...
  @myarray = split /></,$line;
  if ( $prev ne $myarray[0] ) {
    $prev = $myarray[0];
  } else {
    $myarray[0] = "<TAB";
  }
  $line = join '><', @myarray;
  print OUTFILE, $line;
...

##</code><code>##

$line =~ s/<TAB>/\t/;