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

my (@lines);

while (<>) {
    next if /^\s*$/; # skip empty lines
    chomp;
    push @lines, $_;
} continue {
    close ARGV if eof;  # Not eof()!
}

my @dublicatedLines = duplicates @lines;

print Dumper \@lines, \@dublicatedLines;

__END__

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