Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_06187

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, 432

Length: 720
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.24


Found at i:364 original size:24 final size:24

Alignment explanation


    Indices: 337--489  Score: 98
    Period size: 24  Copynumber: 6.2  Consensus size: 24

        327 TGGCACAAGC

                                    
        337 ACAACACCATCCACAGGGACTCCG
          1 ACAACACCATCCACAGGGACTCCG

                 *                    
        361 ACAACTCCGAGT--ACAGGGACTCCG
          1 ACAACACC-A-TCCACAGGGACTCCG

                 *      *           *
        385 ACAACTCCGA-CTACAGGGACTCCA
          1 ACAACACC-ATCCACAGGGACTCCG

                           *           *
        409 ACAACACC-TACCACGGGGACTCCTACC
          1 ACAACACCAT-CCACAGGGACT-C--CG

                     *             *
        436 ACAACACCAACCACAGGGACTCCT
          1 ACAACACCATCCACAGGGACTCCG

              *      * *  *     *   
        460 ACCACACCAACAACGGGGACACCG
          1 ACAACACCATCCACAGGGACTCCG

                  
        484 ACAACA
          1 ACAACA

        490 GGGACAAGCA


Statistics
Matches: 104,  Mismatches: 15, Indels: 20
        0.75            0.11        0.14

Matches are distributed among these distances:
  24   81  0.78
  25    2  0.02
  26    2  0.02
  27   19  0.18

ACGTcount: A:0.35, C:0.40, G:0.17, T:0.08


Consensus pattern (24 bp):   
ACAACACCATCCACAGGGACTCCG

Found at i:443 original size:27 final size:27

Alignment explanation


    Indices: 397--465  Score: 99
    Period size: 27  Copynumber: 2.7  Consensus size: 27

        387 AACTCCGACT

                                   *   
        397 ACAGGGACTCC-A--ACAACACCTACC
          1 ACAGGGACTCCTACCACAACACCAACC

              *                        
        421 ACGGGGACTCCTACCACAACACCAACC
          1 ACAGGGACTCCTACCACAACACCAACC

                              
        448 ACAGGGACTCCTACCACA
          1 ACAGGGACTCCTACCACA

        466 CCAACAACGG


Statistics
Matches: 39,  Mismatches: 3, Indels: 3
        0.87            0.07        0.07

Matches are distributed among these distances:
  24   10  0.26
  25    1  0.03
  27   28  0.72

ACGTcount: A:0.35, C:0.42, G:0.14, T:0.09


Consensus pattern (27 bp):   
ACAGGGACTCCTACCACAACACCAACC

Found at i:465 original size:15 final size:15

Alignment explanation


    Indices: 415--465  Score: 54
    Period size: 15  Copynumber: 3.6  Consensus size: 15

        405 TCCAACAACA

                    *      
        415 CCTACCACGGGGACT
          1 CCTACCACAGGGACT

                          *
        430 CCTACCACA---ACA
          1 CCTACCACAGGGACT

              *            
        442 CCAACCACAGGGACT
          1 CCTACCACAGGGACT

                     
        457 CCTACCACA
          1 CCTACCACA

        466 CCAACAACGG


Statistics
Matches: 28,  Mismatches: 5, Indels: 6
        0.72            0.13        0.15

Matches are distributed among these distances:
  12   10  0.36
  15   18  0.64

ACGTcount: A:0.31, C:0.45, G:0.14, T:0.10


Consensus pattern (15 bp):   
CCTACCACAGGGACT
Done.