diff --git a/modisco b/modisco
index 5088aef..3ef7ecd 100755
--- a/modisco
+++ b/modisco
@@ -185,7 +185,7 @@ if args.cmd == "motifs":
 
 	if sequences.shape[1] < args.window:
 		raise ValueError("Window ({}) cannot be ".format(args.window) +
-			"longer than the sequences".format(sequences.shape))
+			"longer than the sequences {}".format(sequences.shape[1]))
 
 	sequences = sequences.astype('float32')
 	attributions = attributions.astype('float32')
diff --git a/modiscolite/aggregator.py b/modiscolite/aggregator.py
index 876fc3e..933f8c1 100644
--- a/modiscolite/aggregator.py
+++ b/modiscolite/aggregator.py
@@ -41,7 +41,6 @@ def polish_pattern(pattern, min_frac, min_num, track_set, flank, window_size, bg
 
 def _expand_seqlets_to_fill_pattern(pattern, track_set, left_flank_to_add,
 	right_flank_to_add):
-
 	new_seqlets = []
 	for seqlet in pattern.seqlets:
 		left_expansion = left_flank_to_add 
@@ -55,11 +54,11 @@ def _expand_seqlets_to_fill_pattern(pattern, track_set, left_flank_to_add,
 			end = seqlet.end + left_expansion
 		
 		if start >= 0 and end <= track_set.length:
-			seqlet = track_set.create_seqlets(
+			seqlets = track_set.create_seqlets(
 				seqlets=[core.Seqlet(example_idx=seqlet.example_idx,
-					start=start, end=end, is_revcomp=seqlet.is_revcomp)])[0]
-
-			new_seqlets.append(seqlet)
+					start=start, end=end, is_revcomp=seqlet.is_revcomp)])
+			if len(seqlets) > 0:
+				new_seqlets.append(seqlets[0])
 
 	if len(new_seqlets) > 0:
 		return core.SeqletSet(seqlets=new_seqlets)
@@ -299,7 +298,7 @@ def SimilarPatternsCollapser(patterns, track_set,
 
 				within_pattern1_sims = affinitymat.jaccard(
 					flat_pattern1_fwdseqdata[:, :, None], 
-					flat_pattern1_fwdseqdata[:, :, None])[:, :, 0].flatten()
+					flat_pattern1_fwdseqdata[:, :, None])[:, :, 0].flatten()	
 
 				auroc = roc_auc_score(
 					y_true=[0 for x in between_pattern_sims]
@@ -502,4 +501,4 @@ def SimilarPatternsCollapser(patterns, track_set,
 			current_level_nodes = next_level_nodes
 
 	return patterns, PatternMergeHierarchy(root_nodes=current_level_nodes)
-	
\ No newline at end of file
+	
diff --git a/modiscolite/core.py b/modiscolite/core.py
index 639531b..3d0e7f4 100644
--- a/modiscolite/core.py
+++ b/modiscolite/core.py
@@ -21,7 +21,8 @@ def __init__(self, one_hot, contrib_scores, hypothetical_contribs):
 		self.length = len(one_hot[0])
 
 	def create_seqlets(self, seqlets):
-		for seqlet in seqlets:
+		out_seqlets = []        
+		for i,seqlet in enumerate(seqlets):
 			idx = seqlet.example_idx
 			s, e = seqlet.start, seqlet.end
 
@@ -33,8 +34,11 @@ def create_seqlets(self, seqlets):
 				seqlet.sequence = self.one_hot[idx][s:e]
 				seqlet.contrib_scores = self.contrib_scores[idx][s:e]
 				seqlet.hypothetical_contribs = self.hypothetical_contribs[idx][s:e]				
-
-		return seqlets
+                
+			# verify that seqlet is not at the end of the sequence and has some bp set
+			if seqlet.sequence.sum()>0:
+				out_seqlets.append(seqlet)
+		return out_seqlets
 
 class Seqlet(object):
 	def __init__(self, example_idx, start, end, is_revcomp):