use strict;

my $searchString = "GATTACA";
my %subStrings = {};
my @subStrings = ();

sub populate {
  # Fills the hash subStrings with all "allowed" substrings
  # of the argument. Duplicates are avoided by
  # filling a hash instead of an array.
  my ($string) = @_;
  
  return if $string eq "";
  
  my $line = "";
  
  foreach (split "", $string) {
    $line .= $_;
    #print "Added $line\n";
    $subStrings{$line} = "1";
  };
  
  populate( substr( $string, 1 ));
};

populate( $searchString );

# We are only interested in the keys of our hash, 
# longest matches first :
@subStrings = reverse 
              sort { 
               length($a) <=> length($b) # Sort by string length
            || $a cmp $b                 # and then by string content
             } keys %subStrings;

# We read the file line by line :
my ( $line, $substring );
while ($line = <DATA>) {
  my @MatchedSubstrings = ();
  foreach $substring (@subStrings) {
    if ($line =~ /$substring/) {
      push @MatchedSubstrings, $substring;
    };    
  };
  if ($#MatchedSubstrings != -1) {
    print "On line $. : ", join(",", @MatchedSubstrings ),"\n";
  };
};

__DATA__
AGATTACAAA
ZZGATTZZ
GATTAZZ
GATGATTACAZZ
asdfgh
gattaca