diff --git a/src/alignment.r b/src/alignment.r
index d28e028..c9cdacb 100644
--- a/src/alignment.r
+++ b/src/alignment.r
@@ -126,7 +126,7 @@ get_hvr_sequences <- function(sequences, vdj_segments, cores = detectCores()) {
   )
   cys_coordinates <- parallel::mclapply(v_alignment, FUN = get_cys_coordinates)
   cys_df <- as.data.frame(do.call(rbind, cys_coordinates))
-  remaining <- Biostrings::subseq(sequences, start = unlist(cys_df$end))
+  remaining <- Biostrings::subseq(sequences, start = unlist(cys_df$end) + 1)
   j_alignment <- parallel::mcmapply(remaining,
     df$j_seq,
     FUN = align_sequence,