local $, = "\t";
local $\ = "\n";

foreach my $short (qw(
   CACGTG
   GTGCAC
)) {
   my $pos = 0;
   my $len = length($short);
   while (($pos = index($sequence, $short, $pos)) >= 0) {
      print $chr, '+', substr($sequence, $pos, $len);
      $pos += $len;
   }
}