{
  "title": "Sequence motif finder",
  "human_url": "https://happytails.ai/en/developer-tools/sequence-motif-finder/",
  "agent_url": "https://happytails.ai/agents/en/developer-tools/sequence-motif-finder/",
  "language": "en",
  "markdown_url": "https://happytails.ai/en/developer-tools/sequence-motif-finder.md",
  "content": "Sequence motif finder\nLocate overlapping literal or ambiguity-coded motifs in DNA or RNA FASTA, with explicit strand and matching rules.\nHow can we improve this tool?\nReport a problem or share an idea.\nPlease leave out private information. Your message and the tool name go to our team via PostHog.\nHow to use Sequence motif finder\nPaste gap-free DNA or RNA FASTA and enter an IUPAC motif.\nChoose literal, possible or certain matching and one or both strands.\nReview inclusive forward-source coordinates and download every match.\nUseful next steps\nFASTA validator\nFASTA sequence extractor\nSequence reverse complement\nDefine ambiguity matching\nLiteral mode compares symbols. Possible mode accepts intersecting base sets. Certain mode requires every possible sequence base to be included in the motif.\nInterpret strand rows explicitly\nBoth-strand mode searches the motif and its reverse complement. Overlapping matches are retained; palindromic motifs can produce two rows at one position. Matches do not establish biological significance.",
  "content_format": "text/plain",
  "visibility": "public",
  "links": [
    {
      "name": "FASTA validator",
      "url": "https://happytails.ai/en/developer-tools/fasta-validator/"
    },
    {
      "name": "FASTA sequence extractor",
      "url": "https://happytails.ai/en/developer-tools/fasta-sequence-extractor/"
    },
    {
      "name": "Sequence reverse complement",
      "url": "https://happytails.ai/en/developer-tools/sequence-reverse-complement/"
    }
  ],
  "tool": {
    "id": "sequence-motif-finder",
    "category": "developer-tools",
    "built": true,
    "requirements": "Searches every FASTA record case-insensitively and includes overlapping matches. Literal mode compares symbols exactly. Possible mode requires intersecting IUPAC base sets at every position. Certain mode requires every possible sequence base to be allowed by the motif. Both-strand mode also searches the reverse complement of the motif and reports coordinates on the original forward sequence. Palindromic motifs can produce two strand-specific rows at one position. Coordinates are one-based and inclusive. Only linear, gap-free DNA or RNA is supported; this is not alignment, homology, variant or biological significance analysis. Runs locally without uploads or database lookup. Limit: 500000 combined input characters, 2000 records, 2000 validation issues, a 1000-symbol motif, 20000 matches and 10000000 symbol comparisons. Exceeding a limit rejects the complete report. Each export is limited to 3000000 characters; typed CSV allows 200000 values. Preview shows 200 rows. Processing stops after 10 seconds.",
    "implementation": {
      "fields": [
        {
          "key": "alphabet",
          "label": "Sequence alphabet",
          "value": "dna",
          "type": "select",
          "values": [
            "dna",
            "rna"
          ]
        },
        {
          "key": "allowGaps",
          "label": "Allow alignment gaps (-)",
          "value": "false",
          "type": "select",
          "values": [
            "false"
          ]
        },
        {
          "key": "motif",
          "label": "Motif",
          "value": "ACG",
          "type": "text",
          "maxLength": 1000,
          "help": "Use 1 to 1000 IUPAC symbols from the chosen DNA or RNA alphabet. No regular expressions, gaps or wildcards other than IUPAC symbols."
