Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_21276

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: 5448
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28


Found at i:1504 original size:6 final size:6

Alignment explanation


    Indices: 1485--1519  Score: 52
    Period size: 6  Copynumber: 5.8  Consensus size: 6

       1475 TTGCTTTAAC

                      *                    *        
       1485 GGATGA GGACGA GGATGA GGATGA GGAAGA GGATG
          1 GGATGA GGATGA GGATGA GGATGA GGATGA GGATG

       1520 TTGTAACAGA


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
   6   25  1.00

ACGTcount: A:0.34, C:0.03, G:0.51, T:0.11


Consensus pattern (6 bp):   
GGATGA

Found at i:1508 original size:18 final size:18

Alignment explanation


    Indices: 1485--1519  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       1475 TTGCTTTAAC

                     *        
       1485 GGATGAGGACGAGGATGA
          1 GGATGAGGAAGAGGATGA

                             
       1503 GGATGAGGAAGAGGATG
          1 GGATGAGGAAGAGGATG

       1520 TTGTAACAGA


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:0.34, C:0.03, G:0.51, T:0.11


Consensus pattern (18 bp):   
GGATGAGGAAGAGGATGA
Done.