USACO——Bovine Genomics

Bovine Genomics

Farmer John owns N cows with spots and N cows without spots. Having just completed a 

course   in   bovine   genetics,   he   is   convinced   that   the   spots   on   his   cows   are  caused   by 
mutations in the bovine genome. 


At great expense, Farmer John sequences the genomes of his cows. Each genome is a 
string of length M built from the four characters A,   C, G, and   T. When he lines up the 
genomes of his cows, he gets a table like the following, shown here for N=3: 


Positions:        1 2 3 4 5 6 7 ... M 


Spotty Cow 1: A A T C C C A ... T 
Spotty Cow 2: G A T T G C A ... A 
Spotty Cow 3: G G T C G C A ... A 


Plain Cow 1:  A C T C C C A ... G 
Plain Cow 2:  A G T T G C A ... T 
Plain Co