This table is useful with back-translated sequences. This table provides better discrimination. You should be choice this table first when back-translated sequences are used. This parameter controls the scoring of unknown bases in nucleic acid searches. Nmatch specifies how the character N in the query and in the database is matched.
N can match everything or N can match only itself, in the databases or in the query.
XX Use most negative value from table, for N in both the query and the database. The setting of Nmatch you use depends on your meaning for the N character. In DDBJ, GenBank, and EMBl, there are long runs of N's that often represent unknown bases. If you allow these N's to match, using the NN or QX settings, any query will match these sequences and they will all be reported with high scores. On the other hand, N's in the query may mean that any base is acceptable.