As of December 15th 2009, the MetaGene tool is no longer available on the RGD website. Over the years since the tool was first written, most or all of the online resources that MetaGene used have been either moved or changed sufficiently to render the MetaGene tool unusable. During a round of testing in October 2009 we found that all of the "request" submissions that we made via this tool failed. Unfortunately, it took several hours for the tool to determine that the requests had failed making the situation even more problematic. As such the decision was made to remove the tool completely rather than simply leave it as "available but unsupported".
If you are looking for DNA analysis software, here are some alternatives that you can try: