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General Parameters:
	Expect threathold: Expected number of chance matches in a random model. more... 1000 100 10 1 0.1 0.01 0.001 1e-03 1e-04 1e-05 1e-10 1e-20 1e-30 1e-40 1e-50 1e-100 Descriptions: The number of short descriptions of matching sequences reported to the number specified. more ... 10 50 100 250 500 1000 5000 10000 Alignments: Select the maximum number of aligned sequences to display 10 50 100 250 500 1000 5000 10000 WordSize: The length of the seed that initiates an alignment. more... 2 3 6
Filter and Masking:
	Low complexity regions: Mask regions of low compositional complexity that may cause spurious or misleading results. more... SEG Mask lower case letters: Mask any letters that were lower-case in the FASTA input. more...
Scoring Parameters:
	Matrix: Assigns a score for aligning pairs of residues, and determines overall alignment score. more... PAM30 PAM70 PAM250 BLOSUM80 BLOSUM62 BLOSUM45 BLOSUM50 BLOSUM90 Gap Costs (Open/Extend) Cost to create and extend a gap in an alignment. more... (4,4) (2,4) (0,4) (3,3) (6,2) (5,2) (4,2) (2,2) Ungapped Align Perform ungapped alignment only? Compositional adjustments Matrix adjustment method to compensate for amino acid composition of sequences. more... No composition-based statistics (0) Composition-based statistics (1) Conditional composition-based score adjustment (2) Unconditional composition-based score adjustment (3) Genetic Code (only blastx) Standard ( 1 ) Vertebrate Mitochondrial ( 2 ) Yeast Mitochondrial ( 3 ) Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma ( 4 ) Invertebrate Mitochondrial ( 5 ) Ciliate, Dasycladacean and Hexamita Nuclear ( 6 ) Echinoderm and Flatworm Mitochondrial ( 9 ) Euplotid Nuclear ( 10 ) Bacterial, Archaeal and Plant Plastid ( 11 ) Alternative Yeast Nuclear ( 12 ) Ascidian Mitochondrial ( 13 ) Alternative Flatworm Mitochondrial ( 14 ) Chlorophycean Mitochondrial ( 16 ) Trematode Mitochondrial ( 21 ) Scenedesmus obliquus Mitochondrial ( 22 ) Thraustochytrium Mitochondrial ( 23 ) Pterobranchia Mitochondrial ( 24 ) Candidate Division SR1 and Gracilibacteria ( 25 ) Pachysolen tannophilus Nuclear ( 26 ) Karyorelict Nuclear ( 27 ) Condylostoma Nuclear ( 28 ) Mesodinium Nuclear ( 29 ) Peritrich Nuclear ( 30 ) Blastocrithidia Nuclear ( 31 )