N means that in this position you could have any nucleotide (A or T or C or G)- if the N is the result of a low quality sequence, I would first try to find out what the most likely correct sequence is by looking for alternative sequences in genebank.

I agree with Annemarie Honegger . you should have a high quality of the DNA sequence if your aim is to detect rare codon, what you yourself has asked. I would not recommend to use any of the sequence which has "N". As you are already including a lot of manual bias if you are optimizing the "N" yourself, and the analysis is loosing it credibility from the beginning.