Whole-Plasmid Sequencing Check — Consensus vs Your Design
Paste the consensus your sequencing service returned and the map it should be.
🔒 Nothing you paste is logged or stored on our servers
Whole-plasmid nanopore sequencing returns one assembled circular consensus, and then the work starts: the assembler began the circle wherever it landed, half the time it hands back the reverse complement, and a 1 bp indel inside a run of six A's is both the commonest basecalling artefact and exactly what a real frameshift looks like. This tool does those three. Paste your design and the consensus; it works out the rotation and the strand, reports each difference at its position in YOUR numbering, and says which identical-base run each indel sits in. Paste the design as an annotated GenBank record and every difference is also read against its features — silent, missense with the codon number, or a premature stop.
0 bp. An annotated record is what turns a position into “silent in AmpR” or “a stop at codon 41”.
0 bp
How to use the Whole-Plasmid Sequencing Check tool
- 1Paste your design — ideally the annotated GenBank record, which is what turns a position into a consequence.
- 2Paste the consensus FASTA your sequencing service sent back.
- 3Read the verdict, then the difference table: each row carries the change, the feature it lands in, and the homopolymer run if it is in one.
Frequently asked questions
My consensus and my map do not start at the same base. Does that matter?
No. An assembler starts the circle wherever its algorithm landed, so the two almost never line up as written — end to end as linear strings they look about 0% identical. The rotation is found for you, and the result says how far it was and whether the consensus also had to be reverse-complemented.
Is a 1 bp indel a real mutation or a sequencing error?
Nothing in a sequence decides that, so this does not claim to. What it does is tell you when the indel sits inside a run of identical bases, because that is where long-read basecallers miscount and also where real slippage happens. It is the signal to go back to the reads, not a verdict either way.
What does this NOT check?
How much of the plasmid the sequencing actually covered, and whether the prep was homogeneous. A consensus is reported at full length whatever the coverage behind it was, and a mixed population collapses to one sequence before this tool sees it. If you have the reads, sequencing_readback_verify answers both.
More
Related tools
Inspect chromatograms, compare a read with its reference, or screen a whole plate of clones.
Align your reads to your own annotated reference and get what each difference DOES — silent, missense at a named codon, or a premature STOP that ends the protein — not just where it sits.
Paste what you got back and the PCR you say made the insert. It re-derives the insert, finds it in either orientation, and gives you the exact mismatch positions.