"A C D"

##</code><code>##

  /A(.*?)C(.*?)D/

##</code><code>##

  "ABICID"

##</code><code>##

  "A--C-D"

##</code><code>##

  if ($string =~ $test) {
    for my $offset (1 .. $#-) {
      my $start = $-[$offset];
      my $len = $+[$offset] - $start;
      substr($test, $start, $len) = "-" x $len;
    }
    # now extract only the matched extent
    push @hyph_padded_seq, substr($test, $-[0], $+[0] - $-[0]);
  }