diff --git a/src/Mutalyzer.py b/src/Mutalyzer.py
index fe1f1e65de172988d60e33b72f354ef9f922b5c0..9d7564c062700279e05232912c1c1c296afc7446 100644
--- a/src/Mutalyzer.py
+++ b/src/Mutalyzer.py
@@ -879,12 +879,15 @@ def checkDeletionDuplication(start_g, end_g, mutationType, MUU,
 
     roll = __roll(MUU.orig, start_g, end_g)
 
+    # In the case of RNA, check if we roll over a splice site. If so, make
+    # the roll shorter, just up to the splice site.
     shift = roll[1]
     if GenRecordInstance.record.molType == 'n' :
         mRNA = GenRecordInstance.record.geneList[0].transcriptList[0
             ].mRNA.positionList
         for i in mRNA :
             if end_g <= i and end_g + roll[1] > i :
+                # Do a shorter roll, just up to the splice site
                 print "ALARM"
                 shift = i - end_g
                 print shift
@@ -893,7 +896,6 @@ def checkDeletionDuplication(start_g, end_g, mutationType, MUU,
         #for
     #if
 
-
     if shift : # FIXME, The warning may not be apropriate.
         newStart = start_g + shift
         newStop = end_g + shift
@@ -977,12 +979,15 @@ def checkInsertion(start_g, end_g, Arg1, MUU, GenRecordInstance, O) :
     newStop = MUU.shiftpos(start_g) + insertionLength
     roll = __roll(MUU.mutated, newStart + 1, newStop)
 
+    # In the case of RNA, check if we roll over a splice site. If so, make
+    # the roll shorter, just up to the splice site.
     shift = roll[1]
     if GenRecordInstance.record.molType == 'n' :
         mRNA = GenRecordInstance.record.geneList[0].transcriptList[0
             ].mRNA.positionList
         for i in mRNA :
             if newStop <= i and newStop + roll[1] > i :
+                # Do a shorter roll, just up to the splice site
                 print "ALARM"
                 shift = i - newStop
                 print shift