{
 "about": {
  "generatedBy": "pipeline/sequence-toolkit/reference.py",
  "scriptSha256": "1bc66633d1a780a7f255b02743e9258652769ed35b770f193c5d74e0070410d6",
  "recordedOn": "2026-10-06",
  "python": "3.11.15",
  "oracle": "Independent ORF scan (reference.py scan_orfs) with Biopython translations; cross-check NCBI ORFfinder",
  "oracleLicence": "reference.py: MIT; Biopython: Biopython Licence Agreement or BSD-3-Clause; ORFfinder: public domain (NCBI)",
  "rule": "No value in this file comes from the Drybench engine under test.",
  "fixture": "ORFs on three sequences, tables 1, 2 and 11, start codons ATG only (the default) and with the table's alternative initiation codons (brief section 4.3 (4))",
  "tolerance": "Exact: every field of every entry in main, nestedHidden and noStopBeforeEnd, hiddenCount, and the absence of every mustBeAbsent ORF",
  "ruling": "CSO ruling, 6 October 2026 (item 4; corrects brief section 4.1, which was written from memory), and the CSO's confirmation of the same day (item 6)",
  "rules": {
   "startCodons": "atgOnly (the default setting): ATG only. alternativeStarts: ATG and the table's alternative initiation codons, read from gc.prt (input.startCodonList); ORFfinder -s 1",
   "start": "an ORF starts at the most upstream permitted start codon after the previous in-frame stop (or after the start of its frame)",
   "stop": "the table's stop codons, read from gc.prt; end and lengthNt include the stop codon",
   "minimumLength": "codingLengthNt >= 75 (25 codons), counted from the start codon to the codon before the stop, as ORFfinder 0.4.3 counts -ml 75; for an ORF with no stop, the complete codons to the end of the sequence. mustBeAbsent lists the ORFs that counting the stop codon (lengthNt >= 75) would add: none may appear in any list.",
   "noStopBeforeEnd": "an ORF with no in-frame stop before the sequence ends is not in the main list; it is listed separately as 'No stop codon before the sequence ends', ends with the last complete codon of its frame (stopCodon null), and still counts when hiding nested ORFs, as ORFfinder counts it. Such an ORF that is itself nested is hidden like any nested ORF (in nestedHidden with stopCodon null), as ORFfinder hides it: nesting is decided first for every ORF, with or without a stop (CSO confirmation, item 6(b)); this happens once (about.confirmedCases).",
   "nested": "an ORF whose whole span, stop codon included, lies inside the span of another listed ORF (noStopBeforeEnd included), on either strand and in any frame, is nested. Nested ORFs are hidden by default (nestedHidden, with or without a stop) and their number is shown (hiddenCount). main holds the stop-terminated ORFs that are not nested; noStopBeforeEnd the ORFs without a stop that are not nested.",
   "protein": "the ORF translated with the case's table, without the stop; the start codon reads as M (initiator) unless startsAtFrameStart",
   "startsAtFrameStart": "the start codon is the first complete codon of its frame, so no in-frame stop can lie upstream within the sequence: the ORF is flagged 'may begin before the sequence' and that codon is translated as an internal codon (CTG -> L), as ORFfinder does (CSO confirmation, item 6(a); about.confirmedCases)",
   "alternativeStartsCopy": "The start shown is the most upstream permitted start codon after the previous in-frame stop, not a predicted translation start (lacI: annotated GTG at 79, shown from 70). (CSO confirmation, item 6(c), verbatim)",
   "coordinates": "1-based on the given strand; a minus-strand ORF has start > end",
   "frame": "as in translation.json: +1..+3 from positions 1..3 of the given strand, -1..-3 from positions 1..3 of the reverse complement",
   "ids": "orfN numbers all of a case's ORFs (the three lists together) by lower, then upper coordinate; containedIn names the containing ORFs by these ids. The ids are the fixture's own: match ORFs by strand, start and end."
  },
  "orffinderNotes": "ORFfinder 0.4.3 defaults are -s 1, -ml 75 and -n false (nested shown). It reports ORFs with no stop before the sequence end as partial and counts them when hiding nested ORFs (-n t). Every case agrees with ORFfinder (crossCheck.orffinder) on the start, end, partial flag and protein of every ORF and on the ORFs shown by default.",
  "confirmedCases": [
   "ins-mrna, table 1, alternativeStarts: orf6 (464..180) starts with CTG, the first codon of frame -2: no in-frame stop can lie upstream within the sequence, so ORFfinder marks it partial and prints the codon's own amino acid (L) rather than M. CSO confirmation, 6 October 2026, item 6(a): flag it 'may begin before the sequence' and translate that codon as an internal codon, as here.",
   "ins-mrna, table 1, alternativeStarts: orf9 (341..463) has no stop before the sequence ends and lies inside orf6: as a nested ORF it is hidden by default and listed in nestedHidden (stopCodon null), not in noStopBeforeEnd; ORFfinder hides it too (-n t). CSO confirmation, 6 October 2026, item 6(b): nesting is decided first for every ORF, with or without a stop.",
   "ins-mrna, table 11, alternativeStarts: orf7 (464..180) starts with CTG, the first codon of frame -2: no in-frame stop can lie upstream within the sequence, so ORFfinder marks it partial and prints the codon's own amino acid (L) rather than M. CSO confirmation, 6 October 2026, item 6(a): flag it 'may begin before the sequence' and translate that codon as an internal codon, as here."
  ],
  "sequences": [
   {
    "id": "ins-mrna",
    "accession": "NM_000207.3",
    "range": null,
    "description": "Homo sapiens insulin (INS), transcript variant 1, mRNA (RefSeq), whole record",
    "why": "Teaching example (insulin); a nuclear mRNA read with the standard code; AGA/AGG codons make table 2 cut the CDS short.",
    "length": 465,
    "sequence": "AGCCCTCCAGGACAGGCTGCATCAGAAGAGGCCATCAAGCAGATCACTGTCCTTCTGCCATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTGGGGACCTGACCCAGCCGCAGCCTTTGTGAACCAACACCTGTGCGGCTCACACCTGGTGGAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTACACACCCAAGACCCGCCGGGAGGCAGAGGACCTGCAGGTGGGGCAGGTGGAGCTGGGCGGGGGCCCTGGTGCAGGCAGCCTGCAGCCCTTGGCCCTGGAGGGGTCCCTGCAGAAGCGTGGCATTGTGGAACAATGCTGTACCAGCATCTGCTCCCTCTACCAGCTGGAGAACTACTGCAACTAGACGCAGCCCGCAGGCAGCCCCACACCCGCCGCCTCCTGCACCGAGAGAGATGGAATAAAGCCCTTGAACCAGC",
    "sha256": "2132509911c26572e7dfcaea140a3c893ab2cb6ec1d71cfe23b91fcf09ae4ff1",
    "file": "pipeline/sequence-toolkit/inputs/nucleotide/NM_000207.3.gb",
    "retrieved": "2026-10-06T02:24:10Z",
    "naturalTable": 1,
    "licence": "NCBI: no restrictions placed by NCBI on GenBank/RefSeq data (submitter rights may apply)"
   },
   {
    "id": "mt-atp8-atp6-cox3",
    "accession": "NC_012920.1",
    "range": [
     8295,
     9990
    ],
    "description": "Homo sapiens mitochondrion (rCRS), positions 8295-9990: tRNA-Lys, ATP8, ATP6 and COX3",
    "why": "Vertebrate mitochondrial code: TGA is Trp and AGA/AGG are stops; ATP8 and ATP6 overlap in different frames; COX3 ends with an incomplete stop (T, completed by polyadenylation), so its ORF is not stop-terminated in the DNA.",
    "length": 1696,
    "sequence": "CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCATAATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACAAACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCTGTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCTATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCATCAACAACCGACTAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGATAACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTTAATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAACTATCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCACAGTGATTATAGGCTTTCGCTCTAAGATTAAAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGGAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCATCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCACACTTCTAGTAAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGTAAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACGGGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAATTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTCCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCTAATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTTGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCTCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACATCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTTTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTT",
    "sha256": "27920863d5c2e03f14784ddf0a553d59643e759b8cef3ddac95ff8fbf8c19e5c",
    "file": "pipeline/sequence-toolkit/inputs/nucleotide/NC_012920.1_8295-9990.gb",
    "retrieved": "2026-10-06T02:24:11Z",
    "naturalTable": 2,
    "licence": "NCBI: no restrictions placed by NCBI on GenBank/RefSeq data (submitter rights may apply)"
   },
   {
    "id": "ecoli-lacI",
    "accession": "J01636.1",
    "range": [
     1,
     1500
    ],
    "description": "Escherichia coli lactose operon, positions 1-1500: lacI (GTG start) and the start of lacZ",
    "why": "Bacterial code: lacI starts with GTG (Met only with alternative initiation codons on); lacZ runs off the end of the region, so it is not stop-terminated.",
    "length": 1500,
    "sequence": "GACACCATCGAATGGCGCAAAACCTTTCGCGGTATGGCATGATAGCGCCCGGAAGAGAGTCAATTCAGGGTGGTGAATGTGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTCAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGGATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAA",
    "sha256": "3866d793146ad0a0c8c75011f117b5b4ee6a341a971e61f00d9fe85fc1a227b8",
