diff --git a/mhcflurry/encodable_sequences.py b/mhcflurry/encodable_sequences.py
index 8dff8e8f496d8aa96159b6569eb806b36b714771..84e9a2daf26a97359d62950c42a04a3390bec9e4 100644
--- a/mhcflurry/encodable_sequences.py
+++ b/mhcflurry/encodable_sequences.py
@@ -76,6 +76,7 @@ class EncodableSequences(object):
 
         cache_key = (
             "fixed_length_categorical",
+            alignment_method,
             left_edge,
             right_edge,
             max_length)
@@ -123,6 +124,7 @@ class EncodableSequences(object):
         cache_key = (
             "fixed_length_vector_encoding",
             vector_encoding_name,
+            alignment_method,
             left_edge,
             right_edge,
             max_length)