Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_17368

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, 988

Length: 1647
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33


Found at i:407 original size:24 final size:24

Alignment explanation


    Indices: 380--436  Score: 80
    Period size: 24  Copynumber: 2.4  Consensus size: 24

        370 TCCAGTACTT

                           *         
        380 CTGCCTTCGCTG-CTGCAAGCACTC
          1 CTGCCTTCGCTGTC-ACAAGCACTC

                     *              
        404 CTGCCTTCGGTGTCACAAGCACTC
          1 CTGCCTTCGCTGTCACAAGCACTC

                     
        428 CTGCCTTCG
          1 CTGCCTTCG

        437 GTTCAACTGG


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  24   29  0.97
  25    1  0.03

ACGTcount: A:0.12, C:0.40, G:0.21, T:0.26


Consensus pattern (24 bp):   
CTGCCTTCGCTGTCACAAGCACTC

Found at i:598 original size:45 final size:45

Alignment explanation


    Indices: 541--668  Score: 123
    Period size: 45  Copynumber: 2.8  Consensus size: 45

        531 AAGCGCACCA

                             *                            
        541 GCTTTTGGCACTTCTC-TCACTCATGCTTTTGGAGCATCAAATTCT
          1 GCTTTTGGCACTTC-CAACACTCATGCTTTTGGAGCATCAAATTCT

                             *    *  *        **    *    
        586 GCTTTTGGCACTTCCAAGACTCCTGTTTTTGGAGTGTCAAGTTCT
          1 GCTTTTGGCACTTCCAACACTCATGCTTTTGGAGCATCAAATTCT

                     **    *      * *        *    
        631 GCTTTTGGCGTTTCCGACACTCCTTCTTTTGGATCATC
          1 GCTTTTGGCACTTCCAACACTCATGCTTTTGGAGCATC

        669 TTCTACTCCT


Statistics
Matches: 66,  Mismatches: 16, Indels: 2
        0.79            0.19        0.02

Matches are distributed among these distances:
  44    1  0.02
  45   65  0.98

ACGTcount: A:0.15, C:0.26, G:0.19, T:0.41


Consensus pattern (45 bp):   
GCTTTTGGCACTTCCAACACTCATGCTTTTGGAGCATCAAATTCT
Done.