#!/usr/bin/perl -l

# http://perlmonks.org/?node_id=1167857

use strict;
use warnings;

#my $seq = 'ATCGGATCTGGC';
my $seq = 'A-C-G--CTGGC';
my $tag = '___';

$seq =~ s/(?:-*[ATGC]-*){2}/$& =~ s#^-+|-+$##gr . $tag/e;
$seq =~ s/$tag(?:-*[ATGC]-*){4}/$& =~ s#^-+|-+$##gr . $tag/e;

print $seq;
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