while ($seq{$k} =~ /([QGYN]{3,6})/g) {
     my $seq = $1;
     next if $seq =~ /(.)\1\1/;
     print "\n$k";
     print "$seq begins at position ", (pos($seq{$k})-length($s)) , "\n";
}

##</code><code>##

my $length = length $s; # Pull this out of the loop for eff.
my $sequence = $seq{$k};

while ($sequence =~ /([QGYN]{3,6})/g) {
     my $seq = $1;
     my $pos = $-[0] - $length; # @- holds the positions on the last match
     next if $seq =~ /(.)\1\1/;
     print "\n$k $seq begins at position $pos\n";
}