Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_29146

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, 914

Length: 1524
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28


Found at i:238 original size:3 final size:3

Alignment explanation


    Indices: 230--299  Score: 104
    Period size: 3  Copynumber: 23.3  Consensus size: 3

        220 TTAGTATGGA

                                      *                           *        
        230 ATG ATG ATG ATG ATG ATG ATA ATG ATG ATG ATG ATG ATG ATA ATG ATG
          1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG

                * *                      
        278 ATG GTA ATG ATG ATG ATG ATG A
          1 ATG ATG ATG ATG ATG ATG ATG A

        300 CGACGACAAG


Statistics
Matches: 59,  Mismatches: 8, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   3   59  1.00

ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33


Consensus pattern (3 bp):   
ATG

Found at i:255 original size:21 final size:21

Alignment explanation


    Indices: 229--299  Score: 115
    Period size: 21  Copynumber: 3.4  Consensus size: 21

        219 TTTAGTATGG

                                 
        229 AATGATGATGATGATGATGAT
          1 AATGATGATGATGATGATGAT

                                 
        250 AATGATGATGATGATGATGAT
          1 AATGATGATGATGATGATGAT

                      * *        
        271 AATGATGATGGTAATGATGAT
          1 AATGATGATGATGATGATGAT

            *       
        292 GATGATGA
          1 AATGATGA

        300 CGACGACAAG


Statistics
Matches: 47,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  21   47  1.00

ACGTcount: A:0.38, C:0.00, G:0.30, T:0.32


Consensus pattern (21 bp):   
AATGATGATGATGATGATGAT
Done.