diff --git a/porechop/adapters.py b/porechop/adapters.py
index dce7a4f..06ff0e5 100644
--- a/porechop/adapters.py
+++ b/porechop/adapters.py
@@ -25,6 +25,7 @@ def __init__(self, name, start_sequence=None, end_sequence=None, both_ends_seque
             self.start_sequence = both_ends_sequence
             self.end_sequence = both_ends_sequence
         self.best_start_score, self.best_end_score = 0.0, 0.0
+        self.sum_start_scores, self.sum_end_scores = 0.0, 0.0
 
     def best_start_or_end_score(self):
         return max(self.best_start_score, self.best_end_score)
diff --git a/porechop/nanopore_read.py b/porechop/nanopore_read.py
index 8a03776..80f9642 100755
--- a/porechop/nanopore_read.py
+++ b/porechop/nanopore_read.py
@@ -157,11 +157,13 @@ def align_adapter_set(self, adapter_set, end_size, scoring_scheme_vals):
             score, _, _, _ = align_adapter(read_seq_start, adapter_set.start_sequence[1],
                                            scoring_scheme_vals)
             adapter_set.best_start_score = max(adapter_set.best_start_score, score)
+            adapter_set.sum_start_scores += score
         if adapter_set.end_sequence:
             read_seq_end = self.seq[-end_size:]
             score, _, _, _ = align_adapter(read_seq_end, adapter_set.end_sequence[1],
                                            scoring_scheme_vals)
             adapter_set.best_end_score = max(adapter_set.best_end_score, score)
+            adapter_set.sum_end_scores += score
 
     def find_start_trim(self, adapters, end_size, extra_trim_size, end_threshold,
                         scoring_scheme_vals, min_trim_size, check_barcodes, forward_or_reverse):
diff --git a/porechop/porechop.py b/porechop/porechop.py
index 25febe6..8d6d2c6 100755
--- a/porechop/porechop.py
+++ b/porechop/porechop.py
@@ -338,13 +338,13 @@ def choose_barcoding_kit(adapter_sets, verbosity, print_dest):
     for adapter_set in adapter_sets:
         if 'barcode' in adapter_set.name.lower():
             if '(forward)' in adapter_set.name.lower():
-                forward_start_or_end += adapter_set.best_start_or_end_score()
-                forward_start_and_end += adapter_set.best_start_score
-                forward_start_and_end += adapter_set.best_end_score
+                forward_start_or_end += max(adapter_set.sum_start_scores, adapter_set.sum_end_scores)
+                forward_start_and_end += adapter_set.sum_start_scores
+                forward_start_and_end += adapter_set.sum_end_scores
             elif '(reverse)' in adapter_set.name.lower():
-                reverse_start_or_end += adapter_set.best_start_or_end_score()
-                reverse_start_and_end += adapter_set.best_start_score
-                reverse_start_and_end += adapter_set.best_end_score
+                reverse_start_or_end += max(adapter_set.sum_start_scores, adapter_set.sum_end_scores)
+                reverse_start_and_end += adapter_set.sum_start_scores
+                reverse_start_and_end += adapter_set.sum_end_scores
 
     if forward_start_or_end == 0 and reverse_start_or_end == 0:
         sys.exit('Error: no barcodes were found, so Porechop cannot perform barcode demultiplexing')