Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_33721

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, 597

Length: 996
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21


Found at i:655 original size:24 final size:24

Alignment explanation


    Indices: 628--704  Score: 68
    Period size: 24  Copynumber: 3.2  Consensus size: 24

        618 CAAGTCAATG

                       *            
        628 GAGAGGGAAAAACCAAGAAAGCAT
          1 GAGAGGGAAAAGCCAAGAAAGCAT

                 *       *     *     *
        652 GAGAGAGAAGAAGTCAAGTCAA-C-G
          1 GAGAGGGAA-AAGCCAAG-AAAGCAT

                *                   
        676 GAGAAGGAAAAGCCAAGAAAGCAT
          1 GAGAGGGAAAAGCCAAGAAAGCAT

                 
        700 GAGAG
          1 GAGAG

        705 AGAAGAAGAT


Statistics
Matches: 38,  Mismatches: 11, Indels: 8
        0.67            0.19        0.14

Matches are distributed among these distances:
  22    2  0.05
  23    8  0.21
  24   19  0.50
  25    7  0.18
  26    2  0.05

ACGTcount: A:0.51, C:0.12, G:0.32, T:0.05


Consensus pattern (24 bp):   
GAGAGGGAAAAGCCAAGAAAGCAT

Found at i:685 original size:48 final size:48

Alignment explanation


    Indices: 613--712  Score: 173
    Period size: 48  Copynumber: 2.1  Consensus size: 48

        603 GGATTCAGAC

                         *     *                            
        613 GAAGTCAAGTCAATGGAGAGGGAAAAACCAAGAAAGCATGAGAGAGAA
          1 GAAGTCAAGTCAACGGAGAAGGAAAAACCAAGAAAGCATGAGAGAGAA

                                      *                     
        661 GAAGTCAAGTCAACGGAGAAGGAAAAGCCAAGAAAGCATGAGAGAGAA
          1 GAAGTCAAGTCAACGGAGAAGGAAAAACCAAGAAAGCATGAGAGAGAA

                
        709 GAAG
          1 GAAG

        713 ATCCAGATGA


Statistics
Matches: 49,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  48   49  1.00

ACGTcount: A:0.50, C:0.11, G:0.32, T:0.07


Consensus pattern (48 bp):   
GAAGTCAAGTCAACGGAGAAGGAAAAACCAAGAAAGCATGAGAGAGAA

Found at i:705 original size:26 final size:26

Alignment explanation


    Indices: 628--705  Score: 60
    Period size: 23  Copynumber: 3.2  Consensus size: 26

        618 CAAGTCAATG

                *      *              
        628 GAGAGGGAAAAACCAAGAAAGCATGA
          1 GAGAAGGAAAAGCCAAGAAAGCATGA

                         *     *        
        654 GAG-A-GAAGAAGTCAAGTCAA-C--G-
          1 GAGAAGGAA-AAGCCAAG-AAAGCATGA

                                      
        676 GAGAAGGAAAAGCCAAGAAAGCATGA
          1 GAGAAGGAAAAGCCAAGAAAGCATGA

                
        702 GAGA
          1 GAGA

        706 GAAGAAGATC


Statistics
Matches: 38,  Mismatches: 6, Indels: 16
        0.63            0.10        0.27

Matches are distributed among these distances:
  22    5  0.13
  23   10  0.26
  24    6  0.16
  25    8  0.21
  26    9  0.24

ACGTcount: A:0.51, C:0.12, G:0.32, T:0.05


Consensus pattern (26 bp):   
GAGAAGGAAAAGCCAAGAAAGCATGA

Done.