use Algorithm::Permute;
my $needle_chars = 'AAC';
my $haystack = 'AAACACAA';

my $p = Algorithm::Permute->new( [ split //, $needle_chars ], 3 );

my %perms;

while( my @perm = $p->next ) {
    $perms{ join '', @perm }++;
}

my $pos = 0;

while( $pos + 3 < length $haystack ) {
    my $pos_chars = substr $haystack, $pos, 3;
    print $pos_chars, " found at $pos\n"
        if exists $perms{ $pos_chars };
    $pos++;
}