diff --git a/bin/rnamotifs2 b/bin/rnamotifs2
index 6183a95..de6076c 100755
--- a/bin/rnamotifs2
+++ b/bin/rnamotifs2
@@ -27,7 +27,8 @@ for region in ["r1s", "r1e", "r2s", "r2e", "r3s", "r3e"]:
         continue
     if rnamotifs2.data.dist.get("e", None)==None and region[-1]=="e":
         continue
-    rnamotifs2.start(comps, region, 0, 4)
+    # rnamotifs2.data.pth = 4 (default)
+    rnamotifs2.start(comps, region, 0, rnamotifs2.data.pth)
 
 if rnamotifs2.data.data_type=="apa":
     os.system("rnamotifs2.draw_apa -comps %s" % comps)
diff --git a/data/__init__.py b/data/__init__.py
index 1cfd93f..11187cc 100644
--- a/data/__init__.py
+++ b/data/__init__.py
@@ -36,10 +36,13 @@ def read_config(comps):
         continue
     f.close()
 
-    # by default, do not correct for FDR
+    # default values
     if getattr(m, "use_FDR", None)==None:
         setattr(m, "use_FDR", False)
 
+    if getattr(m, "pth", None)==None:
+        setattr(m, "pth", 4)
+
     if getattr(m, "base_motif_thr", None)==None:
         setattr(m, "base_motif_thr", 0.01)