To insert a literal string into a pattern you can use \Q and \E. This insures that any characters that have special meaning in a regex will be escaped and treated as literals.

As for finding all overlapping patterns, see the documentation of pos and the 0 length lookahead operator in perlre. Using pos, 0 length lookahead regexes (look for (?=) might be preferable since the documentation says that (?{...}) is experimental.

use strict;
use warnings;

my $sequence = "GGGGGGGAGAAAAAAAAAAAAAAAGAAGGA";

sub tryPattern {
  my $pattern = shift;
  my $iCount = 0;
  while ($sequence =~ /(?=\Q$pattern\E)/g) {
    $iCount++;
    my $iPos = pos($sequence);
    my $sMatch = substr($sequence, $iPos, 5);
    print "$iPos: $sMatch\n";
    pos($sequence) = $iPos + 1;
  }
  print "total found: $iCount\n";
}

tryPattern($_) foreach qw(AAAAA GGGGG GGAGA GAAGG);
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Best, beth