BlastN

Input
Blast DB   Identifies the database to search.
Database must already be formatted by formatdb.
Nucleotide Query sequence(s)   If the input file contains multiple sequences, BLAST will be run on each sequence in order, and the resulting output will contain concatenated BLAST reports.
Believe the query defline.   Believe the query definition line.
Output
Result   Designates an output file for the search results.
Format   Pairwise (Default)
Query-anchored, showing identities
Query-anchored, no identities
Flat query-anchored, showing identities
Flat query-anchored, no identities
Query-anchored, no identities and blunt ends
Flat query-anchored, no identities and blunt ends
XML Blast output
Tabular
Tabular with comment lines
ASN, text
ASN, binary
Show GI's in deflines  Shows GenInfo Identifier (GI) numbers in definition lines.
A GI is a unique numeric identifier assigned for a sequence in GenBank.
A GI corresponds to an accession version pair.
Produce HTML output   Produces HTML output with [anchor] links from the summary at the top of the report to the alignments farther below.
This option should be used only with the standard report format ("Pairwise (Default)").
Number of Alignments to output  Truncates the report to set number of alignments.
There is no warning when you exceed this limit, so it's generally a good idea to set this value very high unless you're interested only in the top hits.
SeqAlign file (Optional)   SeqAlign output file
Options
MegaBlast search Sets the blastn program to the megablast mode, which is optimized to find near identities very quickly.
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.
Filter query sequence   Filters the query sequence for low-complexity subsequences.
The default setting is ON.
Complexity filtering is generally a good idea, but it may break long HSPs into several smaller HSPs due to low-complexity segments.
This can cause some alignments to fall below the significance threshold and be lost. To prevent this, either turn off filtering (not recommended) or use soft masking, in which the filter is used only in the word seeding phase, but not the extension phase.
DUST with blastn, SEG with others.
Perform gapped alignment Performs gapped alignment.
Setting this to OFF invokes the older, ungapped style of alignment.
You can't perform gapped alignments with tblastx, regardless of this setting.
Open Gap Cost   Initial penalty for opening a gap of length 0. -1 invokes the default behavior, and setting the parameter to zero is impossible, unless the "Perform gapped alignment" option is set to NO, which turns gapping off. The default gap costs for programs other than blastn depend on the scoring matrix.
Extend Gap Cost  The penalty for each gap character. Note that value -1 is synonymous with the default behavior for the "Open Gap Cost" parameter and, it's impossible to set value to zero unless the "Perform gapped alignment" option is set to NO, which turns gapping off. The default gap cost, for programs other than blastn, depends on the scoring matrix.
Gapped Alignment X dropoff value X dropoff value for gapped alignment (in bits);
Zero invokes default behavior; blastn 30, megablast 20, tblastx 0, all others 15.
Nucleotide Mismatch Penalty   Sets the penalty for a nucleotide mismatch. Also see "Nucleotide Match Reward". The choice of [integer] for "Nucleotide Mismatch Penalty" and "Nucleotide Match Reward" are very important because they determine your target frequencies. The default values 1 for "Nucleotide Match Reward" and -3 for "Nucleotide Mismatch Penalty" are most effective for aligning sequences that are 99 percent identical.
Nucleotide Match Reward   Sets the score of a nucleotide match. See also the "Nucleotide Mismatch Penalty" parameter.
Number of DB Seqs to show descriptions   Sets the number of database sequences for which to show the one-line summary descriptions at the top of a BLAST report. You won't be warned if you exceed a value. Also see the "Number of Alignments to output" parameter.
Extending Hits Threshold Neighborhood word threshold score.
Only those words scoring equal to or greater than [value] will seed alignments.
Zero is default; blastp 11, blastn 0, blastx 12, tblastn 13, tblastx 13, megablast 0.
Word size Sets the word size for the initial word search.
The minimum word size for blastn is 7.
DataBase Effective Length   Effective length of the database. Use zero for the real size (Default).
Best Hits Number   The number of best hits from a region to keep.
This option is useful when you want to limit the number of alignments that might pile up in one section of the query. This is most useful if the settings of "Number of Alignments to output" or "Number of DB Seqs to show descriptions" are low, and the abundant alignments push lower scoring alignments off the end of the report.
Off by default, if used a value of 100 is recommended.
Two-hit or Single-hit Algorithm   Specifies the two-hit or single-hit algorithm.
The two-hit option requires two word hits on the same diagonal to extend from either one.
When set to two-hit mode, the "Multiple Hits Window Size" parameter specifies how close the two hits have to be to trigger extension.
Query strands   Chooses which strand of DNA-based queries is searched.
Top Strand
Bottom Strand
Both Strands
Location on query sequence   The location on query sequence.
This lets you limit the search to a subsequence of the query sequence.
For example, to search just the letters from 21 to 50, set the parameter to following:
"21,50"
The alignments won't extend outside the specified region.
In older versions of BLAST, this parameter set the size of the region under control of the "Best Hits Number" parameter.
Search Space Effective Length   Effective length of the search space. Use zero for the real size (Default).
Lower Case Filtering   Use lower case filtering of FASTA sequence.
Ungapped Extension X dropoff value   X dropoff value for ungapped extensions in bits;
Zero invokes default behavior; blastn 20, megablast 10, all others 7.
Final Gapped Alignment X dropoff value   X dropoff value for final gapped alignment in bits;
Sets the X3 dropoff value (in bits) for extensions but is bounded by the value for X2.
Zero invokes default behavior; blastn/megablast 50, tblastx 0, all others 25.
Multiple Hits Window Size   Sets the multiple-hit window size [integer].
When BLAST is set to two-hit mode, this option requires two word hits on the same diagonal to be within [value] letters of each other in order to extend from either one.
The larger the [value], the more sensitive BLAST will be.
Setting [value] to 0 sets the default behavior of 40, except for blastn, whose default is single word hit. To specify one-hit behavior, set 1. Blastn/megablast 0 (Default), all others 40.
Concatenated Queries Number   Sets the number of queries to concatenate in a single search [integer]. Concatenating queries accelerates the search because the database is scanned just one time.
The specified value must be the number of sequences in the query file. if it's less, only the first set of [value] sequences is used.
Also, the output is very different than you would expect. All the query names are listed, and then all the one-line summaries are given, followed by the alignments, and finally, one footer is produced for the whole report. Given this format, it's very difficult to discern which alignments belong to which query.
This option should not be used in its current implementation.
Number of processors   Sets the number of processors to use.
If you have multiple queries, you will get better throughput by executing multiple BLAST searches.
For insensitive searches such as default BLASTN, setting -a to a higher value may not appreciably improve speed if disk I/O is the bottleneck.
Old Engine Use   Force use of old engine.