    "file": "pipeline/sequence-toolkit/inputs/nucleotide/J01636.1_1-1500.gb",
    "retrieved": "2026-10-06T02:24:12Z",
    "naturalTable": 11,
    "licence": "NCBI: no restrictions placed by NCBI on GenBank/RefSeq data (submitter rights may apply)"
   }
  ],
  "geneticCodes": {
   "file": "pipeline/sequence-toolkit/ncbi/gc.prt",
   "version": "4.6",
   "retrieved": "2026-10-06T02:24:29Z",
   "sha256": "2aecbdd09ecc5e0d233c105090a593737298ef93d88f6bc0c1bef26df6051a04",
   "tables": {
    "1": {
     "name": "Standard",
     "stops": [
      "TAA",
      "TAG",
      "TGA"
     ],
     "starts": [
      "ATG",
      "CTG",
      "TTG"
     ],
     "biopythonEqualsGcPrt": true
    },
    "2": {
     "name": "Vertebrate Mitochondrial",
     "stops": [
      "AGA",
      "AGG",
      "TAA",
      "TAG"
     ],
     "starts": [
      "ATA",
      "ATC",
      "ATG",
      "ATT",
      "GTG"
     ],
     "biopythonEqualsGcPrt": true
    },
    "11": {
     "name": "Bacterial, Archaeal and Plant Plastid",
     "stops": [
      "TAA",
      "TAG",
      "TGA"
     ],
     "starts": [
      "ATA",
      "ATC",
      "ATG",
      "ATT",
      "CTG",
      "GTG",
      "TTG"
     ],
     "biopythonEqualsGcPrt": true
    }
   }
  }
 },
 "cases": [
  {
   "id": "ins-mrna.t1.atgOnly",
   "input": {
    "sequenceId": "ins-mrna",
    "table": 1,
    "startCodons": "atgOnly",
    "startCodonList": [
     "ATG"
    ],
    "defaultSetting": true,
    "minimumCodingLengthNt": 75
   },
   "expected": {
    "main": [
     {
      "id": "orf1",
      "strand": "+",
      "frame": 3,
      "start": 60,
      "end": 392,
      "lengthNt": 333,
      "codingLengthNt": 330,
      "lengthAa": 110,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN"
     }
    ],
    "nestedHidden": [
     {
      "id": "orf2",
      "strand": "-",
      "frame": -3,
      "start": 355,
      "end": 206,
      "lengthNt": 150,
      "codingLengthNt": 147,
      "lengthAa": 49,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf1"
      ],
      "protein": "MLVQHCSTMPRFCRDPSRAKGCRLPAPGPPPSSTCPTCRSSASRRVLGV"
     }
    ],
    "hiddenCount": 1,
    "noStopBeforeEnd": [
     {
      "id": "orf3",
      "strand": "+",
      "frame": 2,
      "start": 341,
      "end": 463,
      "lengthNt": 123,
      "codingLengthNt": 123,
      "lengthAa": 41,
      "startCodon": "ATG",
      "stopCodon": null,
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MLYQHLLPLPAGELLQLDAARRQPHTRRLLHRERWNKALEP"
     }
    ],
    "mustBeAbsent": []
   },
   "crossCheck": {
    "biopythonTranslation": "every ORF is Biopython's translation (same table) of its nucleotides, found at its place in the frame translation; one final stop when stopCodon is set, none otherwise",
    "orffinder": {
     "used": true,
     "tool": "NCBI ORFfinder 0.4.3",
     "files": [
      "pipeline/sequence-toolkit/orffinder/ins-mrna.g1.s0.nf.fa",
      "pipeline/sequence-toolkit/orffinder/ins-mrna.g1.s0.nt.fa"
     ],
     "commands": [
      "ORFfinder -in <fasta> -g 1 -s 0 -ml 75 -strand both -outfmt 0 -n f -out <out>",
      "ORFfinder -in <fasta> -g 1 -s 0 -ml 75 -strand both -outfmt 0 -n t -out <out>"
     ],
     "allOrfsAgree": true,
     "shownByDefaultAgree": true,
     "compared": "start, end and protein of every ORF (-n f) and of the ORFs shown by default (-n t); ORFfinder's 'partial' equals stopCodon null or startsAtFrameStart"
    }
   },
   "method": "ORF rules of the CSO ruling of 6 October 2026, as about.rules states them",
   "oracle": "independent scan in reference.py (scan_orfs), cross-checked against Biopython translations and NCBI ORFfinder",
   "source": "pipeline/sequence-toolkit/reference.py (orf)",
   "oracleVersion": "reference.py sha256 1bc66633d1a7; Biopython 1.88",
   "recordedOn": "2026-10-06",
   "notes": []
  },
  {
   "id": "ins-mrna.t1.alternativeStarts",
   "input": {
    "sequenceId": "ins-mrna",
    "table": 1,
    "startCodons": "alternativeStarts",
    "startCodonList": [
     "ATG",
     "CTG",
     "TTG"
    ],
    "defaultSetting": false,
    "minimumCodingLengthNt": 75
   },
   "expected": {
    "main": [
     {
      "id": "orf3",
      "strand": "-",
      "frame": -1,
      "start": 405,
      "end": 22,
      "lengthNt": 384,
      "codingLengthNt": 381,
      "lengthAa": 127,
      "startCodon": "CTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MRAASSCSSSPAGRGSRCWYSIVPQCHASAGTPPGPRAAGCLHQGPRPAPPAPPAGPLPPGGSWVCRRSLVPRTLGRELPPGVSRTGVGSQRLRLGQVPRGPAAPAGAGGASTGPWQKDSDLLDGLF"
     },
     {
      "id": "orf6",
      "strand": "-",
      "frame": -2,
      "start": 464,
      "end": 180,
      "lengthNt": 285,
      "codingLengthNt": 282,
      "lengthAa": 94,
      "startCodon": "CTG",
      "stopCodon": "TAG",
      "startsAtFrameStart": true,
      "nested": false,
      "containedIn": [],
      "protein": "LVQGLYSISLGAGGGGCGAACGLRLVAVVLQLVEGADAGTALFHNATLLQGPLQGQGLQAACTRAPAQLHLPHLQVLCLPAGLGCVEEASFPAH"
     }
    ],
    "nestedHidden": [
     {
      "id": "orf2",
      "strand": "+",
      "frame": 2,
      "start": 17,
      "end": 118,
      "lengthNt": 102,
      "codingLengthNt": 99,
      "lengthAa": 33,
      "startCodon": "CTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf1"
      ],
      "protein": "MHQKRPSSRSLSFCHGPVDAPPAPAGAAGPLGT"
     },
     {
      "id": "orf4",
      "strand": "+",
      "frame": 1,
      "start": 55,
      "end": 138,
      "lengthNt": 84,
      "codingLengthNt": 81,
      "lengthAa": 27,
      "startCodon": "CTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf1",
       "orf3"
      ],
      "protein": "MPWPCGCASCPCWRCWPSGDLTQPQPL"
     },
     {
      "id": "orf5",
      "strand": "+",
      "frame": 3,
      "start": 60,
      "end": 392,
      "lengthNt": 333,
      "codingLengthNt": 330,
      "lengthAa": 110,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf3"
      ],
      "protein": "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN"
     },
     {
      "id": "orf7",
      "strand": "-",
      "frame": -3,
      "start": 355,
      "end": 206,
      "lengthNt": 150,
      "codingLengthNt": 147,
      "lengthAa": 49,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf3",
       "orf5",
       "orf6"
      ],
      "protein": "MLVQHCSTMPRFCRDPSRAKGCRLPAPGPPPSSTCPTCRSSASRRVLGV"
     },
     {
      "id": "orf8",
      "strand": "+",
      "frame": 1,
      "start": 274,
      "end": 450,
      "lengthNt": 177,
      "codingLengthNt": 174,
      "lengthAa": 58,
      "startCodon": "CTG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf6"
      ],
      "protein": "MVQAACSPWPWRGPCRSVALWNNAVPASAPSTSWRTTATRRSPQAAPHPPPPAPREME"
     },
     {
      "id": "orf9",
      "strand": "+",
      "frame": 2,
      "start": 341,
      "end": 463,
      "lengthNt": 123,
      "codingLengthNt": 123,
      "lengthAa": 41,
      "startCodon": "ATG",
      "stopCodon": null,
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf6"
      ],
      "protein": "MLYQHLLPLPAGELLQLDAARRQPHTRRLLHRERWNKALEP"
     }
    ],
    "hiddenCount": 6,
    "noStopBeforeEnd": [
     {
      "id": "orf1",
      "strand": "-",
      "frame": -2,
      "start": 143,
      "end": 3,
      "lengthNt": 141,
      "codingLengthNt": 141,
      "lengthAa": 47,
      "startCodon": "TTG",
      "stopCodon": null,
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MVHKGCGWVRSPEGQQRQQGQEAHPQGHGRRTVICLMASSDAACPGG"
     }
    ],
    "mustBeAbsent": []
   },
   "crossCheck": {
    "biopythonTranslation": "every ORF is Biopython's translation (same table) of its nucleotides, found at its place in the frame translation; one final stop when stopCodon is set, none otherwise",
    "orffinder": {
     "used": true,
     "tool": "NCBI ORFfinder 0.4.3",
     "files": [
      "pipeline/sequence-toolkit/orffinder/ins-mrna.g1.s1.nf.fa",
      "pipeline/sequence-toolkit/orffinder/ins-mrna.g1.s1.nt.fa"
     ],
     "commands": [
      "ORFfinder -in <fasta> -g 1 -s 1 -ml 75 -strand both -outfmt 0 -n f -out <out>",
      "ORFfinder -in <fasta> -g 1 -s 1 -ml 75 -strand both -outfmt 0 -n t -out <out>"
     ],
     "allOrfsAgree": true,
     "shownByDefaultAgree": true,
     "compared": "start, end and protein of every ORF (-n f) and of the ORFs shown by default (-n t); ORFfinder's 'partial' equals stopCodon null or startsAtFrameStart"
    }
   },
   "method": "ORF rules of the CSO ruling of 6 October 2026, as about.rules states them",
   "oracle": "independent scan in reference.py (scan_orfs), cross-checked against Biopython translations and NCBI ORFfinder",
   "source": "pipeline/sequence-toolkit/reference.py (orf)",
   "oracleVersion": "reference.py sha256 1bc66633d1a7; Biopython 1.88",
   "recordedOn": "2026-10-06",
   "notes": [
    "ins-mrna, table 1, alternativeStarts: orf6 (464..180) starts with CTG, the first codon of frame -2: no in-frame stop can lie upstream within the sequence, so ORFfinder marks it partial and prints the codon's own amino acid (L) rather than M. CSO confirmation, 6 October 2026, item 6(a): flag it 'may begin before the sequence' and translate that codon as an internal codon, as here.",
    "ins-mrna, table 1, alternativeStarts: orf9 (341..463) has no stop before the sequence ends and lies inside orf6: as a nested ORF it is hidden by default and listed in nestedHidden (stopCodon null), not in noStopBeforeEnd; ORFfinder hides it too (-n t). CSO confirmation, 6 October 2026, item 6(b): nesting is decided first for every ORF, with or without a stop."
