In-silico PCR
in_silico_pcrPredict PCR products for a template and a pair of primers (IUPAC-aware, allows mismatches, handles circular templates). Primers may carry a non-templated 5' tail — a restriction site, a Gibson arm, a Kozak, a tag: a primer primes on its 3' end, and the tail is carried into the product rather than required to match. start/end are the TEMPLATE-derived span, length is the whole product including tails, and features marks which product bases came from the oligos (present only when there is a tail). Each end reports annealedLength and tailLength.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| circular | No | Treat the template as circular (plasmid). | |
| template | Yes | Nucleotide sequence (raw or FASTA; IUPAC accepted). | |
| forwardPrimer | No | Primer 1, 5'→3'. | |
| maxMismatches | No | Mismatches tolerated per primer (0–10). | |
| reversePrimer | No | Primer 2, 5'→3' (order does not matter). Optional: one primer alone is accepted and reports the products it makes on its own — none, unless the template carries inverted sites it can prime from both ends. | |
| maxProductLength | No | Ignore predicted products longer than this (bp). A SEARCH WINDOW, not a claim about what amplifies: whole-plasmid inverse PCR — the reaction a q5-style site_directed_mutagenesis design is run as — makes one product the size of the plasmid, so raise this for a construct over 50 kb. `suppressedByLength` in the response counts what the window discarded. |