191.52user 153.47system 5:49.44elapsed 98%CPU 

##</code><code>##

open SEQ,  '<', $ARGV[0] or die $!; #plain
open MASK, '<', $ARGV[1] or die $!; #hardmask

while ( my $seq = <SEQ> ) {    ## Read a sequence 
    my $mask = <MASK>;         ## And the corresponding mask

    if ( $mask =~ /^>/ ) {    
        print "$seq";
    }
    else {
        $mask =~ tr[N][ ];         ## Ns => spaces
        print $seq | $mask;        ## bitwise-OR them and print the result;
        
    }
    
}
close SEQ;
close MASK;


##</code><code>##

0.45user 0.07system 0:05.59elapsed 9%CPU 

##</code><code>##

#Seq_name    #Seq_len
2-micron	6318
MT	85779
I	230208
VI	270148
III	316617
IX	439885
VIII	562643
V	576869
XI	666454
X	745745
XIV	784333
II	813178
XIII	924429
XVI	948062
XII	1078175
VII	1090946
XV	1091289
IV	1531918