If the possibility your describe can happen, I think this is a computationally simpler solution: #! perl -slw
use strict;
my @queries = qw[ GCGAT CACGT ];
chomp( my @targets = <DATA> );
for my $q ( @queries ) {
for my $t ( @targets ) {
my $matched = ( $q ^ substr( $t, 0, length( $q ) ) ) =~ tr[\0]
+[\0];
if(
$matched == length( $q )
or $matched == length( $q )-1
and substr( $t, 0, length( $q ) ) =~ tr[N][N] == 1
) {
print "$q matched $t";
}
}
}
__DATA__
GNGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
GCGANBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
CNCGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
GBGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'
Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.
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