Hi I have the code below working. I now need to set a threshold for how many mis-matches can be tolerated and also set a user-provided limit for how many characters are matched at a time (i.e. matches groups of characters rather than one character at a time).
The two strings are being read in from separate files and compared and a dot printed for each matching group.
. I'm a perl beginner and I've tried combinations of pattern matches but with little success. I would appreciate any help in what to change in the code in order to achieve this/ 

#!/usr/bin/perl
use strict;use warnings;
my $i;my $j;my $a;
open (FH1,'<', "./CAM3UCA.txt");
open (FH2,'<', "./TCH3A.txt");
my $seq1 = do { local $/; <FH1> };
my $seq2 = do { local $/; <FH2> };

my @s1=split('',$seq1);
my @s2=split('',$seq2);
my @matrix=();

for($i=0;$i<scalar(@s2);$i++)
{
 for($j=0;$j<scalar(@s1);$j++)
 {
  if($s2[$i] eq $s1[$j])
  {
  $matrix[$i][$j]=".";
  }
  else
  {
  $matrix[$i][$j]=" ";
  }

 }
}

#Printing matrix of dot plot
open (FHOUT,">dotplot.txt") or die "cannot open outfile\n";
print FHOUT " ";
for($a=0;$a<scalar(@s1);$a++)
    {
print FHOUT "$s1[$a]";
}
print FHOUT "\n";
#print FHOUT "\n\n";
for($i=0;$i<scalar(@s2);$i++)
{
    print FHOUT "$s2[$i]";

 for($j=0;$j<scalar(@s1);$j++)
 {

print FHOUT "$matrix[$i][$j]";
 }
  print FHOUT "\n";
#print FHOUT "\n\n";
}

close FH1;
close FH2;
close FHOUT;<br>

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In reply to Matrix plot help by utterlyconfused

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