Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_04281

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, 909

Length: 1516
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22


Found at i:225 original size:3 final size:3

Alignment explanation


    Indices: 217--260  Score: 88
    Period size: 3  Copynumber: 14.7  Consensus size: 3

        207 GGAATTTGAA

                                                                      
        217 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
          1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA

        261 AGATGACGAG


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   41  1.00

ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00


Consensus pattern (3 bp):   
GAG

Found at i:1245 original size:26 final size:27

Alignment explanation


    Indices: 1191--1247  Score: 71
    Period size: 26  Copynumber: 2.1  Consensus size: 27

       1181 GCCTGCTGGA

                             *  *      
       1191 GCTGGGTTCAACCATGGTGTTGCTCCT
          1 GCTGGGTTCAACCATGGAGTGGCTCCT

                         *          *  
       1218 GCTGGGTT-AACCCTGGAGTGGCTGCT
          1 GCTGGGTTCAACCATGGAGTGGCTCCT

                
       1244 GCTG
          1 GCTG

       1248 CTGCACCGGG


Statistics
Matches: 26,  Mismatches: 4, Indels: 1
        0.84            0.13        0.03

Matches are distributed among these distances:
  26   18  0.69
  27    8  0.31

ACGTcount: A:0.11, C:0.25, G:0.35, T:0.30


Consensus pattern (27 bp):   
GCTGGGTTCAACCATGGAGTGGCTCCT
Done.