Here's one way to do it:

$x = "KPHVNVGTIGHVDHGKTTL-------AISHVLAKTYGGEAKDFSQ--------IDNAPKPVLNV
+AFIGHVDAGKSTTVGRLLLDSGTIDPQIIERLKREASEKGKAGFEFAYVMDGLK";

while ($x =~ m/(-+)/g) {
  print pos($x), " ", length($1), "\n";
}
__END__
26 7
53 8
[download]