The scores of each word are added and a global score for the MSP is computed. This shouldn't be a problem since all matching regions will be analyzed, although they will be listed as separate items in the final report. Decreasing this value will find more sequences, possibly uncovering biologically significant matches that might not be statistically significant enough. The search results When the search has finished you will be presented with a report of the results. This helps identify the file contents later on and reminds you of what it is all about.
Next thing is a listing of sequences containing matching regions.
For each of them you get the score of the matches and the number of regions found. The listing will contain the sequence name, this score of the best match, the probability of finding a similar group of scores by chance and the number of matches contained by this sequence. You should never trust blindly the computer , only a human expert can reliably assert possible biological meaningfulness of sequence alignments. This ability of previously reducing the search space often proves rather useful to remove worthless matches or get more easily to the matches you want. Even if your sequence contains ambiguity codes, they are converted to what the program considers to be the most probable sequence before comparison.