This should work. Change the "number of characters" as per your need.You need to modify the code as per your need

#!/usr/bin/perl

use strict;
use warnings;

my $str = ".,a..A,,C..+4ACGTG.,-2TG,,...,a";
$str =~ s/[+-]?\d\w{4}//g;
$str =~ s/[+-]?\d\w+//g;
print $str;
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Update 1: Eliya's method works awesomely well. I learnt something today. Thanks Eliya

Update 2: After several tries, I got this regex and it should also work

#!/usr/bin/perl

use strict;
use warnings;

my $str = ".,a..A,,C..+4ACGTG.,-2TG,,...,a";
$str =~ s/[+|-](\d*)(\w*)/(substr $2, $1)/ge;
print $str;
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