Hello everyone! The problem is the following: I got a pattern of microsatellite, for example (GA)8nGTGT(G)11, and I want to search for all possible targets across the specified locus (2nd chromosome) across all genome assemblies. I tried non-specific software namely BLASTn, however there is no option to choose a specific chromosome as well as to specify all assemblies available. I also tried UGENE but it also searches across one assembly. Could you suggest some tool if there is any, please?
A GUI for
fuzznuc
. Not sure if it will take chromosome sized data via web.