   ]
  },
  {
   "id": "ins-mrna.t2.atgOnly",
   "input": {
    "sequenceId": "ins-mrna",
    "table": 2,
    "startCodons": "atgOnly",
    "startCodonList": [
     "ATG"
    ],
    "defaultSetting": true,
    "minimumCodingLengthNt": 75
   },
   "expected": {
    "main": [
     {
      "id": "orf1",
      "strand": "+",
      "frame": 3,
      "start": 60,
      "end": 392,
      "lengthNt": 333,
      "codingLengthNt": 330,
      "lengthAa": 110,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN"
     }
    ],
    "nestedHidden": [],
    "hiddenCount": 0,
    "noStopBeforeEnd": [],
    "mustBeAbsent": []
   },
   "crossCheck": {
    "biopythonTranslation": "every ORF is Biopython's translation (same table) of its nucleotides, found at its place in the frame translation; one final stop when stopCodon is set, none otherwise",
    "orffinder": {
     "used": true,
     "tool": "NCBI ORFfinder 0.4.3",
     "files": [
      "pipeline/sequence-toolkit/orffinder/ins-mrna.g2.s0.nf.fa",
      "pipeline/sequence-toolkit/orffinder/ins-mrna.g2.s0.nt.fa"
     ],
     "commands": [
      "ORFfinder -in <fasta> -g 2 -s 0 -ml 75 -strand both -outfmt 0 -n f -out <out>",
      "ORFfinder -in <fasta> -g 2 -s 0 -ml 75 -strand both -outfmt 0 -n t -out <out>"
     ],
     "allOrfsAgree": true,
     "shownByDefaultAgree": true,
     "compared": "start, end and protein of every ORF (-n f) and of the ORFs shown by default (-n t); ORFfinder's 'partial' equals stopCodon null or startsAtFrameStart"
    }
   },
   "method": "ORF rules of the CSO ruling of 6 October 2026, as about.rules states them",
   "oracle": "independent scan in reference.py (scan_orfs), cross-checked against Biopython translations and NCBI ORFfinder",
   "source": "pipeline/sequence-toolkit/reference.py (orf)",
   "oracleVersion": "reference.py sha256 1bc66633d1a7; Biopython 1.88",
   "recordedOn": "2026-10-06",
   "notes": []
  },
  {
   "id": "ins-mrna.t2.alternativeStarts",
   "input": {
    "sequenceId": "ins-mrna",
    "table": 2,
    "startCodons": "alternativeStarts",
    "startCodonList": [
     "ATA",
     "ATC",
     "ATG",
     "ATT",
     "GTG"
    ],
    "defaultSetting": false,
    "minimumCodingLengthNt": 75
   },
   "expected": {
    "main": [
     {
      "id": "orf1",
      "strand": "+",
      "frame": 1,
      "start": 34,
      "end": 183,
      "lengthNt": 150,
      "codingLengthNt": 147,
      "lengthAa": 49,
      "startCodon": "ATC",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MKQITVLLPWPCGCASCPCWRCWPSGDLTQPQPLWTNTCAAHTWWKLST"
     },
     {
      "id": "orf2",
      "strand": "+",
      "frame": 3,
      "start": 60,
      "end": 392,
      "lengthNt": 333,
      "codingLengthNt": 330,
      "lengthAa": 110,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN"
     },
     {
      "id": "orf4",
      "strand": "-",
      "frame": -2,
      "start": 443,
      "end": 273,
      "lengthNt": 171,
      "codingLengthNt": 168,
      "lengthAa": 56,
      "startCodon": "ATC",
      "stopCodon": "AGG",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MSLGAGGGGCGAACGLRLVAVVLQLVEGADAGTALFHNATLLQGPLQGQGLQAACT"
     }
    ],
    "nestedHidden": [
     {
      "id": "orf3",
      "strand": "+",
      "frame": 2,
      "start": 68,
      "end": 199,
      "lengthNt": 132,
      "codingLengthNt": 129,
      "lengthAa": 43,
      "startCodon": "GTG",
      "stopCodon": "AGG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MDAPPAPAGAAGPLGTWPSRSLCEPTPVRLTPGGSSLPSVRGT"
     }
    ],
    "hiddenCount": 1,
    "noStopBeforeEnd": [],
    "mustBeAbsent": []
   },
   "crossCheck": {
    "biopythonTranslation": "every ORF is Biopython's translation (same table) of its nucleotides, found at its place in the frame translation; one final stop when stopCodon is set, none otherwise",
    "orffinder": {
     "used": true,
     "tool": "NCBI ORFfinder 0.4.3",
     "files": [
      "pipeline/sequence-toolkit/orffinder/ins-mrna.g2.s1.nf.fa",
      "pipeline/sequence-toolkit/orffinder/ins-mrna.g2.s1.nt.fa"
     ],
     "commands": [
      "ORFfinder -in <fasta> -g 2 -s 1 -ml 75 -strand both -outfmt 0 -n f -out <out>",
      "ORFfinder -in <fasta> -g 2 -s 1 -ml 75 -strand both -outfmt 0 -n t -out <out>"
     ],
     "allOrfsAgree": true,
     "shownByDefaultAgree": true,
     "compared": "start, end and protein of every ORF (-n f) and of the ORFs shown by default (-n t); ORFfinder's 'partial' equals stopCodon null or startsAtFrameStart"
    }
   },
   "method": "ORF rules of the CSO ruling of 6 October 2026, as about.rules states them",
   "oracle": "independent scan in reference.py (scan_orfs), cross-checked against Biopython translations and NCBI ORFfinder",
   "source": "pipeline/sequence-toolkit/reference.py (orf)",
   "oracleVersion": "reference.py sha256 1bc66633d1a7; Biopython 1.88",
   "recordedOn": "2026-10-06",
   "notes": []
  },
  {
   "id": "ins-mrna.t11.atgOnly",
   "input": {
    "sequenceId": "ins-mrna",
    "table": 11,
    "startCodons": "atgOnly",
    "startCodonList": [
     "ATG"
    ],
    "defaultSetting": true,
    "minimumCodingLengthNt": 75
   },
   "expected": {
    "main": [
     {
      "id": "orf1",
      "strand": "+",
      "frame": 3,
      "start": 60,
      "end": 392,
      "lengthNt": 333,
      "codingLengthNt": 330,
      "lengthAa": 110,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN"
     }
    ],
    "nestedHidden": [
     {
      "id": "orf2",
      "strand": "-",
      "frame": -3,
      "start": 355,
      "end": 206,
      "lengthNt": 150,
      "codingLengthNt": 147,
      "lengthAa": 49,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf1"
      ],
      "protein": "MLVQHCSTMPRFCRDPSRAKGCRLPAPGPPPSSTCPTCRSSASRRVLGV"
     }
    ],
    "hiddenCount": 1,
    "noStopBeforeEnd": [
     {
      "id": "orf3",
      "strand": "+",
      "frame": 2,
      "start": 341,
      "end": 463,
      "lengthNt": 123,
      "codingLengthNt": 123,
      "lengthAa": 41,
      "startCodon": "ATG",
      "stopCodon": null,
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MLYQHLLPLPAGELLQLDAARRQPHTRRLLHRERWNKALEP"
     }
    ],
    "mustBeAbsent": []
   },
   "crossCheck": {
    "biopythonTranslation": "every ORF is Biopython's translation (same table) of its nucleotides, found at its place in the frame translation; one final stop when stopCodon is set, none otherwise",
    "orffinder": {
     "used": true,
     "tool": "NCBI ORFfinder 0.4.3",
     "files": [
