The sort is not necessary.

Here is how I would approach it: 

use warnings;
use strict;

my %barcode_hash = (
    1 => ['AGCTCGTTGTTCGATCCA','GAGAGATAGATGATAGTG','TTTT_CCCC',0],
    2 => ['AGCTCGTTGTTCGATCCA','GAGAGATAGATGATAGTG','TTTT_AAAA',0],
    3 => ['AGCTCGTTGTTCGATCCA','GAGAGATAGATGATAGTG','TTTT_BBBB',0],
    4 => ['AGCTCGTTGTTCGATCCA','GAGAGATAGATGATAGTG','TTTT_AAAA',0],
);

Find_and_Increment ('TTTT_AAAA');
Find_and_Increment ('TTTT_CCCC');
Find_and_Increment ('TTTT_AAAA');

#--------------------
sub Find_and_Increment{
    my ($pair) = @_;

    for my $k (keys %barcode_hash){
       next unless ( my $aref = $barcode_hash{$k} ) -> [2] eq $pair;
       $aref->[3]++;
       print "$pair found at $k, $aref->[3] time(s)\n";
    }
}

[download]
Output: 
$ perl search_hash.pl 
TTTT_AAAA found at 4, 1 time(s)
TTTT_AAAA found at 2, 1 time(s)
TTTT_CCCC found at 1, 1 time(s)
TTTT_AAAA found at 4, 2 time(s)
TTTT_AAAA found at 2, 2 time(s)

[download]

        ...Disinformation is not as good as datinformation.               Don't document the program; program the document.

In reply to Re^3: search for particular elements of hash with multiple values by NetWallah
in thread search for particular elements of hash with multiple values by pmpmmpmp

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