$targetseq =~ /.*$probe.*/
simplies to
$targetseq =~ /$probe/
but you probably want to escape the stuff in $probe (which should fix the problem), leaving you with
$targetseq =~ /\Q$probe\E/
which is the same thing as
index($targetseq, $probe) != -1

So

       if ($targetseq=~ /.*$probe.*/) {
          $start = index($targetseq, $probe);
          push(@matchregion,$start);
       }
[download]

becomes

       $start = index($targetseq, $probe);
       push(@matchregion, $start) unless $start == -1;
[download]

I didn't look at improving your alogirthm, just fixing the problem you mentioned (the contents of $probe being treated as a regexp).