#! C:/Perl/bin/perl

use strict;
use warnings;

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

my  @pattern_list = split //, $pattern;
my  $pattern_length = @pattern_list;

for my $x ( 0..((length $string) - $pattern_length) ){
    my $test_string = substr $string, $x, $pattern_length;
    my @result_array = split //, $test_string;
    my $score = 0;
    for my $y ( 0..$#pattern_list ){
        $score++ if $pattern_list[$y] eq $result_array[$y];
    }
    if( $score > 1 ){
        print "String: $test_string, position: $x, score: $score\n";
    }
}
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Results

String: JKJU, position: 1, score: 2
String: JUJH, position: 3, score: 2
String: JHJD, position: 5, score: 2
String: JDJE, position: 7, score: 3
String: JEJE, position: 9, score: 4
String: JEJE, position: 11, score: 4
String: JEDE, position: 13, score: 3
String: DEJO, position: 15, score: 2
String: JOJO, position: 17, score: 2
String: JOJJ, position: 19, score: 2
String: JJJA, position: 21, score: 2
String: JHJS, position: 26, score: 2
String: SHJE, position: 29, score: 2
String: JEFE, position: 31, score: 3
String: FEJU, position: 33, score: 2
String: JUJE, position: 35, score: 3
String: JEJU, position: 37, score: 3
String: JUJK, position: 39, score: 2
[download]