diff --git a/src/sse_banded_LCS_alignment.c b/src/sse_banded_LCS_alignment.c
index 8790c6b..eab489b 100644
--- a/src/sse_banded_LCS_alignment.c
+++ b/src/sse_banded_LCS_alignment.c
@@ -900,6 +900,14 @@ double generic_sse_banded_lcs_align(char* seq1, char* seq2, double threshold, bo
 		lmin = l1;
 	}
 
+	// Check that the sequences are not greater than what can be aligned using the 16 bits registers (as the LCS and alignment lengths are kept on 16 bits)
+	if (lmax > SHRT_MAX)
+	{
+		obi_set_errno(OBI_ALIGN_ERROR);
+		obidebug(1, "\nError: can not align sequences longer than %d (as the LCS and alignment lengths are kept on 16 bits)", SHRT_MAX);
+		return 0; 		// TODO DOUBLE_MIN to flag error
+	}
+
 	// If the score is expressed as a normalized distance, get the corresponding identity
 	if (!similarity_mode && normalize)
 		threshold = 1.0 - threshold;
@@ -995,6 +1003,14 @@ double obiblob_sse_banded_lcs_align(Obi_blob_p seq1, Obi_blob_p seq2, double thr
 		lmin = l1;
 	}
 
+	// Check that the sequences are not greater than what can be aligned using the 16 bits registers (as the LCS and alignment lengths are kept on 16 bits)
+	if (lmax > SHRT_MAX)
+	{
+		obi_set_errno(OBI_ALIGN_ERROR);
+		obidebug(1, "\nError: can not align sequences longer than %d (as the LCS and alignment lengths are kept on 16 bits)", SHRT_MAX);
+		return 0; 		// TODO DOUBLE_MIN to flag error
+	}
+
 	// If the score is expressed as a normalized distance, get the corresponding identity
 	if (!similarity_mode && normalize)
 		threshold = 1.0 - threshold;