Query parameters

Paste your sequence	FASTA format. Length is limited to 20Mb
Or select a file	FASTA format. File size is limited to 20Mb

Databank selection

Databank

General parameters

Expect	The statistical significance threshold for reporting matches. Lowest values are the most stringent.
Word size	The length of the seed that initiates an alignment.

Scoring parameters

Matrix	First number is the reward when two aligned nucleotides match. Second number is the penalty when two aligned nucleotides are different.
Gap costs	Penalties when opening and extending a gap in each alignment.
Compositional adjustments	Matrix adjustment method to compensate for amino acid composition of sequences.

Filters and masking

Low complexity regions	Mask off segments of the query sequence that have low compositional complexity.
Soft masking	Mask only when finding alignment seeds, not during extension.
Mask lower case letters	Filter regions in lower case in query sequence.

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