Assuming it should have stayed, there's a not-only-regex solution:

#!/usr/bin/perl
use warnings;
use strict;
use feature qw{ say };

my @expected = ('AT___CGGA___TCTGGC', 'A-C___-G--CTG___GC');
#                                            ^

my $tag = '___';

for ('ATCGGATCTGGC',
     'A-C-G--CTGGC',
    ) {
    my $seq = $_;
    my $pos = 0;
    my $count_letters = 0;
    for my $stop (2, 6) {
        until ($count_letters == $stop) {
            $seq =~ /([ATGC])/g;
            $pos = pos $seq;
            $count_letters++;
        }
        substr $seq, $pos, 0, $tag;
        pos $seq = $pos + length $tag;
    }
    my $exp = shift @expected;
    say "$seq\t$exp\t", $exp eq $seq;
}
[download]

($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,
[download]