diff --git a/src/alignment.r b/src/alignment.r
index f4bbee4..25facbb 100644
--- a/src/alignment.r
+++ b/src/alignment.r
@@ -35,8 +35,8 @@ construct_full_sequences <- function(vdj_segments, metadata) {
 
 align_sequence <- function(sequence, vdj_segment) {
   return(Biostrings::pairwiseAlignment(
-    pattern = sequence,
-    subject = vdj_segment,
+    subject = sequence,
+    pattern = vdj_segment,
     type = "global-local",
     gapOpening = 1,
   ))