diff --git a/src/main.cpp b/src/main.cpp
index 30f5c368..422ddfce 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -196,7 +196,7 @@ int run_strobealign(int argc, char **argv) {
     map_param.dropoff_threshold = opt.dropoff_threshold;
     map_param.rescue_level = opt.rescue_level;
     map_param.max_tries = opt.max_tries;
-    map_param.use_mcs = false; //opt.r < 200;
+    map_param.use_mcs = true; //opt.r < 200;
     map_param.output_format = (
             opt.is_abundance_out ? OutputFormat::Abundance :
             opt.is_sam_out ? OutputFormat::SAM :