Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_19859

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, 347

Length: 579
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24


Found at i:496 original size:9 final size:10

Alignment explanation


    Indices: 489--545  Score: 55
    Period size: 11  Copynumber: 5.5  Consensus size: 10

        479 AAGAGAAAAC

                      
        489 AAAGAAAAGA
          1 AAAGAAAAGA

                        
        499 AAAGAAAAAGCA
          1 AAAG-AAAAG-A

                  *   
        511 AAAGAAGA-A
          1 AAAGAAAAGA

                       
        520 AAAGAAAATGA
          1 AAAGAAAA-GA

                       
        531 AATA-AAAAGA
          1 AA-AGAAAAGA

                 
        541 AAAGA
          1 AAAGA

        546 GAGGCAAGAG


Statistics
Matches: 39,  Mismatches: 2, Indels: 12
        0.74            0.04        0.23

Matches are distributed among these distances:
   9    9  0.23
  10    9  0.23
  11   15  0.38
  12    6  0.15

ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04


Consensus pattern (10 bp):   
AAAGAAAAGA

Found at i:512 original size:21 final size:20

Alignment explanation


    Indices: 478--545  Score: 66
    Period size: 21  Copynumber: 3.2  Consensus size: 20

        468 ACATTCTTGT

                                  
        478 AAAGAGAAAA-CAAAGAAAAGA
          1 AAAGA-AAAAGCAAA-AAAAGA

                           *     
        499 AAAGAAAAAGCAAAAGAAGAA
          1 AAAGAAAAAGCAAAAAAAG-A

                    * *          
        520 AAAGAAAATGAAATAAAAAGA
          1 AAAGAAAAAGCAA-AAAAAGA

                 
        541 AAAGA
          1 AAAGA

        546 GAGGCAAGAG


Statistics
Matches: 40,  Mismatches: 4, Indels: 6
        0.80            0.08        0.12

Matches are distributed among these distances:
  20    8  0.20
  21   27  0.68
  22    5  0.12

ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03


Consensus pattern (20 bp):   
AAAGAAAAAGCAAAAAAAGA

Found at i:513 original size:6 final size:5

Alignment explanation


    Indices: 489--545  Score: 55
    Period size: 5  Copynumber: 11.0  Consensus size: 5

        479 AAGAGAAAAC

                                             *                       
        489 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
          1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA

                       
        536 AAAGA AAAGA
          1 AAAGA AAAGA

        546 GAGGCAAGAG


Statistics
Matches: 44,  Mismatches: 3, Indels: 10
        0.77            0.05        0.18

Matches are distributed among these distances:
   4    4  0.09
   5   25  0.57
   6   14  0.32
   7    1  0.02

ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04


Consensus pattern (5 bp):   
AAAGA

Found at i:520 original size:15 final size:14

Alignment explanation


    Indices: 489--545  Score: 60
    Period size: 16  Copynumber: 3.7  Consensus size: 14

        479 AAGAGAAAAC

                            
        489 AAAGAAAAGAAAAGAA
          1 AAAGAAAAG--AAGAA

                           
        505 AAAGCAAAAGAAGAA
          1 AAAG-AAAAGAAGAA

                         *  
        520 AAAGAAAATGAAATAA
          1 AAAGAAAA-G-AAGAA

                      
        536 AAAGAAAAGA
          1 AAAGAAAAGA

        546 GAGGCAAGAG


Statistics
Matches: 37,  Mismatches: 1, Indels: 8
        0.80            0.02        0.17

Matches are distributed among these distances:
  14    5  0.14
  15   11  0.30
  16   16  0.43
  17    5  0.14

ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04


Consensus pattern (14 bp):   
AAAGAAAAGAAGAA
Done.