Choose a target database
HanPSC8r1.0-20181105 r1.0 cds sequences - Nucleotide,68610 0 sequences
HanPSC8r1.0-20181105 r1.0 five_prime_utr sequences - Nucleotide,40383 0 sequences
HanPSC8r1.0-20181105 r1.0 gene sequences - Nucleotide,80979 0 sequences
HanPSC8r1.0-20181105 r1.0 mrna sequences - Nucleotide,68610 0 sequences
HanPSC8r1.0-20181105 r1.0 ncrna sequences - Nucleotide,10583 0 sequences
HanPSC8r1.0-20181105 r1.0 prot sequences - Protein,68610 0 sequences
HanPSC8r1.0-20181105 r1.0 rrna sequences - Nucleotide,322 0 sequences
HanPSC8r1.0-20181105 r1.0 three_prime_utr sequences - Nucleotide,42675 0 sequences
HanPSC8r1.0-20181105 r1.0 trna sequences - Nucleotide,1464 0 sequences
HanPSC8r1.0-20181105 reference sequence - Nucleotide,929 0 sequences
choose a program
blastn: Nucleotide-Nucleotide BLAST
blastp: Protein-Protein BLAST
blastx: Translated Query-Protein Subject BLAST
short: Short Nucleotide sequence (primer)-Nucleotide BLAST
tblastn: Protein Query-Translated Subject BLAST
tblastx: Translated Query-Translated Subject BLAST
blastp options
Input query options
Location on the query sequence in 1-based offsets (Format: start-stop)
General search options
Expectation value (E) threshold for saving hits
Cost to open a gap
Cost to extend a gap
Task to execute
blastp
blastp-short
deltablast
Word size for wordfinder algorithm (length of best perfect match)
Scoring matrix name (normally BLOSUM62)
BLOSUM62
BLOSUM80
PAM30
PAM70
BLOSUM45
Minimum word score such that the word is added to the BLAST lookup table
Use composition-based statistics
Composition-based statistics as in NAR 29:2994-3005, 2001
Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally
Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties
no composition-based statistics
Formatting options
Show NCBI GIs in deflines
Number of database sequences to show alignments for
Query filtering options
Apply filtering locations as soft masks
Use lower case filtering in query and subject sequence(s)
Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable)
Restrict search or results
Filtering algorithm ID to apply to the BLAST database as soft masking
Filtering algorithm ID to apply to the BLAST database as hard masking
Percent identity
If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit
Best Hit algorithm overhang value(recommended value : 0.1)
Best Hit algorithm score edge value(recommended value : 0.1)
Maximum number of aligned sequences to keep
Set maximum number of HSPs per subject sequence to save for each query
Statistical options
Effective length of the database
Effective length of the search space
Extension options
X-dropoff value (in bits) for ungapped extensions
Multiple hits window size, use 0 to specify 1-hit algorithm
X-dropoff value (in bits) for preliminary gapped extensions
X-dropoff value (in bits) for final gapped alignment
Perform ungapped alignment only?
Miscellaneous options
Compute locally optimal Smith-Waterman alignments?
blastn options
Input query options
Location on the query sequence in 1-based offsets (Format: start-stop)
Query strand(s) to search against database/subject
both
minus
plus
General search options
Expectation value (E) threshold for saving hits
Cost to open a gap
Cost to extend a gap
Task to execute
blastn
dc-megablast
blastn-short
rmblastn
megablast
Word size for wordfinder algorithm (length of best perfect match)
Penalty for a nucleotide mismatch
Reward for a nucleotide match
Formatting options
Show NCBI GIs in deflines
Number of database sequences to show alignments for
Query filtering options
Apply filtering locations as soft masks
Use lower case filtering in query and subject sequence(s)
Filter query sequence with DUST(Format :'yes','level window linker', or 'no' to disable)
BLAST database containing filtering elements(i . e . : repeats)
Enable WindowMasker filtering using a Taxonomic ID
Enable WindowMasker filtering using this repeats database .
