X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FRnamlFile.java;h=bc6b3855c6b706730a887650c62a21c15da678f9;hb=6819474b5da8df0145cfe2c65ea9445609332c20;hp=da646076cf87abe0e6a5e817e672e4b10fa0ede2;hpb=df4d3a854a8969b957937c8b043f5eaf4b310082;p=jalview.git

diff --git a/src/jalview/io/RnamlFile.java b/src/jalview/io/RnamlFile.java
index da64607..bc6b385 100644
--- a/src/jalview/io/RnamlFile.java
+++ b/src/jalview/io/RnamlFile.java
@@ -126,8 +126,8 @@ public class RnamlFile extends AlignFile
 		  //System.out.println(result.get(0).getAnnotations());
 		  String seq = current.getSeq();
 	
-		  int begin=0;
-		  int end = seq.length()-1;
+		  int begin=1;
+		  int end = seq.length();
 		  
 		  id = current.getName();
 		  seqs[i] = new Sequence(id, seq, begin, end);