If start is not zero, we need to put -- at the start

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 63f791c..ca5bbb3 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -295,6 +295,9 @@ public class Conservation
         Hashtable resultHash ;
         Enumeration enumeration;
 
+        for(int i=0; i<start; i++)
+          consString.append('-');
+
 
         for (int i = start; i <= end; i++)
         {
@@ -343,7 +346,7 @@ public class Conservation
             }
             else
             {
-                consString.append("-");
+                consString.append('-');
             }
         }