#! perl -slw
use strict;

my $s1 = 'GATTACGAGTGGCGCTCGTGTAACGGCA';
my $s2 = 'GATTACG    GCGCTCG   AACGGCA';
my $masked = $s1 ^ $s2;
print scalar $masked =~ tr[\0][0];

my $s3 = 'GATTACGAGTGGCGCTCGTGTAACGGCA';
my $s4 = 'GATTACG                     ';
my $s5 = '  TTACGAG       CGTGTAA     ';
tr[ ][\0] for $s3, $s4, $s5;

$masked = $s3 ^ ( $s4 | $s5 );
print scalar $masked =~ tr[\0][0];

my $s6 = '             GCTCGTG        ';
my $s7 = 'GATTACGAGTGGCGCTCGTGTAACGGCA';
my $s8 = '   TACGAGT                  ';
my $s9 = '        GTGGCGC             ';

tr[ ][\0] for $s6, $s7, $s8, $s9;

$masked = $s7 ^ ( $s6 | $s8 | $s9 );
print scalar $masked =~ tr[\0][0];

__END__
P:\test>junk2
21
16
17