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

my $A = 'ATGGAGTCGACGAATTTGAAGAAT';
my $B = 'xxxxxxATGGAGyxxxTCGAzxxxxCGAATTTGAAxxwGAAT';

my @A = split //, $A;
my $Are = '^(.*)' . join('(.*)', @A) . '(.*)$';
my @introns = ($B =~ m/$Are/);
if (!@introns) {
 die "There was no possible way to match the input.";
}
foreach (0..$#introns) {
 print "$_: $introns[$_] $A[$_]\n";
}