diff --git a/src/align/alt_hsp.cpp b/src/align/alt_hsp.cpp
index 3278511b..255b6ef8 100644
--- a/src/align/alt_hsp.cpp
+++ b/src/align/alt_hsp.cpp
@@ -38,7 +38,7 @@ struct ActiveTarget {
 				masked_seq[h.frame] = dst.ptr(i++);
 			}
 			Letter* seq = masked_seq[h.frame];
-			std::fill(seq + h.subject_range.begin_, seq + h.subject_range.end_, MASK_LETTER);
+			std::fill(seq + h.subject_range.begin_, seq + h.subject_range.end_, SUPER_HARD_MASK);
 		}
 	}
 	Sequence masked(int32_t context) const {
@@ -85,7 +85,7 @@ static TargetVec recompute_alt_hsps(const Sequence* query_seq, const int query_s
 			ActiveTarget& t = targets[hsp.front().swipe_target];
 			list<Hsp>& l = t.match->hsp;
 			l.splice(l.end(), hsp, hsp.begin());
-			std::fill(t.masked_seq[context] + l.back().subject_range.begin_, t.masked_seq[context] + l.back().subject_range.end_, MASK_LETTER);
+			std::fill(t.masked_seq[context] + l.back().subject_range.begin_, t.masked_seq[context] + l.back().subject_range.end_, SUPER_HARD_MASK);
 			t.active |= 1 << context;
 		}
 	}
diff --git a/src/util/sequence/sequence.cpp b/src/util/sequence/sequence.cpp
index f87ca247..cec7600a 100644
--- a/src/util/sequence/sequence.cpp
+++ b/src/util/sequence/sequence.cpp
@@ -96,7 +96,11 @@ void get_title_def(const std::string& s, std::string& title, std::string& def)
 }
 
 bool is_fully_masked(const Sequence& seq) {
-	return std::count(seq.data(), seq.end(), MASK_LETTER) == seq.length();
+	Loc n = 0;
+	for (const Letter* p = seq.data(); p < seq.end(); ++p)
+		if (*p >= TRUE_AA)
+			++n;
+	return n == seq.length();
 }
 
 }}
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