#my $old_seq='ATGC---ACGT---TAGCAAGGTAAAT';
#my $new_seq='----AT-GC----ACGT----TAGCAA----------GGTAAAT---';
print "old seq is\n$old_seq\nnew seq is\n$new_seq\n";

my @old_array = split //, lc ($old_seq);
my @new_array = split //, lc ($new_seq);


my $n_old=0;
my $n_new=0;
my %gaps;
while (my $old_base = shift @old_array){


my $new_base = shift @new_array;
#print "base in oldseq is $old_base, base in newseq is $new_base\n";



if ($old_base eq $new_base){
#	print "match!\n";
	$n_old++;
	$n_new++;
	next;
}
else{
#	print "no match! - must be a new gap at position $n_new new, $n_old old\n";
	my $new_gap_length=0;
	while ($new_base = shift @new_array){
		$n_new++;
		$new_gap_length++;
#		print "newbase is $new_base\n";
		if ($new_base eq $old_base){
#			print "found it - length was $new_gap_length\n";
			$gaps{$n_new-$new_gap_length} = $new_gap_length;
			$n_old++;
			$n_new++;
			last;
		}
		
	}
}
}

foreach (sort {$a <=> $b} keys %gaps){
print "gap at position in new $_, length $gaps{$_}\n";
}