stat is also a nice command to know the detail statistics of the file.
stat <fileName>
How about this oneliner ;)
perl -ne 'chomp;if( />(.*)/){$head = $1; $i=0; next};@a=split("",$_); foreach(@a){$i++;if($_ eq "N" && $s ==0 ){print "$head\t$i"; $s =1}elsif($s==1 && $_ ne "N"){print "\t$i\n";$s=0}}' infile.fa