Ah, i see... thanks for the hint on txt formatting. Theres me rushing into things again. You learn something new everyday. I hope this is more readable. Thanks for your example.
MonkPaul.

sub checkFile()
{
 # print("The path name was: $file");
    print("Opening File...");
    print("File is now open");
    @file = <FILE>;
    print("<BR><BR> @file<BR><BR>");
    while($line = <FILE>)
    {
      chomp($line);
      if($line =~ /([^ACGTacgt])/) {next;}
      else
      {
        @cols = split(/\s/, $line);
        print("@cols");
      }
      print("File is now closed");
    }
}
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