You don't give us much code to go on! Maybe you need to invert the hash so that you can do a reverse look up? Something like:

use strict;
use warnings;
use Data::Dump::Streamer;

my %dnaLookup = (
    wibble => 'AATCAA 2',
    wobble => 'AATCAA 1',
    plibble => 'GATCAA 3',
    plobble => 'GATCAA 1',
    );
my %reverseLookup;

for my $key (keys %dnaLookup) {
    my ($dna, $loc) = split ' ', $dnaLookup{$key};
    
    push @{$reverseLookup{$dna}}, [$key, $loc];
}

Dump (\%reverseLookup);
[download]

Prints:

$HASH1 = {
           AATCAA => [
                       [
                         'wibble',
                         2
                       ],
                       [
                         'wobble',
                         1
                       ]
                     ],
           GATCAA => [
                       [
                         'plobble',
                         1
                       ],
                       [
                         'plibble',
                         3
                       ]
                     ]
         };
[download]