      "pipeline/sequence-toolkit/orffinder/ins-mrna.g11.s0.nf.fa",
      "pipeline/sequence-toolkit/orffinder/ins-mrna.g11.s0.nt.fa"
     ],
     "commands": [
      "ORFfinder -in <fasta> -g 11 -s 0 -ml 75 -strand both -outfmt 0 -n f -out <out>",
      "ORFfinder -in <fasta> -g 11 -s 0 -ml 75 -strand both -outfmt 0 -n t -out <out>"
     ],
     "allOrfsAgree": true,
     "shownByDefaultAgree": true,
     "compared": "start, end and protein of every ORF (-n f) and of the ORFs shown by default (-n t); ORFfinder's 'partial' equals stopCodon null or startsAtFrameStart"
    }
   },
   "method": "ORF rules of the CSO ruling of 6 October 2026, as about.rules states them",
   "oracle": "independent scan in reference.py (scan_orfs), cross-checked against Biopython translations and NCBI ORFfinder",
   "source": "pipeline/sequence-toolkit/reference.py (orf)",
   "oracleVersion": "reference.py sha256 1bc66633d1a7; Biopython 1.88",
   "recordedOn": "2026-10-06",
   "notes": []
  },
  {
   "id": "ins-mrna.t11.alternativeStarts",
   "input": {
    "sequenceId": "ins-mrna",
    "table": 11,
    "startCodons": "alternativeStarts",
    "startCodonList": [
     "ATA",
     "ATC",
     "ATG",
     "ATT",
     "CTG",
     "GTG",
     "TTG"
    ],
    "defaultSetting": false,
    "minimumCodingLengthNt": 75
   },
   "expected": {
    "main": [
     {
      "id": "orf3",
      "strand": "+",
      "frame": 3,
      "start": 21,
      "end": 392,
      "lengthNt": 372,
      "codingLengthNt": 369,
      "lengthAa": 123,
      "startCodon": "ATC",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MRRGHQADHCPSAMALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN"
     },
     {
      "id": "orf4",
      "strand": "-",
      "frame": -1,
      "start": 417,
      "end": 22,
      "lengthNt": 396,
      "codingLengthNt": 393,
      "lengthAa": 131,
      "startCodon": "GTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MWGCLRAASSCSSSPAGRGSRCWYSIVPQCHASAGTPPGPRAAGCLHQGPRPAPPAPPAGPLPPGGSWVCRRSLVPRTLGRELPPGVSRTGVGSQRLRLGQVPRGPAAPAGAGGASTGPWQKDSDLLDGLF"
     },
     {
      "id": "orf7",
      "strand": "-",
      "frame": -2,
      "start": 464,
      "end": 180,
      "lengthNt": 285,
      "codingLengthNt": 282,
      "lengthAa": 94,
      "startCodon": "CTG",
      "stopCodon": "TAG",
      "startsAtFrameStart": true,
      "nested": false,
      "containedIn": [],
      "protein": "LVQGLYSISLGAGGGGCGAACGLRLVAVVLQLVEGADAGTALFHNATLLQGPLQGQGLQAACTRAPAQLHLPHLQVLCLPAGLGCVEEASFPAH"
     }
    ],
    "nestedHidden": [
     {
      "id": "orf2",
      "strand": "+",
      "frame": 2,
      "start": 17,
      "end": 118,
      "lengthNt": 102,
      "codingLengthNt": 99,
      "lengthAa": 33,
      "startCodon": "CTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf1"
      ],
      "protein": "MHQKRPSSRSLSFCHGPVDAPPAPAGAAGPLGT"
     },
     {
      "id": "orf5",
      "strand": "+",
      "frame": 1,
      "start": 34,
      "end": 138,
      "lengthNt": 105,
      "codingLengthNt": 102,
      "lengthAa": 34,
      "startCodon": "ATC",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf1",
       "orf3",
       "orf4"
      ],
      "protein": "MKQITVLLPWPCGCASCPCWRCWPSGDLTQPQPL"
     },
     {
      "id": "orf8",
      "strand": "-",
      "frame": -3,
      "start": 355,
      "end": 206,
      "lengthNt": 150,
      "codingLengthNt": 147,
      "lengthAa": 49,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf3",
       "orf4",
       "orf6",
       "orf7"
      ],
      "protein": "MLVQHCSTMPRFCRDPSRAKGCRLPAPGPPPSSTCPTCRSSASRRVLGV"
     },
     {
      "id": "orf9",
      "strand": "+",
      "frame": 1,
      "start": 274,
      "end": 450,
      "lengthNt": 177,
      "codingLengthNt": 174,
      "lengthAa": 58,
      "startCodon": "CTG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf6",
       "orf7"
      ],
      "protein": "MVQAACSPWPWRGPCRSVALWNNAVPASAPSTSWRTTATRRSPQAAPHPPPPAPREME"
     }
    ],
    "hiddenCount": 4,
    "noStopBeforeEnd": [
     {
      "id": "orf1",
      "strand": "-",
      "frame": -2,
      "start": 146,
      "end": 3,
      "lengthNt": 144,
      "codingLengthNt": 144,
      "lengthAa": 48,
      "startCodon": "GTG",
      "stopCodon": null,
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MLVHKGCGWVRSPEGQQRQQGQEAHPQGHGRRTVICLMASSDAACPGG"
     },
     {
      "id": "orf6",
      "strand": "+",
      "frame": 2,
      "start": 149,
      "end": 463,
      "lengthNt": 315,
      "codingLengthNt": 315,
      "lengthAa": 105,
      "startCodon": "GTG",
      "stopCodon": null,
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MRLTPGGSSLPSVRGTRLLLHTQDPPGGRGPAGGAGGAGRGPWCRQPAALGPGGVPAEAWHCGTMLYQHLLPLPAGELLQLDAARRQPHTRRLLHRERWNKALEP"
     }
    ],
    "mustBeAbsent": []
   },
   "crossCheck": {
    "biopythonTranslation": "every ORF is Biopython's translation (same table) of its nucleotides, found at its place in the frame translation; one final stop when stopCodon is set, none otherwise",
    "orffinder": {
     "used": true,
     "tool": "NCBI ORFfinder 0.4.3",
     "files": [
      "pipeline/sequence-toolkit/orffinder/ins-mrna.g11.s1.nf.fa",
      "pipeline/sequence-toolkit/orffinder/ins-mrna.g11.s1.nt.fa"
     ],
     "commands": [
      "ORFfinder -in <fasta> -g 11 -s 1 -ml 75 -strand both -outfmt 0 -n f -out <out>",
      "ORFfinder -in <fasta> -g 11 -s 1 -ml 75 -strand both -outfmt 0 -n t -out <out>"
     ],
     "allOrfsAgree": true,
     "shownByDefaultAgree": true,
     "compared": "start, end and protein of every ORF (-n f) and of the ORFs shown by default (-n t); ORFfinder's 'partial' equals stopCodon null or startsAtFrameStart"
    }
   },
   "method": "ORF rules of the CSO ruling of 6 October 2026, as about.rules states them",
   "oracle": "independent scan in reference.py (scan_orfs), cross-checked against Biopython translations and NCBI ORFfinder",
   "source": "pipeline/sequence-toolkit/reference.py (orf)",
   "oracleVersion": "reference.py sha256 1bc66633d1a7; Biopython 1.88",
   "recordedOn": "2026-10-06",
   "notes": [
    "ins-mrna, table 11, alternativeStarts: orf7 (464..180) starts with CTG, the first codon of frame -2: no in-frame stop can lie upstream within the sequence, so ORFfinder marks it partial and prints the codon's own amino acid (L) rather than M. CSO confirmation, 6 October 2026, item 6(a): flag it 'may begin before the sequence' and translate that codon as an internal codon, as here."
