#!/usr/bin/perl

use strict;
use warnings;

my @motives = (
  qr(GACG),
  qr(G[A-Z]{2}G),
  qr(GAGG?A),
  qr(Kikeriki)i
);

my %gefunden;
my $zeilennr;
while (my $line = <DATA>) {
  $zeilennr++;
  for my $re (@motives) {
	push @{$gefunden{$re}},$zeilennr if $line =~ $re;
  } 
}

while (my ($k,$v) = each %gefunden) {
  print "$k: ", join(",",@$v),"\n";
}

#ergibt:
#(?-xism:GAGG?A): 1
#(?-xism:GACG): 2
#(?-xism:G[A-Z]{2}G): 1,2
#(?i-xsm:Kikeriki): 4

__DATA__
GAGGA
GACG
Kuh
KikEriKi