diff --git a/primertrim/align.py b/primertrim/align.py
index bfdf761..866ebb2 100644
--- a/primertrim/align.py
+++ b/primertrim/align.py
@@ -111,8 +111,4 @@ def parse(self, f):
                 for field in self.fields:
                     fcn = BLAST_FIELD_TYPES[field]
                     res[field] = fcn(res[field])
-            if res["qstrand"] == "-":
-                qstart_temp = res["qlen"]-res["qend"]+1
-                res["qend"] = res["qlen"]-res["qstart"]+1
-                res["qstart"] = qstart_temp
             yield res
diff --git a/primertrim/matcher.py b/primertrim/matcher.py
index 0740b15..faaec2f 100644
--- a/primertrim/matcher.py
+++ b/primertrim/matcher.py
@@ -141,6 +141,9 @@ def find_in_seqs(self, seqs):
             # Vsearch indexes positions starting with 1
             start_idx = hit["qstart"] - 1
             end_idx = hit["qend"]
+            if hit["qstrand"] == "-":
+                start_idx = hit["qlen"]-hit["qend"]
+                end_idx = hit["qlen"]-hit["qstart"]+1
             assert(start_idx < end_idx)
             seq = seqs[seq_id]
             primerseq = seq[start_idx:end_idx]