Hi monkfan, If i understood your question correctly, it helps you.

use strict;
my %compare = ('[TCG]GGGG[AT]'=>['AGGGGC', 'TGGGGC'], 'TGGGGT'=>['AGGG
+GC','AGGGGC']);

for my $ky (keys (%compare))
{
    my @source = split /GGGG/, $ky;    
    my @arr = @{$compare{$ky}};
    
        print "\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n";
        print "\nSource:\t", $ky;
      print "\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n";
    for my $t (0..$#arr){        
        my @tar = split /GGGG/,$arr[$t];
          print "\nTarget:\t", $arr[$t], "\n";
          my $mis = 0;
            for my $po (0..$#source){                
            if ($tar[$po] !~ m/$source[$po]/){
                $mis++;                        
                print "\nPosition for Mismatch : ",$po + 1 if ($po == 
+0);
                print "\nPosition for Mismatch : ",$po + 5 if ($po == 
+1);
             }
          }
          print "\nNo of Mismatch = $mis\n";          
    }
    print "\n+++++++++++++++++++++++++++++\n";
}
__END__
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Source: [TCG]GGGG[AT]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Target: AGGGGC

Position for Mismatch : 1
Position for Mismatch : 6
No of Mismatch = 2

Target: TGGGGC

Position for Mismatch : 6
No of Mismatch = 1

+++++++++++++++++++++++++++++

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Source: TGGGGT
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Target: AGGGGC

Position for Mismatch : 1
Position for Mismatch : 6
No of Mismatch = 2

Target: AGGGGC

Position for Mismatch : 1
Position for Mismatch : 6
No of Mismatch = 2

+++++++++++++++++++++++++++++

[download]

Regards,
Velusamy R.

eval"print uc\"\\c$_\""for split'','j)@,/6%@0%2,`e@3!-9v2)/@|6%,53!-9@2~j';

In reply to Re: Mismatch Positions of Ambiguous String by Samy_rio
in thread Mismatch Positions of Ambiguous String by monkfan

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