and see if it matches some permutation

Of course, we're all kind of guessing here because that isn't exactly a well-written spec... but I think assuming he wants all permutations is a bit of a leap. I think it may also be a leap to assume he only wants to search for strings of a certain length. He just says that they are "user defined."

I still think this is the right approach though, he just has to track the lengths of his needles and be sure to check substrings of each necessary length (so long as it doesn't go off the end of his haystack.)

Something like this: 

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

my $haystack = shift;
my %needles;

undef @needles{@ARGV};

my @len = sort {$a<=>$b} keys %{{ map { (length,0) } keys %needles }};

my $pos = 0;
my $hlen = length $haystack;
while ($pos + $len[0] <= $hlen) {
    for my $L (@len) {
        last if $pos + $L > $hlen;
        my $substr = substr($haystack, $pos, $L);
        $needles{$substr}++ if exists $needles{$substr};
    }
    $pos++;
}

use Data::Dumper;
print Dumper \%needles;

[download]

Update: 

$ ./973643.pl 'AAAAA AAACACA CAACAAA' AAA AAC ACA CAA
$VAR1 = {
          'AAC' => 2,
          'ACA' => 3,
          'CAA' => 2,
          'AAA' => 5
        };

[download]

-sauoq
"My two cents aren't worth a dime.";

In reply to Re^2: Regex: finding all possible substrings by sauoq
in thread Regex: finding all possible substrings by ssc11008

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