I just learned from Technical Application Scientist that ThermoScientific (Applied Biosystems) is discontinuing the kits ('We are in the process of discontinuing our AFLP Kits. We use to have a Microbial AFLP Kit, but now we only have one module available on the website and some primers.')

I want to use standard enzymes (EcoRI & MspI), my question is about selective primers (see attached  table) that contain additional one or two nucleotides following restriction motif at 3'-end. There are many possible combinations to check

Hi, Marcin

I would strongly suggest to perform an in silico AFLP using the following tool: http://insilico.ehu.es/AFLP/

You may choose the RE type and the selective nucleotide included in the kit for each bacteria in order to test primer combination reproducibility prior to real amplification.

Best wishes

http://insilico.ehu.es/AFLP/