We have identified consensus sequences from many sequences collected from database. There are "n" in many regions. In order to design primers, what should the n be replaced with?
N typically means this region cannot be resolved which can be due to variety of reasons (the sequencing did not reach those bases but was able to reach around 5' and 3' of that region, low quality bases/sequence data, sequence complexity, repeats, etc). If it's a few bases, perhaps the 5' of the primer could potentially tolerate mismatched but generally these regions are hard to amplify for aforementioned reasons. You mentioned it was consensus bases, have a look to see if there's a sequence around non-consensus analysis to get a clue if that region has any data on any of your samples. But as it is a consensus analysis, it hints that a considerable amount of alignments did not form a consensus in that region to resolve the region.
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