#!/usr/bin/perl
use strict;
use warnings;

my %data = ();
while (<DATA>) {
    my ($term1, $term2) = split;
    if (exists $data{$term2}) {
        print "$term2 found in both columns\n";
    }
    $data{$term1} = $term2;
}

__DATA__
NP_041954.1 NP_848263.1
NP_041955.1 NP_041956.1
I_match Not_here_though
I_dont_match I_match