#!/usr/bin/perl -w
use strict;

my $pattern  = "JEJE";
my $string = "EJKJUJHJDJEJEJEDEJOJOJJJAHJHJSHJEFEJUJEJUJKIJS";

# from the $pattern, generate a $regex like this:
my $regex = "JEJE|.EJE|J.JE|JE.E|JEJ.";

# and use it like this:
my (@matches) = $string =~ m/$regex/g;
print join ("\n", @matches), "\n";

__END__
prints:
JDJE
JEJE
JEFE
JUJE