---
title: "Is the template folded over my primer site?"
method: POST
path: "/primer_site_accessibility"
tags: ["Primers & oligos"]
---

# Is the template folded over my primer site?

`POST /primer_site_accessibility`

## Request

- Base URL: `https://seqbench.com/api/v1`
- URL: `https://seqbench.com/api/v1/primer_site_accessibility`
- Auth: none required

Fold the template around each place a primer binds, at the annealing temperature and under DNA parameters, and report how much of the primer's own footprint sits inside a helix. Primer design tools score the oligo — its Tm, its hairpin, its dimers — and leave the template unexamined, while a binding site buried in a stable stem is an ordinary reason a well-designed primer does not amplify. Returns the folded window, its free energy, the paired fraction of the footprint, and how many of the 3'-terminal five bases are paired.

## Request body

- object
  - `template` string, required: The template the primer has to bind — the region of interest, a plasmid, or an amplicon.
  - `primer` string, required: The primer, 5'->3'.
  - `annealingTemp` number: The annealing temperature in Celsius. This is the whole reason the tool exists — structure at 37 C is not structure at 60 C, and the number changes the answer.
  - `windowNt` number: Template to fold around each site, centred on the footprint. 40-200 nt.
  - `circular` boolean: Wrap the window across the origin instead of clipping it.
  - `maxMismatches` number: Mismatches allowed when locating the primer. Defaults to the binding scanner's own rate.

## Response `200`

Tool ran successfully.

- SuccessResponse: Standard success envelope returned by every single-tool call.
  - `ok` unknown, required
  - `tool` string, required: The tool slug that ran.
  - `result` object, required: Tool-specific output object. Its shape depends on the tool — call `GET /{tool}` or see the docs for each tool's fields.
  - `gate` GateResult
    - `pass` boolean, required: True if and only if every hard check passed.
    - `checks` GateCheck[], required
      - `id` string, required
      - `label` string, required
      - `severity` 'hard' | 'soft', required
      - `pass` boolean, required
      - `message` string, required
      - `value` number
      - `threshold` string
    - `notChecked` string[], required: Honest list of what this gate does NOT verify.
  - `provenance` Provenance, required
    - `apiVersion` string, required
    - `tool` union, required: Tool slug, or an array of slugs (one per step) for a workflow.
      - string
      - string[]
    - `generatedAt` string, date-time, required: ISO 8601 timestamp of when the result was generated.

## Other responses

- `400`: Invalid argument or the tool could not run.
- `404`: Unknown tool.
- `429`: Rate limited (metered tools only). Body carries code `rate_limited` and retryable `true`; honor the Retry-After header.
- `503`: A metered tool is momentarily at capacity. The identical request should succeed after Retry-After; body carries code `upstream_unavailable`.

---

[API](https://skmtc.dev/seqbench/apis/seqbench-api.md) · [All operations](https://skmtc.dev/seqbench/apis/seqbench-api/llms.txt) · [OpenAPI document](https://skmtc.dev/seqbench/apis/seqbench-api/revisions/132575216865?raw)