my @a1 = @{$hash{key1}};
my @a2 = @{$hash{key2}};
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You can avoid the copying by using references:

my $a1 = $hash{key1};
my $a2 = $hash{key2};
...
    if ($a1->[$i] eq $a2->[$i]) {
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which is functionally the same as

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

but less to type if you need to access the arrays ($a1/$a2) more than once...