        },
        {
          "key": "mode",
          "label": "Ambiguity matching",
          "value": "possible",
          "type": "select",
          "values": [
            "literal",
            "possible",
            "certain"
          ]
        },
        {
          "key": "strands",
          "label": "Search strands",
          "value": "both",
          "type": "select",
          "values": [
            "forward",
            "both"
          ]
        }
      ],
      "registrationFamily": "sequence-tools",
      "presentation": "metrics",
      "note": "Searches every FASTA record case-insensitively and includes overlapping matches. Literal mode compares symbols exactly. Possible mode requires intersecting IUPAC base sets at every position. Certain mode requires every possible sequence base to be allowed by the motif. Both-strand mode also searches the reverse complement of the motif and reports coordinates on the original forward sequence. Palindromic motifs can produce two strand-specific rows at one position. Coordinates are one-based and inclusive. Only linear, gap-free DNA or RNA is supported; this is not alignment, homology, variant or biological significance analysis. Runs locally without uploads or database lookup. Limit: 500000 combined input characters, 2000 records, 2000 validation issues, a 1000-symbol motif, 20000 matches and 10000000 symbol comparisons. Exceeding a limit rejects the complete report. Each export is limited to 3000000 characters; typed CSV allows 200000 values. Preview shows 200 rows. Processing stops after 10 seconds.",
      "inputMaxLength": 500000,
      "inputErrorCode": "SEQUENCE_INPUT",
      "example": {
        "input": ">sample unchanged description\nACGTrynACGT\n",
        "options": {
          "alphabet": "dna",
          "allowGaps": "false",
          "motif": "ACG",
          "mode": "possible",
          "strands": "both"
        }
      },
      "experience": {
        "automatic": false,
        "single": false,
        "inputMaxLength": 500000,
        "inputMode": "text",
        "label": "Your text",
        "placeholder": "Type or paste your input…",
        "help": "Up to 500,000 characters. Review the settings before running.",
        "action": null
      },
      "mode": "explicit",
      "interactive": false
    },
    "execution": "Browser interface",
    "api": null,
    "browser_agent": {
      "supported": true,
      "name": "run_current_tool",
      "discovery": "WebMCP on the human page in a supporting browser",
      "verification": "See audit/API-AUDIT.md; availability is not verification"
    }
  },
  "markdown": "# Sequence motif finder\n\n- Human page: https://happytails.ai/en/developer-tools/sequence-motif-finder/\n- Markdown: https://happytails.ai/en/developer-tools/sequence-motif-finder.md\n- Structured JSON: https://happytails.ai/agents/en/developer-tools/sequence-motif-finder/index.json\n- Visibility: public\n\n## Tool capabilities\n\n| Property | Value |\n| --- | --- |\n| Tool ID | `sequence-motif-finder` |\n| Category | developer-tools |\n| Implementation | Registered implementation. Registration alone is not a production-quality guarantee. |\n| Browser execution | Use the visible action or interactive controls. |\n| Browser processing | Browser; see tool notes for network behavior. |\n| HTTP API | Not callable through HTTP. |\n| Browser-agent interface | run_current_tool |\n\n### Implementation notes\n\nSearches every FASTA record case-insensitively and includes overlapping matches. Literal mode compares symbols exactly. Possible mode requires intersecting IUPAC base sets at every position. Certain mode requires every possible sequence base to be allowed by the motif. Both-strand mode also searches the reverse complement of the motif and reports coordinates on the original forward sequence. Palindromic motifs can produce two strand-specific rows at one position. Coordinates are one-based and inclusive. Only linear, gap-free DNA or RNA is supported; this is not alignment, homology, variant or biological significance analysis. Runs locally without uploads or database lookup. Limit: 500000 combined input characters, 2000 records, 2000 validation issues, a 1000-symbol motif, 20000 matches and 10000000 symbol comparisons. Exceeding a limit rejects the complete report. Each export is limited to 3000000 characters; typed CSV allows 200000 values. Preview shows 200 rows. Processing stops after 10 seconds.