Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_25195

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, 250

Length: 417
ACGTcount: A:0.37, C:0.18, G:0.34, T:0.11


Found at i:109 original size:14 final size:14

Alignment explanation


    Indices: 92--180  Score: 54
    Period size: 14  Copynumber: 5.6  Consensus size: 14

         82 ATGAAGGAGA

                          
         92 AAGCAGAAGCAGCG
          1 AAGCAGAAGCAGCG

                             
        106 AAGCAGAAGACAATG-G
          1 AAGCAGAAG-C-A-GCG

                             
        122 AGACCGCAGAAGCAGCG
          1 A-A--GCAGAAGCAGCG

                            * 
        139 AAGCAGAAGACAATGGAG
          1 AAGCAGAAG-C-A--GCG

               *           
        157 ACAACAGAAGCAGCG
          1 A-AGCAGAAGCAGCG

                     
        172 AAGCAGAAG
          1 AAGCAGAAG

        181 ACCAGAGGAG


Statistics
Matches: 59,  Mismatches: 4, Indels: 24
        0.68            0.05        0.28

Matches are distributed among these distances:
  14   23  0.39
  15    5  0.08
  16    6  0.10
  17    6  0.10
  18    5  0.08
  19   14  0.24

ACGTcount: A:0.46, C:0.19, G:0.33, T:0.02


Consensus pattern (14 bp):   
AAGCAGAAGCAGCG

Found at i:131 original size:33 final size:33

Alignment explanation


    Indices: 87--182  Score: 165
    Period size: 33  Copynumber: 2.9  Consensus size: 33

         77 AGAGCATGAA

                 *                           
         87 GGAGAAAGCAGAAGCAGCGAAGCAGAAGACAAT
          1 GGAGACAGCAGAAGCAGCGAAGCAGAAGACAAT

                  *                          
        120 GGAGACCGCAGAAGCAGCGAAGCAGAAGACAAT
          1 GGAGACAGCAGAAGCAGCGAAGCAGAAGACAAT

                   *                      
        153 GGAGACAACAGAAGCAGCGAAGCAGAAGAC
          1 GGAGACAGCAGAAGCAGCGAAGCAGAAGAC

        183 CAGAGGAGCC


Statistics
Matches: 59,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  33   59  1.00

ACGTcount: A:0.46, C:0.19, G:0.33, T:0.02


Consensus pattern (33 bp):   
GGAGACAGCAGAAGCAGCGAAGCAGAAGACAAT
Done.