#! /usr/bin/perl -l
use strict;
use warnings;

{ 
	my @POOL = qw( A C G T );

	sub mutate {
		my $str = shift;					# original sequence
		my @positions = @_;					# get all positions for mutations

		for my $pos ( @positions ) {				# check each position
			
			my $original = substr $str, $pos-1, 1;		# determine original

			my @replacer = grep { $_ ne $original } @POOL;	# exclude original from replacement list

			substr( $str, $pos-1, 1) = $replacer[ rand @replacer ]; # replace original with a random item
		}

		# return mutated sequence
		return $str;
	}
}

my $sequence = "ACTA";
print mutate($sequence,3,4);  # mutate at 3rd and 4th position of sequence