---
title: "Find unwanted regulatory elements in a construct"
method: POST
path: "/operon_scan"
tags: ["Enzymes & cloning"]
---

# Find unwanted regulatory elements in a construct

`POST /operon_scan`

## Request

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

Scan a multi-gene construct, on both strands, for the sequence that quietly breaks operons: promoter-like -35/-10 pairs (including ones pointing backwards, which make antisense RNA), Shine-Dalgarno sequences positioned in front of an internal start codon, terminator-shaped hairpins with a U-tract, out-of-frame start codons inside a declared CDS, and exact direct repeats. Reports what MATCHED and how far it sits from consensus — it does not score a match or claim it transcribes. For an estimated promoter strength use promoter_predict; for a translation rate use rbs_predict.

## Request body

- object
  - `sequence` string, required: The construct, raw, FASTA or GenBank. Max 100,000 bp.
  - `maxPromoterMismatches` integer: Total mismatches allowed across both consensus boxes (default 1). 0 finds only perfect consensus, which real promoters rarely are; above 2 the hit rate on random DNA climbs fast.
  - `cdsStart` integer: 1-based start of a coding sequence. Given with cdsEnd, out-of-frame start codons inside it are reported — without them that check is skipped, because 'out of frame' has no meaning until a frame is declared.
  - `cdsEnd` integer: 1-based end of that coding sequence.

## 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)