#!/usr/bin/perl
use strict;
use feature qw{ say };
use warnings;

sub test {
    my ($array1ref, $array2ref) = @_;

    my @array1 = @$array1ref;
    my @array2 = @$array2ref;
    my $count = 0;
    foreach my $element (@array1) {
        foreach my $element2 (@array2) {
            if ($element eq $element2) {
                warn "$element $element2 same";
                $count++;
            } else {
                warn "$element $element2 different";
            }
        }
    }
    return $count
}

my $same = test([qw[ A T C G T C G A G C G ]],
                [qw[ A C G T C C T G T C G ]]);
say "$same matches.";
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Or, do you want to walk both the arrays at the same time? Then you can use indices:

sub test {
    my ($array1ref, $array2ref) = @_;

    my $count = 0;
    for my $idx (0 .. $#$array1ref) {
        my $element  = $array1ref->[$idx];
        my $element2 = $array2ref->[$idx];
        if ($element eq $element2) {
            warn "$element $element2 same";
            $count++;
        } else {
            warn "$element $element2 different";
        }
    }
    return $count
}
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Update: You can also just use shift, but you shouldn't use it on the dereferences directly if you want to keep the original arguments to the function unchanged.

sub test {
    my ($array1ref, $array2ref) = @_;
    my @array1 = @$array1ref;
    my @array2 = @$array2ref;

    my $count = 0;
    for my $idx (0 .. $#array1) {
        $count++ if shift @array1 eq shift @array2;
    }
    return $count
}
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($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,
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