Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_20437

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: 2676
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27


Found at i:358 original size:3 final size:3

Alignment explanation


    Indices: 337--412  Score: 53
    Period size: 3  Copynumber: 25.3  Consensus size: 3

        327 GAGGCATGCT

                  *           *           *   *   *           *           *
        337 CAG CAA CAG CAG CAT CAG CAG CAA CAA CAA CAG CAG CAT CAG CAG CAA
          1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG

              *   *               *       *      
        385 CAA CAA CAG CAG CAG CAA CAG CAA CAG C
          1 CAG CAG CAG CAG CAG CAG CAG CAG CAG C

        413 CACAGCAACA


Statistics
Matches: 59,  Mismatches: 14, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
   3   59  1.00

ACGTcount: A:0.45, C:0.34, G:0.18, T:0.03


Consensus pattern (3 bp):   
CAG

Found at i:369 original size:24 final size:24

Alignment explanation


    Indices: 340--419  Score: 124
    Period size: 24  Copynumber: 3.3  Consensus size: 24

        330 GCATGCTCAG

                                    
        340 CAACAGCAGCATCAGCAGCAACAA
          1 CAACAGCAGCATCAGCAGCAACAA

                                    
        364 CAACAGCAGCATCAGCAGCAACAA
          1 CAACAGCAGCATCAGCAGCAACAA

                       *  *        *
        388 CAACAGCAGCAGCAACAGCAACAG
          1 CAACAGCAGCATCAGCAGCAACAA

             *      
        412 CCACAGCA
          1 CAACAGCA

        420 ACAGCCACAA


Statistics
Matches: 52,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  24   52  1.00

ACGTcount: A:0.45, C:0.35, G:0.17, T:0.03


Consensus pattern (24 bp):   
CAACAGCAGCATCAGCAGCAACAA

Found at i:409 original size:18 final size:18

Alignment explanation


    Indices: 337--446  Score: 93
    Period size: 18  Copynumber: 6.3  Consensus size: 18

        327 GAGGCATGCT

                       *  *   
        337 CAGCAACAGCAGCATCAG
          1 CAGCAACAGCAACAGCAG

                    *         
        355 CAGCAACAACAACAGCAG
          1 CAGCAACAGCAACAGCAG

              *  *        *  *
        373 CATCAGCAGCAACAACAA
          1 CAGCAACAGCAACAGCAG

                 *           *
        391 CAGCAGCAGCAACAGCAA
          1 CAGCAACAGCAACAGCAG

                *             
        409 CAGCCACAGCAACAGC--
          1 CAGCAACAGCAACAGCAG

                               
        425 CA-CAAC-GCCAACAGCAG
          1 CAGCAACAG-CAACAGCAG

                 
        442 CAGCA
          1 CAGCA

        447 GCGAAGAGAA


Statistics
Matches: 75,  Mismatches: 13, Indels: 8
        0.78            0.14        0.08

Matches are distributed among these distances:
  14    1  0.01
  15   10  0.13
  16    2  0.03
  17    2  0.03
  18   60  0.80

ACGTcount: A:0.44, C:0.36, G:0.18, T:0.02


Consensus pattern (18 bp):   
CAGCAACAGCAACAGCAG

Found at i:417 original size:6 final size:6

Alignment explanation


    Indices: 337--424  Score: 86
    Period size: 6  Copynumber: 14.7  Consensus size: 6

        327 GAGGCATGCT

                        *   *  *          *         *   *  *       
        337 CAGCAA CAGCAG CATCAG CAGCAA CAACAA CAGCAG CATCAG CAGCAA
          1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA

              *         *                   *             
        385 CAACAA CAGCAG CAGCAA CAGCAA CAGCCA CAGCAA CAGC
          1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGC

        425 CACAACGCCA


Statistics
Matches: 66,  Mismatches: 16, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
   6   66  1.00

ACGTcount: A:0.44, C:0.35, G:0.18, T:0.02


Consensus pattern (6 bp):   
CAGCAA

Done.