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

use strict;
use warnings;

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

Str:  AGACGAGTA
Mask: 00111110

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

# Solution 2:
my $s_mask = unpack ("b*",$mask);
...
  $pos++;
}
print "\n";

Res: AGxxxxxTA