Hi, Firstly i'd like to thank everyone that took the time to help me yesterday. I now have another slight problem....on the same lines. Anyway, i am trying to align two short sequences of DNA and mark on mismatches, which i have done. Yesterday i got help trying to interleave and wrap the output to print 60 chars per line.. my problem is now that i need to interleave the mismatch markings aswell, this part isn't working. the snippet of code that i have is below; 
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);

}

[download]
The desired output would look like this; 

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

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

[download]
but so far it looks like this; 
ATGCATGACTACT
CTGAATGCTGACT
CGTCTGACTATAA

ATGACTTGAC
CTATGACTGA
CCGATGACTG

[download]
so for some reason it thinks that $mismatches is a string of DNA nOt the combination of * and - that were in the subroutine. If anyone can help i'd really appreciate it.

In reply to more interweaving by Anonymous Monk

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