>perl -wMstrict -le
"my @queries = qw[ GCGAT CACGT ];
 ;;
 my @targets = qw(GNGATNNN GCGANBBB CNCGTNNN   CBCGTNNN  );
 ;;
 for my $q (@queries) {
   for my $t (@targets) {
     my $matched = ($q ^ substr($t, 0, length $q)) =~ tr[\0][\0];
     if($matched >= (length($q) - 1)) {
       print qq{'$q' matched '$t'};
       }
     }
   }
"
'GCGAT' matched 'GNGATNNN'
'GCGAT' matched 'GCGANBBB'
'CACGT' matched 'CNCGTNNN'
'CACGT' matched 'CBCGTNNN'