It is often worth the effort to look for a module even to do simple tasks. In this case consider the function 'intersect' in the module Array::Utils. An added benefit is that although your spec 'compare value of 2 arrays' is ambiguous, the word 'intersect' is not. It says exactly what you mean.

$type Dnamonk3.pl
use strict;
use warnings;
use Array::Utils qw(intersect);
my @array1 = ("A2","A5","C1","G0","T3","T4");
my @array2 = ("A2","A3","A5","G1","G0","G4");
{
    local $, = ',';
    print intersect(@array1, @array2);
}


$perl Dnamonk3.pl
A2,A5,G0
[download]