Thanks that clarified things. What’s happening here is that Jalview simply does not have any sequence feature information to add to the image. The image map generator was only designed to embed the tooltip and URL link information associated with sequence annotation (see http://www.jalview.org/help/html/features/featuresFormat.html ). It would, of course, be possible to enhance the generator to embed more information (e.g. row column position, annotation score data, etc) - but we haven’t had any requests for this. What would you like to do ?