What have you tried? What didn't work? See How do I post a question effectively?. In general, we can be more helpful when we can see where you've had difficulty and can gauge your experience.

As I understand your spec, you can use regular expressions to locate where in your masks your codes fall and then use the special variables @- and @+ along with substr to extract the appropriate characters. Something like:

#!/usr/bin/perl
use strict;
use warnings;

my @searches = qw(
                    .LLL
                    LLLL
                    .RRR
                    RRRR
                );
                
my @file = <DATA>;
chomp @file;

for my $search (@searches) {
    for my $line (@file) {
        my ($string, $mask) = split /\s+/, $line, 2;
        my @matches;
        while ($mask =~ /\Q$search\E/g) {
            my $start = $-[0];
            my $end   = $+[0];
            push @matches, substr $string, $start, $end - $start;
        }
        local $" = ",";
        print "$line\t\t@matches\n";
    }
}


__DATA__
THAETURQU                 .LLL..RRR
JURYATAUTIOPW             .LLL...LL.RRR
TURIWOWQNQQUTYRIOPWMNHF   L..L..LLLL.LL.R..L.LLLL
[download]

Note I used \Q and \E to escape metacharacters since . has special meaning in regular expressions. See perlretut on info on how to build regular expressions.