Restrict search or results
Filtering algorithm ID to apply to the BLAST database as soft masking
Filtering algorithm ID to apply to the BLAST database as hard masking
Percent identity
If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit
Best Hit algorithm overhang value(recommended value : 0.1)
Best Hit algorithm score edge value(recommended value : 0.1)
Maximum number of aligned sequences to keep
Set maximum number of HSPs per subject sequence to save for each query
Statistical options
Effective length of the database
Effective length of the search space
Extension options
X-dropoff value (in bits) for ungapped extensions
Multiple hits window size, use 0 to specify 1-hit algorithm
X-dropoff value (in bits) for preliminary gapped extensions
X-dropoff value (in bits) for final gapped alignment
Use non-greedy dynamic programming extension
Minimum raw gapped score to keep an alignment in the preliminary gapped and traceback stages
Perform ungapped alignment only?
Number of off-diagonals to search for the 2nd hit, use 0 to turn off
Discontiguous MegaBLAST options
Discontiguous MegaBLAST template type
coding_and_optimal
coding
optimal
Discontiguous MegaBLAST template length
16
21
18
blastx options
Input query options
Location on the query sequence in 1-based offsets (Format: start-stop)
Query strand(s) to search against database/subject
both
minus
plus
Genetic code to use to translate query
Blepharisma Macronuclear (15)
Yeast Mitochondrial (3)
Vertebrate Mitochondrial (2)
Echinoderm Mitochondrial (9)
Euplotid Nuclear (10)
Standard (1)
Mold Mitochondrial; ... (4)
Alternative Yeast Nuclear (12)
Ciliate Nuclear; ... (6)
Ascidian Mitochondrial (13)
Bacteria and Archaea (11)
Flatworm Mitochondrial (14)
Invertebrate Mitochondrial (5)
General search options
Expectation value (E) threshold for saving hits
Cost to open a gap
Cost to extend a gap
Word size for wordfinder algorithm (length of best perfect match)
Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments (a negative value disables linking)
Scoring matrix name (normally BLOSUM62)
BLOSUM45
PAM70
BLOSUM80
BLOSUM62
PAM30
Minimum word score such that the word is added to the BLAST lookup table
Use composition-based statistics
no composition-based statistics
Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally
Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties
Composition-based statistics as in NAR 29:2994-3005, 2001
Formatting options
Show NCBI GIs in deflines
Number of database sequences to show alignments for
Query filtering options
Apply filtering locations as soft masks
Use lower case filtering in query and subject sequence(s)
Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable)
Restrict search or results
Filtering algorithm ID to apply to the BLAST database as soft masking
Filtering algorithm ID to apply to the BLAST database as hard masking
Percent identity
If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit
Best Hit algorithm overhang value(recommended value : 0.1)
Best Hit algorithm score edge value(recommended value : 0.1)
Maximum number of aligned sequences to keep
Set maximum number of HSPs per subject sequence to save for each query
Statistical options
Effective length of the database
Effective length of the search space
Extension options
X-dropoff value (in bits) for ungapped extensions
Multiple hits window size, use 0 to specify 1-hit algorithm
X-dropoff value (in bits) for preliminary gapped extensions
X-dropoff value (in bits) for final gapped alignment
Perform ungapped alignment only?
