I used to use GeneJockey to check my primers for non-specific binding to my gene. There is a function called Matrix (I think) that would check for homology between my primers and my gene. It will then display a colour-coded plot showing the homology in different regions of the gene. For example, a region of yellow indicates low homology (ie non-specific priming is unlikely) and a black region means high homology (ie non-specific binding is highly probable). However, that program is for Mac OS9 and I don't use Mac anymore. I'm also not sure what this kind of analysis is called. Does anyone know of any software for Windows (preferably freeware) or online tools that can perform this kind of analysis? Thanks!