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

my $length = length $s; # Pull this out of the loop for eff.
my $sequence = $seq{$k};
...
     next if $seq =~ /(.)\1\1/;
     print "\n$k $seq begins at position $pos\n";
}