while (read($fh, my $char, 1) && $eof) {
    
	if ($char =~ m/[ACGT]/ ) {
		$i++;

		if ($i >= $start_genome && $i < $end_genome) {
	    	push (@genome, $char);		
		} elsif ($i > $end_genome) {
			$eof = 0;
		        # do the searching here, instead of outside the loop!
		}
    	
   }
}