Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_16285

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: 2805
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25


Found at i:526 original size:24 final size:24

Alignment explanation


    Indices: 373--531  Score: 207
    Period size: 24  Copynumber: 6.8  Consensus size: 24

        363 GAGGCATGCT

                    *               
        373 CAGCAACAACAGCAGCAGCAACAA
          1 CAGCAACAGCAGCAGCAGCAACAA

              *                 *  *
        397 CAACAACAGCAGCA--A-CAGCAG
          1 CAGCAACAGCAGCAGCAGCAACAA

                 *                  
        418 CAGCAGCAGCAGCAGCAGCAACAA
          1 CAGCAACAGCAGCAGCAGCAACAA

                                    
        442 CAGCAACAGCAGCAGCAGCAACAA
          1 CAGCAACAGCAGCAGCAGCAACAA

                                    
        466 CAGCAACAGCAGCAGCAGCAACAA
          1 CAGCAACAGCAGCAGCAGCAACAA

              *     *     *         
        490 CAACAACAACAGCAACAGCAACAA
          1 CAGCAACAGCAGCAGCAGCAACAA

                 * *          
        514 CAGCAGCCGCAGCAGCAG
          1 CAGCAACAGCAGCAGCAG

        532 TCTCCCCAGC


Statistics
Matches: 115,  Mismatches: 17, Indels: 6
        0.83            0.12        0.04

Matches are distributed among these distances:
  21   16  0.14
  22    1  0.01
  23    1  0.01
  24   97  0.84

ACGTcount: A:0.46, C:0.34, G:0.20, T:0.00


Consensus pattern (24 bp):   
CAGCAACAGCAGCAGCAGCAACAA

Found at i:544 original size:3 final size:3

Alignment explanation


    Indices: 382--531  Score: 120
    Period size: 3  Copynumber: 50.0  Consensus size: 3

        372 TCAGCAACAA

                          *   *   *   *           *                        
        382 CAG CAG CAG CAA CAA CAA CAA CAG CAG CAA CAG CAG CAG CAG CAG CAG
          1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG

                      *   *       *                   *   *       *        
        430 CAG CAG CAA CAA CAG CAA CAG CAG CAG CAG CAA CAA CAG CAA CAG CAG
          1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG

                      *   *   *   *   *       *       *   *          *     
        478 CAG CAG CAA CAA CAA CAA CAA CAG CAA CAG CAA CAA CAG CAG CCG CAG
          1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG

                   
        526 CAG CAG
          1 CAG CAG

        532 TCTCCCCAGC


Statistics
Matches: 127,  Mismatches: 20, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
   3  127  1.00

ACGTcount: A:0.45, C:0.34, G:0.21, T:0.00


Consensus pattern (3 bp):   
CAG

Found at i:1349 original size:6 final size:6

Alignment explanation


    Indices: 1338--1388  Score: 56
    Period size: 6  Copynumber: 9.2  Consensus size: 6

       1328 TGGCTCAGTT

                                      *        *                   
       1338 GCAACA GCAACA G---CA GCAACT GCAACA ACAACA GCAACA GCAACA
          1 GCAACA GCAACA GCAACA GCAACA GCAACA GCAACA GCAACA GCAACA

                    
       1383 G-AACA G
          1 GCAACA G

       1389 TAGCTCACAG


Statistics
Matches: 38,  Mismatches: 4, Indels: 7
        0.78            0.08        0.14

Matches are distributed among these distances:
   3    3  0.08
   5    5  0.13
   6   30  0.79

ACGTcount: A:0.49, C:0.31, G:0.18, T:0.02


Consensus pattern (6 bp):   
GCAACA

Done.