diff --git a/src/alignment.cpp b/src/alignment.cpp
index b9dce5a260..e8a1496793 100644
--- a/src/alignment.cpp
+++ b/src/alignment.cpp
@@ -1321,8 +1321,10 @@ pair<int32_t, int32_t> compute_template_lengths(const int64_t& pos1, const vecto
     // And find the distance
     int32_t dist = max_end - min_start;
     
-    if (pos1 < pos2) {
-        // Count read 1 as the overall "leftmost", so its value will be positive
+    if (bounds1.first < bounds2.first || (bounds1.first == bounds2.first && bounds1.second < bounds2.second)) {
+        // Count read 1 as the overall "leftmost" if it starts earlier or
+        // starts at the same point and ends earlier, so its value will be
+        // positive
         return make_pair(dist, -dist);
     } else {
         // Count read 2 as the overall leftmost
diff --git a/src/unittest/alignment.cpp b/src/unittest/alignment.cpp
index a4b19df860..a29441977c 100644
--- a/src/unittest/alignment.cpp
+++ b/src/unittest/alignment.cpp
@@ -335,8 +335,8 @@ TEST_CASE("Template length for HTS output formats is outermost to outermost when
 
 TEST_CASE("Template length for HTS output formats is outermost to outermost when read 2 is a suffix of read 1", "[alignment][tlen]") {
     auto lengths = compute_template_lengths(1000, {{151, 'M'}}, 1141, {{10, 'M'}});
-    REQUIRE(lengths.first == -151); // Read 1 is the leftmost since it starts earliest
-    REQUIRE(lengths.second == 151);
+    REQUIRE(lengths.first == 151); // Read 1 is the leftmost since it starts earliest
+    REQUIRE(lengths.second == -151);
 }
 
 TEST_CASE("Template length for HTS output formats is outermost to outermost when read 1 and read 2 have identical coordinates", "[alignment][tlen]") {