#!/usr/bin/perl -w
use strict;

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

my $Are = join '(.*?)', '^', (map "($_)", $A =~ /(.)/sg), '$';

(my @introns = $B =~ m/$Are/)
	or die "There was no possible way to match the input.";

my @seq;
while(@introns) {
	my $match = shift @introns;
	if(@seq and not $match) {
		$seq[-1] .= shift @introns || '';
		next;
	}
	push @seq, $match;
}

print "$A\n@seq\n";

__END__
ATGGAGTCGACGAATTTGAAGAAT
xxxxxx ATGGAG yxxx TCGA zxxxx CGAATTTGAA xxw GAAT