Input
Remote DataBase	Select remote DB: Non-Redundant - All GenBank, EMBL and DDBJ Non-Redundant sequences (but no EST, STS, GSS, or phase 0, 1 or 2 HTGS sequences). WGS entries are also excluded. No longer "Non-Redundant". EST - Database for entries from Estimated Sequence Tags (EST) division of GenBank, EMBL and DDBJ. Human EST - H.Sapiens subset of Estimated Sequence Tags. Mouse EST - M.Musculus subset of Estimated Sequence Tags. Other EST - EST other than Human or Mouse. GSS - Genomic Survey Sequence, includes single-pass genomic data, exon-trapped sequences, and Alu PCR sequences. HTGS - Unfinished High Throughput Genomic Sequences: phases 0, 1 and 2. Finished, phase 3 HTG sequences are in NR. Patented sequences (PAT) - Nucleotides from the Patent division of GenBank. Patented sequences - Nucleotides from the Patent division of GenBank.. Monthly Sequences (Month) - All new or revised GenBank, EMBL and DDBJ sequences released updated in the last 30 days. Alu repeats - Select Alu repeats from REPBASE, suitable for masking Alu repeats from query sequences. STS - Database of GenBank, EMBL and DDBJ sequences from STS Division. Chromosomic Sequences - Complete genomes, complete chromosomes, or concatenated genomic contigs from NCBI Reference Sequence Project. Vector fragments (UniVec) - The UniVec non-redundant vector fragment sequences. Whole Genome Shotguns (WGS) - Whole Genome Shotgun sequence assembly. Custom - Specify the database of your interest.
Query sequence(s)	Place your query file with nucleotide sequences in FASTA format.
Location on query sequence	Location on the query sequence in 1-based offsets (Format: start-stop).
Query strand(s)	Query strand(s) to search against database: Both strands Plus strand Minus strand
Output
Result	Designates an output file for the search results: Pairwise aligning Query-anchored, showing identities Query-anchored, no identities Flat query-anchored, showing identities Flat query-anchored, no identities XML Blast output Tabular Tabular with comment lines ASN, text ASN, binary Comma-separated values BLAST archive format (ASN.1)
Options
Expectation value	Sets the threshold expectation value for keeping alignments.This is the E from the Karlin-Altschul equation that describes how often an alignment with a given score is expected to occur at random. min=0, max=1000
Perform gapped alignment	Performs gapped alignment. Setting this to OFF invokes the older, ungapped style of alignment. A gap cost includes a value to open the gap and a value to extend the gap by a base. Following the convention of the command-line applications, these costs are listed as positive numbers here. MegaBLAST uses a specialized algorithm to calculate the default gap costs for a reward/penalty pair that is described in PMID:10890397. Briefly, the default megaBLAST cost to open a gap is zero and the cost to extend a gap two letters is given by the absolute value of two mismatches minus one match. For example, given a reward of 1 and penalty of -5, the cost to extend a gap by one letter is 5.5. The default gap costs for other tasks supported by the blastn application is 5 to open a gap and 2 to extend one base.
Cost to open a gap	Initial penalty for opening a gap of length 0. The default gap costs for programs other than blastn depend on the scoring matrix.
Cost to extend a gap	The penalty for each gap character.