############ outer loop###################
  foreach my $fileSeq(@sequences)  # loop through all the sequences
  {
    $counter++;
    $seqobj = '';
    print("<BR>$counter<BR>");
    $seqobj = Bio::PrimarySeq->new ( -seq => $fileSeq, -alphabet => 'dna');      # create an object of the sequence
    print("<BR>Sequence object created....all going well so far...<BR>");

############ inner loop ###################    
    foreach $element(@enzymes)  # look through all the enzymes for each sequence
    {
      $newObject = '';
      $newObject = new Bio::Tools::RestrictionEnzyme(-NAME =>$element);      # create an object of the enzyme
      print("<BR>Enzyme object created for enzyme : $element<BR>");
      
      $cutSeq = $newObject->site();                                          # show the cut site for the enzyme
      
      $anotate = $newObject->annotate_seq($seqobj);                    # annotate the sequence at cut site
      print("<BR>Sequence virtually labelled....<BR>");
      
      @cut = $newObject->cut_seq($seqobj);                            # virtualy cut the sequnce using the enzyme
      print("<BR>Sequence virtually cut....<BR>");
      
      print("<TABLE BORDER=2>");                                     # produce output
      print("<TR><TD><B>Sequence number $counter</B></TR></TD>");
      print("<TR><TD>");
      print("The cleavage site is $cutSeq for enzyme $element denoted by \" ^ \"<BR></TD></TR>");
      print("<TR><TD>The annotated sequence is given below along with the digested sequence<BR>");
      print("<B>Annotated:</B>$anotate<BR>");
      print("<B>Digested:</B>@cut</TD></TR>");
      print("</TABLE><BR><BR>");
    } ############ END inner loop ################### 
    print("Loop finished... returning to the start<BR>");
  }############ END outer loop ###################