my @data;
while(<>) {
	push @data, $_;
}

foreach my $line (@data) {
	my @temp_array = split "\t", $line; # Split columns into an array
	$temp_array[1] =~ tr/\"\-\/,/ /; #Change all potential word endings to a single space
	$temp_array[1] =~ tr/\(\)//d; # Remove parentheses to avoid mishaps during pattern matching
	$temp_array[2] =~ tr/\"\-\/,/ /; #Same as above
	$temp_array[2] =~ tr/\(\)//d; #Same as above
	my @words = split " ", $temp_array[1]; # Split first phrase into individual words
	for(my $i = 0; $i < @words; $i++) {
		my $match_count = 1;
		if(length ($words[$i]) < 3) { next; }
		elsif(length ($words[$i]) < 5) {
			if($words[$i] =~ /$temp_array[2]/i) {
					print "Match $match_count (probable): $words[$i]\n";
					$match_count++;
			}
			else { next; }
		}
		else {
			if($words[$i] =~ /$temp_array[2]/i) {
					print "Match $match_count: $words[$i] \n";
					$match_count++;
			}
			else { next; }
		}
	}
}

##</code><code>##


MIP_00001 	Chromosomal replication initiator protein dnaA 	 chromosomal replication initiationprotein
MIP_00002 	DNA polymerase III subunit beta 	 DNA polymerase III subunit beta
MIP_00003 	DNA replication and repair protein recF 	 recombination protein F
MIP_00004 	Hypothetical protein 	 hypothetical protein Rv0004
MIP_00006 	DNA gyrase subunit B 	 DNA gyrase subunit B