Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_11757

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: 4161
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24


Found at i:1117 original size:6 final size:6

Alignment explanation


    Indices: 1108--1157  Score: 64
    Period size: 6  Copynumber: 8.3  Consensus size: 6

       1098 GGAGAGGGAG

                                    **           *             *   
       1108 CGAGAA CGAGAA CGAGAA CGACTA CGAGAA CGGGAA CGAGAA CGTGAA
          1 CGAGAA CGAGAA CGAGAA CGAGAA CGAGAA CGAGAA CGAGAA CGAGAA

              
       1156 CG
          1 CG

       1158 TTTGCGCATC


Statistics
Matches: 37,  Mismatches: 7, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
   6   37  1.00

ACGTcount: A:0.42, C:0.20, G:0.34, T:0.04


Consensus pattern (6 bp):   
CGAGAA

Found at i:1200 original size:18 final size:18

Alignment explanation


    Indices: 1177--1211  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       1167 CTTGGAGCGA

                              
       1177 CGGGAGAAGGAAAGAGAG
          1 CGGGAGAAGGAAAGAGAG

                       *     
       1195 CGGGAGAAGGAGAGAGA
          1 CGGGAGAAGGAAAGAGA

       1212 ACGAGAGCGC


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.43, C:0.06, G:0.51, T:0.00


Consensus pattern (18 bp):   
CGGGAGAAGGAAAGAGAG
Done.