my @a1 = @{$hash{key1}};
my @a2 = @{$hash{key2}};

##</code><code>##

my $a1 = $hash{key1};
my $a2 = $hash{key2};
...
    if ($a1->[$i] eq $a2->[$i]) {

##</code><code>##

    if ($hash{key1}->[$i] eq $hash{key2}->[$i]) {