Str:  AGACGAGTA
Mask: 001111100
---------------
Res:  AGxxxxxTA

##</code><code>##

use strict;
use warnings;

my $seq = "AGACGAGTA";
my $mask=''; vec ($mask,$_,1)=1 for (2..6);
print "Str:  $seq\n";
print "Mask: ", unpack ("b*",$mask),"\n";

##</code><code>##

Str:  AGACGAGTA
Mask: 00111110

##</code><code>##

#Solution 1:
my @mask = split "",unpack ("b*",$mask);
my @seq = split "",$seq;
print "Res:  ";
print map {! shift @mask ? $_ : "x"} @seq;
print "\n";

##</code><code>##

# Solution 2:
my $s_mask = unpack ("b*",$mask);
my $pos=0;
print "Res:  ";
while ($pos < length($seq)){
  no warnings;  ## $s_mask could be shorter than $seq
  print ! substr($s_mask,$pos,1) ? substr($seq,$pos,1) : "x";
  $pos++;
}
print "\n";

##</code><code>##

Res: AGxxxxxTA