Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_06399

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, 795

Length: 1326
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32


Found at i:1078 original size:105 final size:104

Alignment explanation


    Indices: 950--1161  Score: 361
    Period size: 105  Copynumber: 2.0  Consensus size: 104

        940 TCTGACAAAA

                                                                             
        950 AGGGTCTATATTCCACATCATTTAAGGTTCCCGATGTTTATGGTGTTTTCCAATTCAAGGTCGAG
          1 AGGGTCTATATTCCACATCATTTAAGGTTCCCGATGTTTATGGTGTTTTCCAATTCAAGGTCGAG

                       *       *            *       
       1015 CACCAAAAGCTTGGTTATACAAGTTTATCCCTTTCAAAGC
         66 CACCAAAAGCTAGG-TATAAAAGTTTATCCCTGTCAAAGC

                            *                                            *   
       1055 AGGGTCTATATTCCACTTCATTTAAGGTTCCCGATGTTTATGGTGTTTTCCAATTCAAGGTTGAG
          1 AGGGTCTATATTCCACATCATTTAAGGTTCCCGATGTTTATGGTGTTTTCCAATTCAAGGTCGAG

            *                                      
       1120 TACCAAAAGCTAGGTATAAAAGTTTATCCCTGTCAAAGC
         66 CACCAAAAGCTAGGTATAAAAGTTTATCCCTGTCAAAGC

               
       1159 AGG
          1 AGG

       1162 CCATATAGAC


Statistics
Matches: 101,  Mismatches: 6, Indels: 1
        0.94            0.06        0.01

Matches are distributed among these distances:
 104   26  0.26
 105   75  0.74

ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34


Consensus pattern (104 bp):   
AGGGTCTATATTCCACATCATTTAAGGTTCCCGATGTTTATGGTGTTTTCCAATTCAAGGTCGAG
CACCAAAAGCTAGGTATAAAAGTTTATCCCTGTCAAAGC
Done.