus size: 24

        405 AGAAAGAACT

                *            *      
        415 GAAAAGGAGAAGGAACGTGAAAAG
          1 GAAAGGGAGAAGGAACGCGAAAAG

                                *   
        439 GAAAGGGAGAAGGAACGCGAGAAG
          1 GAAAGGGAGAAGGAACGCGAAAAG

                         
        463 GAAAGGGAGAAGG
          1 GAAAGGGAGAAGG

        476 CTGAAAGCAA


Statistics
Matches: 34,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  24   34  1.00

ACGTcount: A:0.49, C:0.05, G:0.44, T:0.02


Consensus pattern (24 bp):   
GAAAGGGAGAAGGAACGCGAAAAG
Done.