Maximum number of aligned sequences to display (the actual number of alignments may be greater than this).
The length of the seed that initiates an alignment. more...
Automatically adjust word size and other parameters to improve results for short queries.
Matrix
PAM30 PAM70 BLOSUM80 BLOSUM62 BLOSUM45 [?]
Assigns a score for aligning pairs of residues, and determines overall alignment score. more...
Match/Mismatch Scores
Reward and penalty for matching and mismatching bases. more...
Gap Costs
Cost to create and extend a gap in an alignment. more...
Compositional adjustments
Matrix adjustment method to compensate for amino acid composition of sequences. more...
Mask regions of low compositional complexity that may cause spurious or misleading results. more...
Mask repeat elements of the specified species that may lead to spurious or misleading results. more...
Mask query while producing seeds used to scan database, but not for extensions. more...
Mask any letters that were lower-case in the FASTA input. more...