   ]
  },
  {
   "id": "mt-atp8-atp6-cox3.t1.atgOnly",
   "input": {
    "sequenceId": "mt-atp8-atp6-cox3",
    "table": 1,
    "startCodons": "atgOnly",
    "startCodonList": [
     "ATG"
    ],
    "defaultSetting": true,
    "minimumCodingLengthNt": 75
   },
   "expected": {
    "main": [
     {
      "id": "orf1",
      "strand": "-",
      "frame": -1,
      "start": 139,
      "end": 62,
      "lengthNt": 78,
      "codingLengthNt": 75,
      "lengthAa": 25,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MRNSVRSMGVIMVGHTVVFSWGISL"
     },
     {
      "id": "orf2",
      "strand": "+",
      "frame": 3,
      "start": 72,
      "end": 224,
      "lengthNt": 153,
      "codingLengthNt": 150,
      "lengthAa": 50,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MPQLNTTVWPTIITPILLTLFLITQLKILNTNYHLPPSPKPIKIKNYNKP"
     },
     {
      "id": "orf4",
      "strand": "-",
      "frame": -2,
      "start": 462,
      "end": 139,
      "lengthNt": 324,
      "codingLengthNt": 321,
      "lengthAa": 107,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MIKDTSIRDQVRPLVLCMVIICFEVSLISHCWVVISRLLMRYLEVGINRGGNRMISTAAGRPRIVGAMNEANRFSFILVLRVCYNFLFLWALVREVGGSLCLIFLVG"
     },
     {
      "id": "orf6",
      "strand": "-",
      "frame": -2,
      "start": 684,
      "end": 499,
      "lengthNt": 186,
      "codingLengthNt": 183,
      "lengthAa": 61,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MSRLMVSIITSMGIRGVGVPCGKKWARAFLILERKPIITVPAHKGMAMARFIDSWVVGVNE"
     },
     {
      "id": "orf7",
      "strand": "-",
      "frame": -2,
      "start": 807,
      "end": 685,
      "lengthNt": 123,
      "codingLengthNt": 120,
      "lengthAa": 40,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MISVEGRLMVDIARVALPIRCMSRWPAVMLAVRRTARAIG"
     },
     {
      "id": "orf8",
      "strand": "+",
      "frame": 2,
      "start": 743,
      "end": 913,
      "lengthNt": 171,
      "codingLengthNt": 168,
      "lengthAa": 56,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MHLIGSATLAISTINLPSTLIIFTILILLTILEIAVALIQAYVFTLLVSLYLHDNT"
     },
     {
      "id": "orf9",
      "strand": "-",
      "frame": -1,
      "start": 958,
      "end": 881,
      "lengthNt": 78,
      "codingLengthNt": 75,
      "lengthAa": 25,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MGWVLLYDRHVIGGSLCVVVQVEAY"
     },
     {
      "id": "orf10",
      "strand": "+",
      "frame": 3,
      "start": 957,
      "end": 1361,
      "lengthNt": 405,
      "codingLengthNt": 402,
      "lengthAa": 134,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MTPNRGPLSPPNDLRPSHVISLPLHNAPHTRPTNQHTNHIPMMARCNTRKHIPRPPHTTCPKRPSIRDNPIYYLRSFFLRRIFLSLLPLQPSPYPPIRRALAPNRHHPAKSPRSPTPKHIRITRIRSINHLSSP"
     }
    ],
    "nestedHidden": [
     {
      "id": "orf3",
      "strand": "+",
      "frame": 2,
      "start": 95,
      "end": 214,
      "lengthNt": 120,
      "codingLengthNt": 117,
      "lengthAa": 39,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MAHHNYPHTPYTIPHHPTKNIKHKLPPTSLTKAHKNKKL"
     },
     {
      "id": "orf5",
      "strand": "+",
      "frame": 2,
      "start": 233,
      "end": 376,
      "lengthNt": 144,
      "codingLengthNt": 141,
      "lengthAa": 47,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4"
      ],
      "protein": "MNENLFASFIAPTILGLPAAVLIILFPPLLIPTSKYLINNRLITTQQ"
     }
    ],
    "hiddenCount": 2,
    "noStopBeforeEnd": [],
    "mustBeAbsent": [
     {
      "strand": "-",
      "frame": -3,
      "start": 257,
      "end": 183,
      "lengthNt": 75,
      "codingLengthNt": 72
     },
     {
      "strand": "-",
      "frame": -3,
      "start": 1010,
      "end": 936,
      "lengthNt": 75,
      "codingLengthNt": 72
     },
     {
      "strand": "-",
      "frame": -3,
      "start": 1679,
      "end": 1605,
      "lengthNt": 75,
      "codingLengthNt": 72
     }
    ]
   },
   "crossCheck": {
    "biopythonTranslation": "every ORF is Biopython's translation (same table) of its nucleotides, found at its place in the frame translation; one final stop when stopCodon is set, none otherwise",
    "orffinder": {
     "used": true,
     "tool": "NCBI ORFfinder 0.4.3",
     "files": [
      "pipeline/sequence-toolkit/orffinder/mt-atp8-atp6-cox3.g1.s0.nf.fa",
      "pipeline/sequence-toolkit/orffinder/mt-atp8-atp6-cox3.g1.s0.nt.fa"
     ],
     "commands": [
      "ORFfinder -in <fasta> -g 1 -s 0 -ml 75 -strand both -outfmt 0 -n f -out <out>",
      "ORFfinder -in <fasta> -g 1 -s 0 -ml 75 -strand both -outfmt 0 -n t -out <out>"
     ],
     "allOrfsAgree": true,
     "shownByDefaultAgree": true,
     "compared": "start, end and protein of every ORF (-n f) and of the ORFs shown by default (-n t); ORFfinder's 'partial' equals stopCodon null or startsAtFrameStart"
    }
   },
   "method": "ORF rules of the CSO ruling of 6 October 2026, as about.rules states them",
   "oracle": "independent scan in reference.py (scan_orfs), cross-checked against Biopython translations and NCBI ORFfinder",
   "source": "pipeline/sequence-toolkit/reference.py (orf)",
   "oracleVersion": "reference.py sha256 1bc66633d1a7; Biopython 1.88",
   "recordedOn": "2026-10-06",
   "notes": []
  },
  {
   "id": "mt-atp8-atp6-cox3.t1.alternativeStarts",
   "input": {
    "sequenceId": "mt-atp8-atp6-cox3",
    "table": 1,
    "startCodons": "alternativeStarts",
    "startCodonList": [
     "ATG",
     "CTG",
     "TTG"
    ],
    "defaultSetting": false,
    "minimumCodingLengthNt": 75
   },
   "expected": {
    "main": [
     {
      "id": "orf1",
      "strand": "-",
      "frame": -1,
      "start": 139,
      "end": 62,
      "lengthNt": 78,
      "codingLengthNt": 75,
      "lengthAa": 25,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MRNSVRSMGVIMVGHTVVFSWGISL"
     },
     {
      "id": "orf2",
      "strand": "+",
      "frame": 3,
      "start": 72,
      "end": 224,
      "lengthNt": 153,
      "codingLengthNt": 150,
      "lengthAa": 50,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MPQLNTTVWPTIITPILLTLFLITQLKILNTNYHLPPSPKPIKIKNYNKP"
     },
     {
      "id": "orf4",
      "strand": "-",
      "frame": -2,
      "start": 462,
      "end": 139,
      "lengthNt": 324,
      "codingLengthNt": 321,
      "lengthAa": 107,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MIKDTSIRDQVRPLVLCMVIICFEVSLISHCWVVISRLLMRYLEVGINRGGNRMISTAAGRPRIVGAMNEANRFSFILVLRVCYNFLFLWALVREVGGSLCLIFLVG"
     },
     {
      "id": "orf6",
      "strand": "-",
      "frame": -2,
      "start": 684,
      "end": 499,
      "lengthNt": 186,
      "codingLengthNt": 183,
      "lengthAa": 61,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MSRLMVSIITSMGIRGVGVPCGKKWARAFLILERKPIITVPAHKGMAMARFIDSWVVGVNE"
     },
     {
      "id": "orf7",
      "strand": "-",
      "frame": -2,
      "start": 807,
      "end": 685,
      "lengthNt": 123,
      "codingLengthNt": 120,
      "lengthAa": 40,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MISVEGRLMVDIARVALPIRCMSRWPAVMLAVRRTARAIG"
     },
     {
      "id": "orf8",
      "strand": "+",
      "frame": 2,
      "start": 698,
      "end": 913,
      "lengthNt": 216,
      "codingLengthNt": 213,
      "lengthAa": 71,
      "startCodon": "CTG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MAVRLTANITAGHLLMHLIGSATLAISTINLPSTLIIFTILILLTILEIAVALIQAYVFTLLVSLYLHDNT"
     },
     {
      "id": "orf9",
      "strand": "-",
      "frame": -1,
      "start": 982,
      "end": 881,
      "lengthNt": 102,
      "codingLengthNt": 99,
      "lengthAa": 33,
      "startCodon": "CTG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MRGPLLGVMGWVLLYDRHVIGGSLCVVVQVEAY"
     },
     {
      "id": "orf10",
      "strand": "+",
      "frame": 3,
      "start": 957,
      "end": 1361,
      "lengthNt": 405,
      "codingLengthNt": 402,
      "lengthAa": 134,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MTPNRGPLSPPNDLRPSHVISLPLHNAPHTRPTNQHTNHIPMMARCNTRKHIPRPPHTTCPKRPSIRDNPIYYLRSFFLRRIFLSLLPLQPSPYPPIRRALAPNRHHPAKSPRSPTPKHIRITRIRSINHLSSP"
