#!/usr/bin/perl
use strict;
use warnings;
use 5.014;

my @stops = (2,6); # group by 2 then 4 (6 == 2 + 4)

my $tag = '___';

for ('ATCGGATCTGGC', 'A-C-G--CTGGC') {
    my $seq = $_;
    
    for our $s (@stops) { # necessary to use 'our' instead of 'my'
        $seq =~ s/
             ( # begin capture
                    
                  (??{                       # dynamic regex
                      "(?:[TAGC][^TAGC]*)" . # group to apply quantifier to
                      "{" . ($s-1) . "}"   . # quantifier
                      "[TAGC]"               # end token
                  })                         # end dynamic reference
                    
              ) # end capture
        /$1$tag/x; # end of substitution
    }
    $seq =~ s/__-+/__/g;
    say $seq;
}

__END__
C:\Old_Data\perlp>perl dynamic_regex.pl
AT___CGGA___TCTGGC
A-C___G--CTG___GC

C:\Old_Data\perlp>