And... that made me realize that this:

sub FindPositions {
    my $string = $_[0];
    my $id = $_[1];

    # slice out the appropriate part of the string
    ($string) = $string =~ /(><a name = $id>.*?<\/pre>)/s;

  my @positions = $string =~ m/<a name = $id>.*?Query: (\d+).*?Sbjct: 
+(\d+).*?<\/pre>/s;
  push (@positions, $string =~ m/<a name = $id>.*Query: \d+\s+[a-z]+ (
+\d+)\n.*\nSbjct: \d+\s+[a-z]+ (\d+)\n<\/pre>/s);

    return @positions;
}
[download]

works too. First and last. Hmm. Anyway...