user-defined upper limit for the number of target sequences returned
Alignment
region of similarity between target and query sequences
E-value
a BLAST statistic representing the significance of an alignment, values close to zero
indicate high sequence similarity with low probability of the similarity occurring by chance
Identities
the number of exact nucleotide matches over the alignment, expressed as a fraction
and a percentage
Query Coverage
the length of the query sequence that matches the target sequence in the
alignment
Bit Score
a BLAST statistic measuring the quality of an alignment, higher values indicate a
more significant match
Span
the length of the alignment, including gaps
About Search by Sequence
Search by Sequence performs a nucleotide-nucleotide BLAST search against Addgene’s plasmid sequence database.
BLAST returns plasmids with similarity to the query sequence.
Results are sorted by E-value, a statistic from BLAST that describes the significance of a match.
Lower values are considered better matches.
FASTA headers and numbers at the beginning of each line will be removed.
The query should only contain DNA characters.
Tips for Success
Enter a distinct sequence that is an important, differentiating feature. For example, the coding region of
a gene, instead of the plasmid origin of replication.
Inspect the percent identity, query coverage, and alignment details to determine if a result match is satisfactory.
Visit the corresponding plasmid webpage to view additional details about a matching plasmid.
If no results are returned:
Try a different isoform or region of the desired sequence.
Choose a different BLAST database. Try the general “All Addgene Plasmids” (default selection),
instead of a specific database, such as “Plant Expression Plasmids”
Try selecting a different BLAST algorithm:
megablast: Designed for comparing sequences within the same, or closely related, species.
Default selection.
blastn: Designed for comparing sequences from different species. May return additional results,
if exact species match is not required.
blastn-short: Optimized for searching with shorter sequences (<= 30 nucleotides)
but can still be effective with slightly larger sequences.
There may not be a match in our database.
You can adjust the Max Results setting on the results page from 25 to 500. If many sequences share the same top E-value,
only a truncated set of equally high-scoring matches will be shown. Set the Max Results to 500 to see more matches.
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synthetic autoregulatory gene circuit made by inserting an intron containing the mouse mir-124–3 gene into mCherry. Contains the miR-124-regulated 3′UTR of the Vamp3 gene with three siRNA-like sites
For expression of mouse talin-1 (residues 1-2299) with C-terminal deletion of dimerization domain and R13 (∆R13-DD) in mammalian cells. Contains C-terminal EGFP tag.
Retroviral vector with CMV promoter driving mutant form of acetyltransferase and CH3 domains fragment of human p300 (EP300) (WY1466-1467AS in AT domain).
synthetic autoregulatory gene circuit made by inserting an intron containing the mouse mir-124–3 gene into mCherry. Contains the miR-124-regulated 3′UTR of the Vamp3 gene with seven bulge target sites
PiggyBac-based transposon vector plasmid which encodes the expression units of liver-enriched transcription factor genes (hHNF1α-hHNF3β-hCEBPα-hCEBPβ-hCEBP-γ) under control of the TRE/PCMVmin promoter
Plasmid for easy cloning of a sgRNA sequence. The Plasmid contain a tRNA promoter to facilitate the expression of any sgRNA sequence and also expresses eSpCas9(1.1)
3rd generation lentiviral vector that expresses shRNA under the mouse U6 promoter. A CMV-EGFP reporter cassette is included in the vector to monitor expression.