my $mismatches = get_mismatches ($genome1, $genome2);


my @strings = ($genome1, $mismatches, $genome2);

for (my $x = 0; $x < length ($strings [0]); $x +=60)    {

  print join ("\n", map (substr ($strings[$_], $x, 60), 0..2 )). "\n\n";

 }

sub get_mismatches {

  ($genome1, $genome2) = @_;
  my ($length) = length ($genome1);
  my $position;
  my $count = 0;

  print "\n\n";

   for ($position = 0; $position < $length; ++$position)  {

     if (substr($genome1, $position, 1) eq substr ($genome2, $position, 1))
       {
         print "-";
       }

      else {
         print "*";
        }
  }
return ($genome1, $genome2);

}


##</code><code>##


ACACTTGCATACTGATC
--*****-****---**
ACTACGACTGCATGACT

TGACTGCACT
*********-
CATGATATGT


##</code><code>##

ATGCATGACTACT
CTGAATGCTGACT
CGTCTGACTATAA

ATGACTTGAC
CTATGACTGA
CCGATGACTG