Miscellaneous options
Compute locally optimal Smith-Waterman alignments?
tblastn options
Input query options
Location on the query sequence in 1-based offsets (Format: start-stop)
General search options
Expectation value (E) threshold for saving hits
Cost to open a gap
Cost to extend a gap
Word size for wordfinder algorithm (length of best perfect match)
Genetic code to use to translate database/subjects
Blepharisma Macronuclear (15)
Yeast Mitochondrial (3)
Vertebrate Mitochondrial (2)
Standard (1)
Mold Mitochondrial; ... (4)
Echinoderm Mitochondrial (9)
Euplotid Nuclear (10)
Ascidian Mitochondrial (13)
Bacteria and Archaea (11)
Ciliate Nuclear; ... (6)
Alternative Yeast Nuclear (12)
Invertebrate Mitochondrial (5)
Flatworm Mitochondrial (14)
Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments (a negative value disables linking)
Scoring matrix name (normally BLOSUM62)
BLOSUM45
PAM70
PAM30
BLOSUM80
BLOSUM62
Minimum word score such that the word is added to the BLAST lookup table
Formatting options
Show NCBI GIs in deflines
Number of database sequences to show alignments for
Query filtering options
Apply filtering locations as soft masks
Use lower case filtering in query and subject sequence(s)
Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable)
Restrict search or results
Filtering algorithm ID to apply to the BLAST database as soft masking
Filtering algorithm ID to apply to the BLAST database as hard masking
Percent identity
If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit
Best Hit algorithm overhang value(recommended value : 0.1)
Best Hit algorithm score edge value(recommended value : 0.1)
Maximum number of aligned sequences to keep
Set maximum number of HSPs per subject sequence to save for each query
Statistical options
Effective length of the database
Effective length of the search space
Extension options
X-dropoff value (in bits) for ungapped extensions
Multiple hits window size, use 0 to specify 1-hit algorithm
tblastx options
Input query options
Location on the query sequence in 1-based offsets (Format: start-stop)
Query strand(s) to search against database/subject
both
plus
minus
Genetic code to use to translate query
Flatworm Mitochondrial (14)
Invertebrate Mitochondrial (5)
Ciliate Nuclear; ... (6)
Bacteria and Archaea (11)
Ascidian Mitochondrial (13)
Alternative Yeast Nuclear (12)
Mold Mitochondrial; ... (4)
Standard (1)
Euplotid Nuclear (10)
Echinoderm Mitochondrial (9)
Vertebrate Mitochondrial (2)
Yeast Mitochondrial (3)
Blepharisma Macronuclear (15)
General search options
Expectation value (E) threshold for saving hits
Cost to open a gap
Cost to extend a gap
Word size for wordfinder algorithm (length of best perfect match)
Scoring matrix name (normally BLOSUM62)
BLOSUM45
PAM70
BLOSUM80
BLOSUM62
PAM30
Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments (a negative value disables linking)
Minimum word score such that the word is added to the BLAST lookup table
Genetic code to use to translate database/subjects
Vertebrate Mitochondrial (2)
Yeast Mitochondrial (3)
Blepharisma Macronuclear (15)
Euplotid Nuclear (10)
Echinoderm Mitochondrial (9)
Mold Mitochondrial; ... (4)
Standard (1)
Alternative Yeast Nuclear (12)
Bacteria and Archaea (11)
Ascidian Mitochondrial (13)
Ciliate Nuclear; ... (6)
Invertebrate Mitochondrial (5)
Flatworm Mitochondrial (14)
Formatting options
Show NCBI GIs in deflines
Number of database sequences to show alignments for
Query filtering options
Apply filtering locations as soft masks
Use lower case filtering in query and subject sequence(s)
Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable)
Restrict search or results
Filtering algorithm ID to apply to the BLAST database as soft masking
Filtering algorithm ID to apply to the BLAST database as hard masking
Percent identity
If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit
Best Hit algorithm overhang value(recommended value : 0.1)
Best Hit algorithm score edge value(recommended value : 0.1)
Maximum number of aligned sequences to keep
Set maximum number of HSPs per subject sequence to save for each query
Statistical options
Effective length of the database
Effective length of the search space
Extension options
X-dropoff value (in bits) for ungapped extensions
Multiple hits window size, use 0 to specify 1-hit algorithm
short options
General search options
Percent identity
Expectation value (E) threshold for saving hits
Cost to open a gap
Cost to extend a gap