     },
     {
      "id": "orf11",
      "strand": "+",
      "frame": 1,
      "start": 1399,
      "end": 1632,
      "lengthNt": 234,
      "codingLengthNt": 231,
      "lengthAa": 77,
      "startCodon": "CTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MLITILLGLYFTLLQASEYFESPFTISDGIYGSTFFVATGFHGLHVIIGSTFLTICFIRQLIFHFTSKHHFGFEAAA"
     }
    ],
    "nestedHidden": [
     {
      "id": "orf3",
      "strand": "+",
      "frame": 2,
      "start": 95,
      "end": 214,
      "lengthNt": 120,
      "codingLengthNt": 117,
      "lengthAa": 39,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MAHHNYPHTPYTIPHHPTKNIKHKLPPTSLTKAHKNKKL"
     },
     {
      "id": "orf5",
      "strand": "+",
      "frame": 2,
      "start": 221,
      "end": 376,
      "lengthNt": 156,
      "codingLengthNt": 153,
      "lengthAa": 51,
      "startCodon": "CTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4"
      ],
      "protein": "MRTKMNENLFASFIAPTILGLPAAVLIILFPPLLIPTSKYLINNRLITTQQ"
     }
    ],
    "hiddenCount": 2,
    "noStopBeforeEnd": [
     {
      "id": "orf12",
      "strand": "+",
      "frame": 3,
      "start": 1563,
      "end": 1694,
      "lengthNt": 132,
      "codingLengthNt": 132,
      "lengthAa": 44,
      "startCodon": "CTG",
      "stopCodon": null,
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MLHPPTNISLYIQTSLWLRSRRLILAFCRCGLTISVCLHLLMRV"
     }
    ],
    "mustBeAbsent": [
     {
      "strand": "-",
      "frame": -3,
      "start": 257,
      "end": 183,
      "lengthNt": 75,
      "codingLengthNt": 72
     },
     {
      "strand": "-",
      "frame": -3,
      "start": 1010,
      "end": 936,
      "lengthNt": 75,
      "codingLengthNt": 72
     },
     {
      "strand": "-",
      "frame": -2,
      "start": 1140,
      "end": 1066,
      "lengthNt": 75,
      "codingLengthNt": 72
     },
     {
      "strand": "-",
      "frame": -3,
      "start": 1679,
      "end": 1605,
      "lengthNt": 75,
      "codingLengthNt": 72
     }
    ]
   },
   "crossCheck": {
    "biopythonTranslation": "every ORF is Biopython's translation (same table) of its nucleotides, found at its place in the frame translation; one final stop when stopCodon is set, none otherwise",
    "orffinder": {
     "used": true,
     "tool": "NCBI ORFfinder 0.4.3",
     "files": [
      "pipeline/sequence-toolkit/orffinder/mt-atp8-atp6-cox3.g1.s1.nf.fa",
      "pipeline/sequence-toolkit/orffinder/mt-atp8-atp6-cox3.g1.s1.nt.fa"
     ],
     "commands": [
      "ORFfinder -in <fasta> -g 1 -s 1 -ml 75 -strand both -outfmt 0 -n f -out <out>",
      "ORFfinder -in <fasta> -g 1 -s 1 -ml 75 -strand both -outfmt 0 -n t -out <out>"
     ],
     "allOrfsAgree": true,
     "shownByDefaultAgree": true,
     "compared": "start, end and protein of every ORF (-n f) and of the ORFs shown by default (-n t); ORFfinder's 'partial' equals stopCodon null or startsAtFrameStart"
    }
   },
   "method": "ORF rules of the CSO ruling of 6 October 2026, as about.rules states them",
   "oracle": "independent scan in reference.py (scan_orfs), cross-checked against Biopython translations and NCBI ORFfinder",
   "source": "pipeline/sequence-toolkit/reference.py (orf)",
   "oracleVersion": "reference.py sha256 1bc66633d1a7; Biopython 1.88",
   "recordedOn": "2026-10-06",
   "notes": []
  },
  {
   "id": "mt-atp8-atp6-cox3.t2.atgOnly",
   "input": {
    "sequenceId": "mt-atp8-atp6-cox3",
    "table": 2,
    "startCodons": "atgOnly",
    "startCodonList": [
     "ATG"
    ],
    "defaultSetting": true,
    "minimumCodingLengthNt": 75
   },
   "expected": {
    "main": [
     {
      "id": "orf1",
      "strand": "+",
      "frame": 3,
      "start": 72,
      "end": 278,
      "lengthNt": 207,
      "codingLengthNt": 204,
      "lengthAa": 68,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MPQLNTTVWPTMITPMLLTLFLITQLKMLNTNYHLPPSPKPMKMKNYNKPWEPKWTKICSLHSLPPQS"
     },
     {
      "id": "orf4",
      "strand": "+",
      "frame": 2,
      "start": 233,
      "end": 913,
      "lengthNt": 681,
      "codingLengthNt": 678,
      "lengthAa": 226,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MNENLFASFIAPTILGLPAAVLIILFPPLLIPTSKYLINNRLITTQQWLIKLTSKQMMTMHNTKGRTWSLMLVSLIIFIATTNLLGLLPHSFTPTTQLSMNLAMAIPLWAGTVIMGFRSKIKNALAHFLPQGTPTPLIPMLVIIETISLLIQPMALAVRLTANITAGHLLMHLIGSATLAMSTINLPSTLIIFTILILLTILEIAVALIQAYVFTLLVSLYLHDNT"
     }
    ],
    "nestedHidden": [
     {
      "id": "orf2",
      "strand": "+",
      "frame": 2,
      "start": 95,
      "end": 214,
      "lengthNt": 120,
      "codingLengthNt": 117,
      "lengthAa": 39,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf1"
      ],
      "protein": "MAHHNYPHTPYTIPHHPTKNIKHKLPPTSLTKAHKNKKL"
     },
     {
      "id": "orf3",
      "strand": "-",
      "frame": -3,
      "start": 257,
      "end": 177,
      "lengthNt": 81,
      "codingLengthNt": 78,
      "lengthAa": 26,
      "startCodon": "ATG",
      "stopCodon": "AGG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf1"
      ],
      "protein": "MKRTDFRSFWFSGFVMIFYFYGLWWG"
     },
     {
      "id": "orf6",
      "strand": "-",
      "frame": -1,
      "start": 1111,
      "end": 995,
      "lengthNt": 117,
      "codingLengthNt": 114,
      "lengthAa": 38,
      "startCodon": "ATG",
      "stopCodon": "AGG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf5"
      ],
      "protein": "MCFLVLHRAIIGMWLVCWLVGLVWGALWSGSEITWLGR"
     },
     {
      "id": "orf7",
      "strand": "-",
      "frame": -1,
      "start": 1330,
      "end": 1235,
      "lengthNt": 96,
      "codingLengthNt": 93,
      "lengthAa": 31,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf5"
      ],
      "protein": "MRVMRMCLGVGLLGDLAGWCLLGASALLIGG"
     }
    ],
    "hiddenCount": 4,
    "noStopBeforeEnd": [
     {
      "id": "orf5",
      "strand": "+",
      "frame": 1,
      "start": 913,
      "end": 1695,
      "lengthNt": 783,
      "codingLengthNt": 783,
      "lengthAa": 261,
      "startCodon": "ATG",
      "stopCodon": null,
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MTHQSHAYHMVKPSPWPLTGALSALLMTSGLAMWFHFHSMTLLMLGLLTNTLTMYQWWRDVTRESTYQGHHTPPVQKGLRYGMILFITSEVFFFAGFFWAFYHSSLAPTPQLGGHWPPTGITPLNPLEVPLLNTSVLLASGVSITWAHHSLMENNRNQMIQALLITILLGLYFTLLQASEYFESPFTISDGIYGSTFFVATGFHGLHVIIGSTFLTICFIRQLMFHFTSKHHFGFEAAAWYWHFVDVVWLFLYVSIYWWGS"
     }
    ],
    "mustBeAbsent": []
   },
   "crossCheck": {
    "biopythonTranslation": "every ORF is Biopython's translation (same table) of its nucleotides, found at its place in the frame translation; one final stop when stopCodon is set, none otherwise",
    "orffinder": {
     "used": true,
     "tool": "NCBI ORFfinder 0.4.3",
     "files": [
      "pipeline/sequence-toolkit/orffinder/mt-atp8-atp6-cox3.g2.s0.nf.fa",
      "pipeline/sequence-toolkit/orffinder/mt-atp8-atp6-cox3.g2.s0.nt.fa"
     ],
     "commands": [
      "ORFfinder -in <fasta> -g 2 -s 0 -ml 75 -strand both -outfmt 0 -n f -out <out>",
      "ORFfinder -in <fasta> -g 2 -s 0 -ml 75 -strand both -outfmt 0 -n t -out <out>"
     ],
     "allOrfsAgree": true,
     "shownByDefaultAgree": true,
     "compared": "start, end and protein of every ORF (-n f) and of the ORFs shown by default (-n t); ORFfinder's 'partial' equals stopCodon null or startsAtFrameStart"
    }
   },
   "method": "ORF rules of the CSO ruling of 6 October 2026, as about.rules states them",
   "oracle": "independent scan in reference.py (scan_orfs), cross-checked against Biopython translations and NCBI ORFfinder",
   "source": "pipeline/sequence-toolkit/reference.py (orf)",
   "oracleVersion": "reference.py sha256 1bc66633d1a7; Biopython 1.88",
   "recordedOn": "2026-10-06",
   "notes": []
  },
  {
   "id": "mt-atp8-atp6-cox3.t2.alternativeStarts",
   "input": {
    "sequenceId": "mt-atp8-atp6-cox3",
    "table": 2,
    "startCodons": "alternativeStarts",
    "startCodonList": [
     "ATA",
     "ATC",
     "ATG",
     "ATT",
     "GTG"
    ],
    "defaultSetting": false,
