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

my $oldstring = 'ATTGC---AGTCCATGC------ATGC';
my $newstring = 'AT-TGC---AGTCCATGC--------ATGC';

my @oldstring= ($oldstring=~ /(-*)(?:A|C|G|T|$)/g);
my @newstring= ($newstring=~ /(-*)(?:A|C|G|T|$)/g);

my $pos= 0;
for (my $i= 0; $i < @oldstring; ++$i) {
	if ( $oldstring[$i] ne $newstring[$i]) {
		print length($newstring[$i]) - length($oldstring[$i])," at position ",$pos,'-',$pos+length($oldstring[$i]),"\n";
	}
	$pos+=  length($oldstring[$i])+1;
}