\n\n### Inputs and settings\n\nText input: Your text.\n\nExample or placeholder shown in the interface (not a validated fixture):\n\n```text\nType or paste your input…\n```\n\nUp to 500,000 characters. Review the settings before running.\n\n| Setting | Meaning | Control type | Default | Constraints |\n| --- | --- | --- | --- | --- |\n| `alphabet` | Sequence alphabet | select | \"dna\" | Allowed: dna, rna |\n| `allowGaps` | Allow alignment gaps (-) | select | \"false\" | Allowed: false |\n| `motif` | Motif | text | \"ACG\" |  |\n| `mode` | Ambiguity matching | select | \"possible\" | Allowed: literal, possible, certain |\n| `strands` | Search strands | select | \"both\" | Allowed: forward, both |\n\n### Browser-agent workflow\n\n1. Open the human page in a browser that supports WebMCP.\n2. Discover the interface exposed by that page; use its actual schema.\n3. Select files on the page first when the tool requires files.\n4. Call `run_current_tool` with valid input and settings.\n5. Inspect the returned result or error and the displayed output. Retrieve files from the displayed download links.\n\nCalls do not automatically copy or download results. Browser permissions still apply. Interface availability alone is not proof of successful execution.\n\n### Planning specification\n\nSearches every FASTA record case-insensitively and includes overlapping matches. Literal mode compares symbols exactly. Possible mode requires intersecting IUPAC base sets at every position. Certain mode requires every possible sequence base to be allowed by the motif. Both-strand mode also searches the reverse complement of the motif and reports coordinates on the original forward sequence. Palindromic motifs can produce two strand-specific rows at one position. Coordinates are one-based and inclusive. Only linear, gap-free DNA or RNA is supported; this is not alignment, homology, variant or biological significance analysis. Runs locally without uploads or database lookup. Limit: 500000 combined input characters, 2000 records, 2000 validation issues, a 1000-symbol motif, 20000 matches and 10000000 symbol comparisons. Exceeding a limit rejects the complete report. Each export is limited to 3000000 characters; typed CSV allows 200000 values. Preview shows 200 rows. Processing stops after 10 seconds.\n\nThis describes intended requirements. Use the implementation notes, interface schema and observed output to determine current support.\n\n### Complete machine-readable capability record\n\n```json\n{\n  \"id\": \"sequence-motif-finder\",\n  \"category\": \"developer-tools\",\n  \"built\": true,\n  \"requirements\": \"Searches every FASTA record case-insensitively and includes overlapping matches. Literal mode compares symbols exactly. Possible mode requires intersecting IUPAC base sets at every position. Certain mode requires every possible sequence base to be allowed by the motif. Both-strand mode also searches the reverse complement of the motif and reports coordinates on the original forward sequence. Palindromic motifs can produce two strand-specific rows at one position. Coordinates are one-based and inclusive. Only linear, gap-free DNA or RNA is supported; this is not alignment, homology, variant or biological significance analysis. Runs locally without uploads or database lookup. Limit: 500000 combined input characters, 2000 records, 2000 validation issues, a 1000-symbol motif, 20000 matches and 10000000 symbol comparisons. Exceeding a limit rejects the complete report. Each export is limited to 3000000 characters; typed CSV allows 200000 values. Preview shows 200 rows. Processing stops after 10 seconds.\",\n  \"implementation\": {\n    \"fields\": [\n      {\n        \"key\": \"alphabet\",\n        \"label\": \"Sequence alphabet\",\n        \"value\": \"dna\",\n        \"type\": \"select\",\n        \"values\": [\n          \"dna\",\n          \"rna\"\n        ]\n      },\n      {\n        \"key\": \"allowGaps\",\n        \"label\": \"Allow alignment gaps (-)\",\n        \"value\": \"false\",\n        \"type\": \"select\",\n        \"values\": [\n          \"false\"\n        ]\n      },\n      {\n        \"key\": \"motif\",\n        \"label\": \"Motif\",\n        \"value\": \"ACG\",\n        \"type\": \"text\",\n        \"maxLength\": 1000,\n        \"help\": \"Use 1 to 1000 IUPAC symbols from the chosen DNA or RNA alphabet. No regular expressions, gaps or wildcards other than IUPAC symbols.