Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_35341

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: 2162
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21


Found at i:581 original size:48 final size:49

Alignment explanation


    Indices: 508--778  Score: 268
    Period size: 48  Copynumber: 5.5  Consensus size: 49

        498 GCAACCGCCG

                          *     *                     *      
        508 CCGCCTCCGAAAGAGACGCAGACGCTGTTTATGCAACAGCCACCGT-CT
          1 CCGCCTCCGAAAGAAACGCAAACGCTGTTTATGCAACAGCCAGCGTCCT

            *             *                      *   *       
        556 GCGCCTCCGAAAGAGACGCAAACGCTGTTTATGCAACCGCCTGC-TCCT
          1 CCGCCTCCGAAAGAAACGCAAACGCTGTTTATGCAACAGCCAGCGTCCT

                    *  *        *   *          * *   *       
        604 CCGCCTCCTAAGGAAACGCAGACGTTGTTTATGCAGCCGCCGGC-TCCT
          1 CCGCCTCCGAAAGAAACGCAAACGCTGTTTATGCAACAGCCAGCGTCCT

                       *                              *       
        652 CCGCCTCCGAAGGAAACGCAAACGCTGTTTATGCAACCA-CCGGC-TCCT
          1 CCGCCTCCGAAAGAAACGCAAACGCTGTTTATGCAA-CAGCCAGCGTCCT

                                                            *       
        700 CCGCCTCCGAAAGAAACGCAAACGCAAACGCTGTTTATGCAACCA-CCGGCG-CCT
          1 CCGCCTCC----GAAA-G-AAACGCAAACGCTGTTTATGCAA-CAGCCAGCGTCCT

                                     
        754 CCGCCTCCGAAAGAAACGCAAACGC
          1 CCGCCTCCGAAAGAAACGCAAACGC

        779 AAACGCTGTT


Statistics
Matches: 195,  Mismatches: 19, Indels: 18
        0.84            0.08        0.08

Matches are distributed among these distances:
  47    1  0.01
  48  142  0.73
  49    2  0.01
  50    4  0.02
  52    3  0.02
  53    1  0.01
  54   42  0.22

ACGTcount: A:0.25, C:0.37, G:0.22, T:0.16


Consensus pattern (49 bp):   
CCGCCTCCGAAAGAAACGCAAACGCTGTTTATGCAACAGCCAGCGTCCT

Found at i:657 original size:96 final size:96

Alignment explanation


    Indices: 508--778  Score: 321
    Period size: 96  Copynumber: 2.8  Consensus size: 96

        498 GCAACCGCCG

                           *                      *   **      *             *
        508 CCGCCTCCGAAA-GAGACGCAGACGCTGTTTATGCAACAGCCACCGT-CTGCGCCTCCGAAAGAG
          1 CCGCCTCC-AAAGGAAACGCAGACGCTGTTTATGCAACCGCCGGC-TCCTCCGCCTCCGAAAGAA

                                   *  *      
        571 ACGCAAACGCTGTTTATGCAACCGCCTGCTCCT
         64 ACGCAAACGCTGTTTATGCAACCACCGGCTCCT

                    *               *          *                       *     
        604 CCGCCTCCTAAGGAAACGCAGACGTTGTTTATGCAGCCGCCGGCTCCTCCGCCTCCGAAGGAAAC
          1 CCGCCTCCAAAGGAAACGCAGACGCTGTTTATGCAACCGCCGGCTCCTCCGCCTCCGAAAGAAAC

                                           
        669 GCAAACGCTGTTTATGCAACCACCGGCTCCT
         66 GCAAACGCTGTTTATGCAACCACCGGCTCCT

                                      *                 *     *              
        700 CCGCCTCCGAAAGAAACGCAAACGCAAACGCTGTTTATGCAACCACCGGCGCCTCCGCCTCCGAA
          1 CCGCCTCC-AAAG----G-AAACGCAGACGCTGTTTATGCAACCGCCGGCTCCTCCGCCTCCGAA

                          
        765 AGAAACGCAAACGC
         60 AGAAACGCAAACGC

        779 AAACGCTGTT


Statistics
Matches: 148,  Mismatches: 19, Indels: 10
        0.84            0.11        0.06

Matches are distributed among these distances:
  95    3  0.02
  96   87  0.59
  97    3  0.02
 101    1  0.01
 102   54  0.36

ACGTcount: A:0.25, C:0.37, G:0.22, T:0.16


Consensus pattern (96 bp):   
CCGCCTCCAAAGGAAACGCAGACGCTGTTTATGCAACCGCCGGCTCCTCCGCCTCCGAAAGAAAC
GCAAACGCTGTTTATGCAACCACCGGCTCCT

Found at i:675 original size:54 final size:54

Alignment explanation


    Indices: 571--795  Score: 294
    Period size: 48  Copynumber: 4.4  Consensus size: 54

        561 TCCGAAAGAG

                                   *  *               *           
        571 ACGCAAACGCTGTTTATGCAACCGCCTGCTCCTCCGCCTCC-TAAG----G-AA
          1 ACGCAAACGCTGTTTATGCAACCACCGGCTCCTCCGCCTCCGAAAGAAACGCAA

                 *   *          *  *                              
        619 ACGCAGACGTTGTTTATGCAGCCGCCGGCTCCTCCGCCTCCG-AAG----G-AA
          1 ACGCAAACGCTGTTTATGCAACCACCGGCTCCTCCGCCTCCGAAAGAAACGCAA

                                                                  
        667 ACGCAAACGCTGTTTATGCAACCACCGGCTCCTCCGCCTCCGAAAGAAACGCAA
          1 ACGCAAACGCTGTTTATGCAACCACCGGCTCCTCCGCCTCCGAAAGAAACGCAA

                                         *                        
        721 ACGCAAACGCTGTTTATGCAACCACCGGCGCCTCCGCCTCCGAAAGAAACGCAA
          1 ACGCAAACGCTGTTTATGCAACCACCGGCTCCTCCGCCTCCGAAAGAAACGCAA

                                 
        775 ACGCAAACGCTGTTTATGCAA
          1 ACGCAAACGCTGTTTATGCAA

        796 TCGCCGCCAA


Statistics
Matches: 161,  Mismatches: 9, Indels: 8
        0.90            0.05        0.04

Matches are distributed among these distances:
  48   81  0.50
  49    3  0.02
  53    1  0.01
  54   76  0.47

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


Consensus pattern (54 bp):   
ACGCAAACGCTGTTTATGCAACCACCGGCTCCTCCGCCTCCGAAAGAAACGCAA
Done.