thanks for this non-destructive method! ;) I am now trying to get more complicated and have written a sub-routine to calculate the mis-matches between the two sequences, ideally i want it to print out like this; 

AGACACTACTGCTG
 *****    ***
ACTACTTACCATCG

[download]
If you see what i mean. I tried to plug the $mismatches into the code you gave me but its not working. it thinks $mismatches is another string! 

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";
  
   }

[download]
The subroutine get_mismatches works perfectly well. Can you see why its going wrong? e.g the above code prints this; 

TGTATCTACTGACTGAC
TGTATCTACTGACTGAC
TGTATCTACTGACTGAC

ATCTG
ATCTG
ATCTG

[download]

In reply to Re: Re: trivial wrapping by Anonymous Monk
in thread trivial wrapping by Anonymous Monk

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