Hi,

Here is my substring approach.

use strict;
use warnings;
my $str = 'TTCTTCT';
my $tar = 'ATGTTCT';
my $i =0;
while (length($str)) {
    if (substr($str,0,1) eq '[') {
       my $index = index $str,']';
       my $m = substr($str,0,$index+1);
       print "Mismatch at index $i\n" unless (substr($tar,$i,1)=~/$m/)
+;
       substr($str,0,$index+1)="";
    }
    else {
       print "Mismatch at index $i\n" unless (substr($str,0,1) eq subs
+tr($tar,$i,1));
       substr($str,0,1)="";
    }   
    $i++;
}
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