#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;
use List::MoreUtils 'duplicates';

my (@keys, @values);

while (<>) {
    next if /^\s*$/; # skip empty lines
    chomp;
    my ($key, $value) = split /\s+/;
    push @keys, $key;
    push @values, $value;
} continue {
    close ARGV if eof;  # Not eof()!
}

my @duplicatedKeys = duplicates @keys;
my @duplicatedValues = duplicates @values;

print Dumper \@keys, \@values, \@duplicatedKeys, \@duplicatedValues;

__END__

$ perl test.pl File1.txt File3.txt
$VAR1 = [
          'ID121',
          'ID122',
          'ID145',
          'ID157',
          'ID181',
          'ID962',
          'ID567',
          'ID921',
          'ID121',
          'ID612',
          'ID122',
          'ID745',
          'ID145',
          'ID157'
        ];
$VAR2 = [
          'ABC14',
          'EFG87',
          'XYZ43',
          'TSR11',
          'ABC31',
          'YTS27',
          'POH70',
          'BAMD80',
          'ABC14',
          'FLOW12',
          'EFG87',
          'KIDP36',
          'XYZ43',
          'TSR11'
        ];
$VAR3 = [
          'ID121',
          'ID122',
          'ID145',
          'ID157'
        ];
$VAR4 = [
          'ABC14',
          'EFG87',
          'XYZ43',
          'TSR11'
        ];