diff --git a/src/alignment.r b/src/alignment.r
index 03470d3..de1c8bf 100644
--- a/src/alignment.r
+++ b/src/alignment.r
@@ -110,8 +110,9 @@ get_cys_coordinates <- function(alignment) {
   insertion <- unlist(Biostrings::insertion(alignment))
   deletion <- unlist(Biostrings::deletion(alignment))
   delta_coordinates <- handle_indels(insertion, deletion, cys, alignment)
-  cys_start <- cys$start + delta_coordinates$start
-  cys_end <- cys$end + delta_coordinates$end
+  read_start <- unlist(start(Biostrings::Views(alignment)))
+  cys_start <- cys$start + delta_coordinates$start + read_start - 1
+  cys_end <- cys$end + delta_coordinates$end + read_start
   return(list("start" = cys_start, "end" = cys_end))
 }