Thanks. I wasn't entirely clear on the input format, each file has a number of those data elements in it (i.e. the example is one file); which I need to extract by ID number. I have altered your code to this (where $id_flag is triggered once we come across the appropriate ID number):

sub FindPositions {
  my $string = $_[0];
  my $id = $_[1];
    
  my ($firstQ, $firstS);
  my ($lastQ, $lastS);
  my $id_flag;
  my $line;
    
  # pipe-ize the string
  my $string_pipe = new FileHandle("echo \'$string\' |") or die;

  while (!(defined($id_flag) && defined($firstQ) && defined($firstS)))
  {
    $line = <$string_pipe>;
    $id_flag = 1 if ($line =~ /<a name = $id>/);
    $firstQ = $1 if ($line =~ /^Query:\s+?(\d+)[\sgcat]*(\d+)/) && do{
+$lastQ=$2};
    $firstS = $1 if ($line =~ /^Sbjct:\s+?(\d+)[\sgcat]*(\d+)/) && do{
+$lastS=$2};
  }
    
  foreach $line (<$string_pipe>)
  {
    $lastQ = $2 if ($line =~ /^Query:\s+?(\d+)[\sgcat]*(\d+)/);
    $lastS = $2 if ($line =~ /^Sbjct:\s+?(\d+)[\sgcat]*(\d+)/);
  }
  return ($firstQ, $firstS, $lastQ, $lastS);
}
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But I'm not sure how to make it grab the appropriate ending values. As is it grabs the last ones in the file.

Thanks