    "minimumCodingLengthNt": 75
   },
   "expected": {
    "main": [
     {
      "id": "orf1",
      "strand": "+",
      "frame": 3,
      "start": 72,
      "end": 278,
      "lengthNt": 207,
      "codingLengthNt": 204,
      "lengthAa": 68,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MPQLNTTVWPTMITPMLLTLFLITQLKMLNTNYHLPPSPKPMKMKNYNKPWEPKWTKICSLHSLPPQS"
     },
     {
      "id": "orf3",
      "strand": "-",
      "frame": -3,
      "start": 320,
      "end": 177,
      "lengthNt": 144,
      "codingLengthNt": 141,
      "lengthAa": 47,
      "startCodon": "ATA",
      "stopCodon": "AGG",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MEGEMEWSVLRRVGLGLWGQWMKRTDFRSFWFSGFVMIFYFYGLWWG"
     },
     {
      "id": "orf4",
      "strand": "+",
      "frame": 2,
      "start": 233,
      "end": 913,
      "lengthNt": 681,
      "codingLengthNt": 678,
      "lengthAa": 226,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MNENLFASFIAPTILGLPAAVLIILFPPLLIPTSKYLINNRLITTQQWLIKLTSKQMMTMHNTKGRTWSLMLVSLIIFIATTNLLGLLPHSFTPTTQLSMNLAMAIPLWAGTVIMGFRSKIKNALAHFLPQGTPTPLIPMLVIIETISLLIQPMALAVRLTANITAGHLLMHLIGSATLAMSTINLPSTLIIFTILILLTILEIAVALIQAYVFTLLVSLYLHDNT"
     }
    ],
    "nestedHidden": [
     {
      "id": "orf2",
      "strand": "+",
      "frame": 2,
      "start": 95,
      "end": 214,
      "lengthNt": 120,
      "codingLengthNt": 117,
      "lengthAa": 39,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf1"
      ],
      "protein": "MAHHNYPHTPYTIPHHPTKNIKHKLPPTSLTKAHKNKKL"
     },
     {
      "id": "orf5",
      "strand": "+",
      "frame": 1,
      "start": 307,
      "end": 423,
      "lengthNt": 117,
      "codingLengthNt": 114,
      "lengthAa": 38,
      "startCodon": "ATT",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4"
      ],
      "protein": "MSPSIDPHLQMSHQQPTNHHPTMTNQTNLKTNDNHTQH"
     },
     {
      "id": "orf6",
      "strand": "-",
      "frame": -2,
      "start": 420,
      "end": 340,
      "lengthNt": 81,
      "codingLengthNt": 78,
      "lengthAa": 26,
      "startCodon": "GTG",
      "stopCodon": "AGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4",
       "orf5"
      ],
      "protein": "MLCMVIICFEVSLISHCWVVISRLLM"
     },
     {
      "id": "orf8",
      "strand": "-",
      "frame": -1,
      "start": 1168,
      "end": 995,
      "lengthNt": 174,
      "codingLengthNt": 171,
      "lengthAa": 57,
      "startCodon": "ATA",
      "stopCodon": "AGG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf7"
      ],
      "protein": "MGLSRIEGLFGQVVCGGLGMCFLVLHRAIIGMWLVCWLVGLVWGALWSGSEITWLGR"
     },
     {
      "id": "orf9",
      "strand": "-",
      "frame": -3,
      "start": 1127,
      "end": 1050,
      "lengthNt": 78,
      "codingLengthNt": 75,
      "lengthAa": 25,
      "startCodon": "GTG",
      "stopCodon": "AGG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf7",
       "orf8"
      ],
      "protein": "MWWPWYVLSRVTSRHHWYMVSVLVS"
     },
     {
      "id": "orf10",
      "strand": "-",
      "frame": -1,
      "start": 1339,
      "end": 1235,
      "lengthNt": 105,
      "codingLengthNt": 102,
      "lengthAa": 34,
      "startCodon": "ATA",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf7"
      ],
      "protein": "MLLMRVMRMCLGVGLLGDLAGWCLLGASALLIGG"
     },
     {
      "id": "orf11",
      "strand": "+",
      "frame": 2,
      "start": 1427,
      "end": 1510,
      "lengthNt": 84,
      "codingLengthNt": 81,
      "lengthAa": 27,
      "startCodon": "ATT",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf7"
      ],
      "protein": "MLPSYKPQSTSSLPSPFPTASTAQHFL"
     }
    ],
    "hiddenCount": 7,
    "noStopBeforeEnd": [
     {
      "id": "orf7",
      "strand": "+",
      "frame": 1,
      "start": 910,
      "end": 1695,
      "lengthNt": 786,
      "codingLengthNt": 786,
      "lengthAa": 262,
      "startCodon": "ATA",
      "stopCodon": null,
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MMTHQSHAYHMVKPSPWPLTGALSALLMTSGLAMWFHFHSMTLLMLGLLTNTLTMYQWWRDVTRESTYQGHHTPPVQKGLRYGMILFITSEVFFFAGFFWAFYHSSLAPTPQLGGHWPPTGITPLNPLEVPLLNTSVLLASGVSITWAHHSLMENNRNQMIQALLITILLGLYFTLLQASEYFESPFTISDGIYGSTFFVATGFHGLHVIIGSTFLTICFIRQLMFHFTSKHHFGFEAAAWYWHFVDVVWLFLYVSIYWWGS"
     }
    ],
    "mustBeAbsent": [
     {
      "strand": "+",
      "frame": 1,
      "start": 505,
      "end": 579,
      "lengthNt": 75,
      "codingLengthNt": 72
     }
    ]
   },
   "crossCheck": {
    "biopythonTranslation": "every ORF is Biopython's translation (same table) of its nucleotides, found at its place in the frame translation; one final stop when stopCodon is set, none otherwise",
    "orffinder": {
     "used": true,
     "tool": "NCBI ORFfinder 0.4.3",
     "files": [
      "pipeline/sequence-toolkit/orffinder/mt-atp8-atp6-cox3.g2.s1.nf.fa",
      "pipeline/sequence-toolkit/orffinder/mt-atp8-atp6-cox3.g2.s1.nt.fa"
     ],
     "commands": [
      "ORFfinder -in <fasta> -g 2 -s 1 -ml 75 -strand both -outfmt 0 -n f -out <out>",
      "ORFfinder -in <fasta> -g 2 -s 1 -ml 75 -strand both -outfmt 0 -n t -out <out>"
     ],
     "allOrfsAgree": true,
     "shownByDefaultAgree": true,
     "compared": "start, end and protein of every ORF (-n f) and of the ORFs shown by default (-n t); ORFfinder's 'partial' equals stopCodon null or startsAtFrameStart"
    }
   },
   "method": "ORF rules of the CSO ruling of 6 October 2026, as about.rules states them",
   "oracle": "independent scan in reference.py (scan_orfs), cross-checked against Biopython translations and NCBI ORFfinder",
   "source": "pipeline/sequence-toolkit/reference.py (orf)",
   "oracleVersion": "reference.py sha256 1bc66633d1a7; Biopython 1.88",
   "recordedOn": "2026-10-06",
   "notes": []
  },
  {
   "id": "mt-atp8-atp6-cox3.t11.atgOnly",
   "input": {
    "sequenceId": "mt-atp8-atp6-cox3",
    "table": 11,
    "startCodons": "atgOnly",
    "startCodonList": [
     "ATG"
    ],
    "defaultSetting": true,
    "minimumCodingLengthNt": 75
   },
   "expected": {
    "main": [
     {
      "id": "orf1",
      "strand": "-",
      "frame": -1,
      "start": 139,
      "end": 62,
      "lengthNt": 78,
      "codingLengthNt": 75,
      "lengthAa": 25,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MRNSVRSMGVIMVGHTVVFSWGISL"
     },
     {
      "id": "orf2",
      "strand": "+",
      "frame": 3,
      "start": 72,
      "end": 224,
      "lengthNt": 153,
      "codingLengthNt": 150,
      "lengthAa": 50,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MPQLNTTVWPTIITPILLTLFLITQLKILNTNYHLPPSPKPIKIKNYNKP"
     },
     {
      "id": "orf4",
      "strand": "-",
      "frame": -2,
      "start": 462,
      "end": 139,
      "lengthNt": 324,
      "codingLengthNt": 321,
      "lengthAa": 107,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MIKDTSIRDQVRPLVLCMVIICFEVSLISHCWVVISRLLMRYLEVGINRGGNRMISTAAGRPRIVGAMNEANRFSFILVLRVCYNFLFLWALVREVGGSLCLIFLVG"
     },
     {
      "id": "orf6",
      "strand": "-",
      "frame": -2,
      "start": 684,
      "end": 499,
      "lengthNt": 186,
      "codingLengthNt": 183,
      "lengthAa": 61,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MSRLMVSIITSMGIRGVGVPCGKKWARAFLILERKPIITVPAHKGMAMARFIDSWVVGVNE"
     },
     {
      "id": "orf7",
      "strand": "-",
      "frame": -2,
      "start": 807,
      "end": 685,
      "lengthNt": 123,
      "codingLengthNt": 120,
      "lengthAa": 40,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MISVEGRLMVDIARVALPIRCMSRWPAVMLAVRRTARAIG"
     },
     {
      "id": "orf8",
      "strand": "+",
      "frame": 2,
      "start": 743,
      "end": 913,
      "lengthNt": 171,
      "codingLengthNt": 168,
      "lengthAa": 56,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MHLIGSATLAISTINLPSTLIIFTILILLTILEIAVALIQAYVFTLLVSLYLHDNT"
     },
     {
      "id": "orf9",
      "strand": "-",
      "frame": -1,
      "start": 958,
      "end": 881,
      "lengthNt": 78,
      "codingLengthNt": 75,
