@input = <INPUT>;
$query1_name = $input[0];
$query1 = $input[1];
$query2_name = $input[2];
$query2 = $input[3];
$query3_name = $input[4];
$query3 = $input[5];
$query4_name = $input[6];
$query4 = $input[7];

@query1 = split ('', $query1);
@query2 = split ('', $query2); 
@query3 = split ('', $query3);
@query4 = split ('', $query4);

$length1 = scalar @query1;
$length2 = scalar @query2;
$length3 = scalar @query3;
$length4 = scalar @query4;

while ($counter <= $length1)
{
	$query1nt = $query1[$counter];
 	$query2nt = $query2[$counter];
 	$query3nt = $query3[$counter];
 	$query4nt = $query4[$counter];

	if ($query1nt ne $query2nt)
	{
		if ($query1nt ne '-' && $query2nt ne '-')
			{
			++$count_sub;
 			}
 	}		
	elsif ($query1nt ne $query3nt)
	{
		if ($query1nt ne "-" && $query3nt ne "-")
			{
			++$count_sub;
			}
	}
	elsif ($query1nt ne $query4nt)
	{
		if ($query1nt ne "-" && $query4nt ne "-")
			{
			++$count_sub;
			}
	}		
	else
	{
		++$count_same;
		print "else, hello\n";
		
	}	
}
$totallength = $count_sub + $count_same;

print "The number of subs is $count_sub. The number of matches is $count_same.\n\n";

print "To check, $totallength should equal the length of the alignment.\n\n";

exit;