Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_39036

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, 612

Length: 1020
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31


Found at i:271 original size:69 final size:69

Alignment explanation


    Indices: 180--308  Score: 188
    Period size: 69  Copynumber: 1.9  Consensus size: 69

        170 AACTATCGAA

                *                   *                         *              
        180 GGAATTATTTCAAGATTTGGCTCCTTTAG-TGTGGAATTCATTGGGTACTGTAGCTGCACTCATA
          1 GGAACTATTTCAAGATTTGGCTCCGTT-GTTGTGGAATTCATTGGGTACTATAGCTGCACTCATA

                 
        244 GAGAG
         65 GAGAG

                                                   *  *        *        
        249 GGAACTATTTCAAGATTTGGCTCCGTTGTTGTGGAATTCTTTTGGTACTATTGCTGCACT
          1 GGAACTATTTCAAGATTTGGCTCCGTTGTTGTGGAATTCATTGGGTACTATAGCTGCACT

        309 TCTACAGGAG


Statistics
Matches: 53,  Mismatches: 6, Indels: 2
        0.87            0.10        0.03

Matches are distributed among these distances:
  68    1  0.02
  69   52  0.98

ACGTcount: A:0.22, C:0.16, G:0.25, T:0.38


Consensus pattern (69 bp):   
GGAACTATTTCAAGATTTGGCTCCGTTGTTGTGGAATTCATTGGGTACTATAGCTGCACTCATAG
AGAG
Done.