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Load a plasmid
Click here or drag and drop a DNA file (.gb / .gbk / .ape / .dna / .fasta / .fastq) anywhere on this page.
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Plasmid
Feature Types
mismatches
0
1×
(overrides per-feature custom colors while checked)
| Type | Label | Location | Strand | Size |
|---|
No enzymes enabled
Matches
| Enzyme | Site | Temp | Strand | Site location | Top-strand cut | Bottom-strand cut |
|---|
Predicted gel
Enable one or more enzymes above to see predicted fragments and a virtual gel. Ladder: NEB 1 kb Plus DNA Ladder.
Alignment viewer
Drop
.gb / .gbk / .dna / .fasta / .ab1 files here to align against the current reference — sequencing reads or another plasmid for side-by-side comparison.
Pre-computed consensus assemblies (Plasmidsaurus, pLannotate, etc.) work best; Sanger .ab1 reads are treated as partial reads.
Drop reads or a reference plasmid here
No reads loaded. Click ＋ Add file, ＋ From vault, or drop files above.
Primer annealing
Primers collected from every plasmid in your vault, matched against this plasmid's sequence (both strands, wraps at origin if circular).
Exact full-length binding only.
CRISPR PAM scanner
Finds protospacers for SpCas9 (NGG, 20 nt 5' of PAM), SaCas9 (NNGRRT, 21 nt 5' of PAM),
and Cas12a (TTTV, 23 nt 3' of PAM). Both strands; circular plasmids wrap at the origin.
No off-target / efficiency scoring — basic site detection only.
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