open (DATEI2, "> $upload_directory/$datei2") or die "Couldn't open: $!";
while ($i < length ($seq) ) {
	 ...
	 if ($ii == 50) {
	     print DATEI2 "\n>$kopf\n$dna";          
	     $dna = "";
	     $seq_dna = "";
	     $ii = 0;
	     $iii++;
	   }
}
close DATEI2;