The fix is something like:

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