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CGGCGGAAAACTGTCCTCCGTGC   mouse
CGACGGAACATTCTCCTCCGCGC   rat 
...
CGACGGAAGACTCTCCTCCGTGC   chimp
 
00100000302011000000100   -> number of subst per site (max parsimony)

use Data::Dumper;
use List::MoreUtils qw(uniq);
...
    return @mincol;
}