\"\n      },\n      {\n        \"key\": \"mode\",\n        \"label\": \"Ambiguity matching\",\n        \"value\": \"possible\",\n        \"type\": \"select\",\n        \"values\": [\n          \"literal\",\n          \"possible\",\n          \"certain\"\n        ]\n      },\n      {\n        \"key\": \"strands\",\n        \"label\": \"Search strands\",\n        \"value\": \"both\",\n        \"type\": \"select\",\n        \"values\": [\n          \"forward\",\n          \"both\"\n        ]\n      }\n    ],\n    \"registrationFamily\": \"sequence-tools\",\n    \"presentation\": \"metrics\",\n    \"note\": \"Searches every FASTA record case-insensitively and includes overlapping matches. Literal mode compares symbols exactly. Possible mode requires intersecting IUPAC base sets at every position. Certain mode requires every possible sequence base to be allowed by the motif. Both-strand mode also searches the reverse complement of the motif and reports coordinates on the original forward sequence. Palindromic motifs can produce two strand-specific rows at one position. Coordinates are one-based and inclusive. Only linear, gap-free DNA or RNA is supported; this is not alignment, homology, variant or biological significance analysis. Runs locally without uploads or database lookup. Limit: 500000 combined input characters, 2000 records, 2000 validation issues, a 1000-symbol motif, 20000 matches and 10000000 symbol comparisons. Exceeding a limit rejects the complete report. Each export is limited to 3000000 characters; typed CSV allows 200000 values. Preview shows 200 rows. Processing stops after 10 seconds.\",\n    \"inputMaxLength\": 500000,\n    \"inputErrorCode\": \"SEQUENCE_INPUT\",\n    \"example\": {\n      \"input\": \">sample unchanged description\\nACGTrynACGT\\n\",\n      \"options\": {\n        \"alphabet\": \"dna\",\n        \"allowGaps\": \"false\",\n        \"motif\": \"ACG\",\n        \"mode\": \"possible\",\n        \"strands\": \"both\"\n      }\n    },\n    \"experience\": {\n      \"automatic\": false,\n      \"single\": false,\n      \"inputMaxLength\": 500000,\n      \"inputMode\": \"text\",\n      \"label\": \"Your text\",\n      \"placeholder\": \"Type or paste your input…\",\n      \"help\": \"Up to 500,000 characters. Review the settings before running.\",\n      \"action\": null\n    },\n    \"mode\": \"explicit\",\n    \"interactive\": false\n  },\n  \"execution\": \"Browser interface\",\n  \"api\": null,\n  \"browser_agent\": {\n    \"supported\": true,\n    \"name\": \"run_current_tool\",\n    \"discovery\": \"WebMCP on the human page in a supporting browser\",\n    \"verification\": \"See audit/API-AUDIT.md; availability is not verification\"\n  }\n}\n```\n\n## Page guide\n\nLocate overlapping literal or ambiguity-coded motifs in DNA or RNA FASTA, with explicit strand and matching rules.\n\nHow can we improve this tool?\n\nReport a problem or share an idea.\n\nPlease leave out private information. Your message and the tool name go to our team via PostHog.\n\n### How to use Sequence motif finder\n\n1. Paste gap-free DNA or RNA FASTA and enter an IUPAC motif.\n2. Choose literal, possible or certain matching and one or both strands.\n3. Review inclusive forward-source coordinates and download every match.\n\n## Useful next steps\n\n- [FASTA validator](https://happytails.ai/en/developer-tools/fasta-validator/) ([Markdown](https://happytails.ai/en/developer-tools/fasta-validator.md))\n\n- [FASTA sequence extractor](https://happytails.ai/en/developer-tools/fasta-sequence-extractor/) ([Markdown](https://happytails.ai/en/developer-tools/fasta-sequence-extractor.md))\n\n- [Sequence reverse complement](https://happytails.ai/en/developer-tools/sequence-reverse-complement/) ([Markdown](https://happytails.ai/en/developer-tools/sequence-reverse-complement.md))\n\n## Define ambiguity matching\n\nLiteral mode compares symbols. Possible mode accepts intersecting base sets. Certain mode requires every possible sequence base to be included in the motif.\n\n### Interpret strand rows explicitly\n\nBoth-strand mode searches the motif and its reverse complement. Overlapping matches are retained; palindromic motifs can produce two rows at one position. Matches do not establish biological significance.\n"
}