You're dealing with characters (or octects), not bits, so you need to set 8 bits in the mask instead of 1 for each letter. substr is a good alternative to vec for doing that. Perl even has Bitwise String Operators (see perlop) that allow you to do bit operations on entire strings "at once". 

my $str  = 'AGACGAGTA';

my $mask = "\xFF" x length($str);
substr($mask, $_, 1, "\x00") for 2..6;

my $res = $str & $mask;
$res =~ s/\x00/x/g;

print("$res\n");

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You can avoid the regexp call: 

my $str = 'AGACGAGTA';

my $mask = "\xFF" x length($str);
substr($mask, $_, 1, "\x00") for 2..6;

my $x = 'x' x length($str);
my $res = ($str & $mask) | ($x & ~$mask);

print("$res\n");

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Of course, you really don't need the mask at all. 

my $str = 'AGACGAGTA';

my $res = $str;
substr($res, $_, 1, "x") for 2..6;

print("$res\n");

[download]

Update: Added the last two snippets.

In reply to Re: Masking part of a string by ikegami
in thread Masking part of a string by citromatik

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