Another way could be to use Tie::File and grep.

use strict;
use warnings;

use Tie::File;

die "File does not exist" unless -f $ARGV[0];

tie my @file, 'Tie::File', $ARGV[0] or die "Could not tie file";

if ( grep !/^[actg]+$/i, @file )
{
        print "BAD\n";
}
else
{
        print "OK\n";
}
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Update: Inefficent see below update by ikegami