I hope this meet your needs:

#! /usr/bin/perl

use strict;
use warnings;
use Data::Dumper;

# your pairs
my @pairs = ([1,2],[3,4],[5,6]);

# sources
my @array1 = (1,5);
my @array2 = (3,6);
my @array3 = (2,4);

my @locations;

for my $pair(@pairs){
  my @loc_array;
  for my $item(@$pair){
    my $location;
    if(grep{$_ == $item}@array1){
       $location = "array1";
    }
    elsif(grep{$_ == $item}@array2){
       $location = "array2";
    }
    else{
       $location = "array3";
    }
    push(@loc_array,$location);
  }
  push(@locations,\@loc_array);
}
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