Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_12300

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, 613

Length: 1023
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25


Found at i:701 original size:42 final size:42

Alignment explanation


    Indices: 635--718  Score: 114
    Period size: 42  Copynumber: 2.0  Consensus size: 42

        625 GCTATGCATC

                           *                *         
        635 GTAACGAGTGGGTGGGAAACGCTGACCGCTGGGTTGCCGGAT
          1 GTAACGAGTGGGTGGAAAACGCTGACCGCTGGCTTGCCGGAT

                *    *         *     *                
        677 GTAATGAGTTGGTGGAAAATGCTGATCGCTGGCTTGCCGGAT
          1 GTAACGAGTGGGTGGAAAACGCTGACCGCTGGCTTGCCGGAT

        719 TTCTTGAGGT


Statistics
Matches: 36,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  42   36  1.00

ACGTcount: A:0.20, C:0.17, G:0.39, T:0.24


Consensus pattern (42 bp):   
GTAACGAGTGGGTGGAAAACGCTGACCGCTGGCTTGCCGGAT

Found at i:979 original size:12 final size:12

Alignment explanation


    Indices: 941--986  Score: 51
    Period size: 12  Copynumber: 3.8  Consensus size: 12

        931 TATGACCAGA

                         
        941 AAGACAGAAAAA-
          1 AAGA-AGAAAAAG

             *           
        953 ATGAA-AAAAAGG
          1 AAGAAGAAAAA-G

                        
        965 AAGAAGAAAAAG
          1 AAGAAGAAAAAG

                      
        977 AAGAAGAAAA
          1 AAGAAGAAAA

        987 CAAACAAACT


Statistics
Matches: 29,  Mismatches: 2, Indels: 6
        0.78            0.05        0.16

Matches are distributed among these distances:
  10    5  0.17
  11    1  0.03
  12   18  0.62
  13    5  0.17

ACGTcount: A:0.74, C:0.02, G:0.22, T:0.02


Consensus pattern (12 bp):   
AAGAAGAAAAAG
Done.