      "lengthAa": 25,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MGWVLLYDRHVIGGSLCVVVQVEAY"
     },
     {
      "id": "orf10",
      "strand": "+",
      "frame": 3,
      "start": 957,
      "end": 1361,
      "lengthNt": 405,
      "codingLengthNt": 402,
      "lengthAa": 134,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MTPNRGPLSPPNDLRPSHVISLPLHNAPHTRPTNQHTNHIPMMARCNTRKHIPRPPHTTCPKRPSIRDNPIYYLRSFFLRRIFLSLLPLQPSPYPPIRRALAPNRHHPAKSPRSPTPKHIRITRIRSINHLSSP"
     }
    ],
    "nestedHidden": [
     {
      "id": "orf3",
      "strand": "+",
      "frame": 2,
      "start": 95,
      "end": 214,
      "lengthNt": 120,
      "codingLengthNt": 117,
      "lengthAa": 39,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MAHHNYPHTPYTIPHHPTKNIKHKLPPTSLTKAHKNKKL"
     },
     {
      "id": "orf5",
      "strand": "+",
      "frame": 2,
      "start": 233,
      "end": 376,
      "lengthNt": 144,
      "codingLengthNt": 141,
      "lengthAa": 47,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4"
      ],
      "protein": "MNENLFASFIAPTILGLPAAVLIILFPPLLIPTSKYLINNRLITTQQ"
     }
    ],
    "hiddenCount": 2,
    "noStopBeforeEnd": [],
    "mustBeAbsent": [
     {
      "strand": "-",
      "frame": -3,
      "start": 257,
      "end": 183,
      "lengthNt": 75,
      "codingLengthNt": 72
     },
     {
      "strand": "-",
      "frame": -3,
      "start": 1010,
      "end": 936,
      "lengthNt": 75,
      "codingLengthNt": 72
     },
     {
      "strand": "-",
      "frame": -3,
      "start": 1679,
      "end": 1605,
      "lengthNt": 75,
      "codingLengthNt": 72
     }
    ]
   },
   "crossCheck": {
    "biopythonTranslation": "every ORF is Biopython's translation (same table) of its nucleotides, found at its place in the frame translation; one final stop when stopCodon is set, none otherwise",
    "orffinder": {
     "used": true,
     "tool": "NCBI ORFfinder 0.4.3",
     "files": [
      "pipeline/sequence-toolkit/orffinder/mt-atp8-atp6-cox3.g11.s0.nf.fa",
      "pipeline/sequence-toolkit/orffinder/mt-atp8-atp6-cox3.g11.s0.nt.fa"
     ],
     "commands": [
      "ORFfinder -in <fasta> -g 11 -s 0 -ml 75 -strand both -outfmt 0 -n f -out <out>",
      "ORFfinder -in <fasta> -g 11 -s 0 -ml 75 -strand both -outfmt 0 -n t -out <out>"
     ],
     "allOrfsAgree": true,
     "shownByDefaultAgree": true,
     "compared": "start, end and protein of every ORF (-n f) and of the ORFs shown by default (-n t); ORFfinder's 'partial' equals stopCodon null or startsAtFrameStart"
    }
   },
   "method": "ORF rules of the CSO ruling of 6 October 2026, as about.rules states them",
   "oracle": "independent scan in reference.py (scan_orfs), cross-checked against Biopython translations and NCBI ORFfinder",
   "source": "pipeline/sequence-toolkit/reference.py (orf)",
   "oracleVersion": "reference.py sha256 1bc66633d1a7; Biopython 1.88",
   "recordedOn": "2026-10-06",
   "notes": []
  },
  {
   "id": "mt-atp8-atp6-cox3.t11.alternativeStarts",
   "input": {
    "sequenceId": "mt-atp8-atp6-cox3",
    "table": 11,
    "startCodons": "alternativeStarts",
    "startCodonList": [
     "ATA",
     "ATC",
     "ATG",
     "ATT",
     "CTG",
     "GTG",
     "TTG"
    ],
    "defaultSetting": false,
    "minimumCodingLengthNt": 75
   },
   "expected": {
    "main": [
     {
      "id": "orf1",
      "strand": "-",
      "frame": -1,
      "start": 163,
      "end": 62,
      "lengthNt": 102,
      "codingLengthNt": 99,
      "lengthAa": 33,
      "startCodon": "GTG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MFNIFSWVMRNSVRSMGVIMVGHTVVFSWGISL"
     },
     {
      "id": "orf2",
      "strand": "+",
      "frame": 3,
      "start": 72,
      "end": 224,
      "lengthNt": 153,
      "codingLengthNt": 150,
      "lengthAa": 50,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MPQLNTTVWPTIITPILLTLFLITQLKILNTNYHLPPSPKPIKIKNYNKP"
     },
     {
      "id": "orf4",
      "strand": "-",
      "frame": -2,
      "start": 474,
      "end": 139,
      "lengthNt": 336,
      "codingLengthNt": 333,
      "lengthAa": 111,
      "startCodon": "GTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MAIKMIKDTSIRDQVRPLVLCMVIICFEVSLISHCWVVISRLLMRYLEVGINRGGNRMISTAAGRPRIVGAMNEANRFSFILVLRVCYNFLFLWALVREVGGSLCLIFLVG"
     },
     {
      "id": "orf7",
      "strand": "+",
      "frame": 2,
      "start": 443,
      "end": 559,
      "lengthNt": 117,
      "codingLengthNt": 114,
      "lengthAa": 38,
      "startCodon": "ATA",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MLVSLIIFIATTNLLGLLPHSFTPTTQLSINLAMAIPL"
     },
     {
      "id": "orf8",
      "strand": "-",
      "frame": -2,
      "start": 684,
      "end": 499,
      "lengthNt": 186,
      "codingLengthNt": 183,
      "lengthAa": 61,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MSRLMVSIITSMGIRGVGVPCGKKWARAFLILERKPIITVPAHKGMAMARFIDSWVVGVNE"
     },
     {
      "id": "orf10",
      "strand": "+",
      "frame": 2,
      "start": 569,
      "end": 913,
      "lengthNt": 345,
      "codingLengthNt": 342,
      "lengthAa": 114,
      "startCodon": "GTG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MIIGFRSKIKNALAHFLPQGTPTPLIPILVIIETISLLIQPIALAVRLTANITAGHLLMHLIGSATLAISTINLPSTLIIFTILILLTILEIAVALIQAYVFTLLVSLYLHDNT"
     },
     {
      "id": "orf12",
      "strand": "-",
      "frame": -1,
      "start": 1015,
      "end": 881,
      "lengthNt": 135,
      "codingLengthNt": 132,
      "lengthAa": 44,
      "startCodon": "ATC",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MTWLGRRSLGGLRGPLLGVMGWVLLYDRHVIGGSLCVVVQVEAY"
     },
     {
      "id": "orf13",
      "strand": "+",
      "frame": 3,
      "start": 924,
      "end": 1361,
      "lengthNt": 438,
      "codingLengthNt": 435,
      "lengthAa": 145,
      "startCodon": "ATC",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MTCLSYSKTQPMTPNRGPLSPPNDLRPSHVISLPLHNAPHTRPTNQHTNHIPMMARCNTRKHIPRPPHTTCPKRPSIRDNPIYYLRSFFLRRIFLSLLPLQPSPYPPIRRALAPNRHHPAKSPRSPTPKHIRITRIRSINHLSSP"
     },
     {
      "id": "orf18",
      "strand": "+",
      "frame": 1,
      "start": 1366,
      "end": 1632,
      "lengthNt": 267,
      "codingLengthNt": 264,
      "lengthAa": 88,
      "startCodon": "ATA",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MENNRNQIIQALLITILLGLYFTLLQASEYFESPFTISDGIYGSTFFVATGFHGLHVIIGSTFLTICFIRQLIFHFTSKHHFGFEAAA"
     }
    ],
    "nestedHidden": [
     {
      "id": "orf3",
      "strand": "+",
      "frame": 2,
      "start": 95,
      "end": 214,
      "lengthNt": 120,
      "codingLengthNt": 117,
      "lengthAa": 39,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MAHHNYPHTPYTIPHHPTKNIKHKLPPTSLTKAHKNKKL"
     },
     {
      "id": "orf5",
      "strand": "+",
      "frame": 1,
      "start": 208,
      "end": 423,
      "lengthNt": 216,
      "codingLengthNt": 213,
      "lengthAa": 71,
      "startCodon": "ATT",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4"
      ],
      "protein": "MITNPENQNERKSVRFIHCPHNPRPTRRSTDHSISPSIDPHLQISHQQPTNHHPTMTNQTNLKTNDNHTQH"
     },
     {
      "id": "orf6",
      "strand": "+",
      "frame": 2,
      "start": 221,
      "end": 376,
      "lengthNt": 156,
      "codingLengthNt": 153,
      "lengthAa": 51,
      "startCodon": "CTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4",
       "orf5"
      ],
      "protein": "MRTKMNENLFASFIAPTILGLPAAVLIILFPPLLIPTSKYLINNRLITTQQ"
     },
     {
      "id": "orf9",
      "strand": "+",
      "frame": 1,
      "start": 505,
      "end": 591,
      "lengthNt": 87,
      "codingLengthNt": 84,
      "lengthAa": 28,
      "startCodon": "ATT",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf8"
      ],
      "protein": "MYTNHPTIYKPSHGHPLMSGHSDYRLSL"
     },
     {
      "id": "orf11",
      "strand": "-",
      "frame": -2,
      "start": 858,
      "end": 685,
      "lengthNt": 174,
      "codingLengthNt": 171,
      "lengthAa": 57,
      "startCodon": "ATT",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf10"
      ],
      "protein": "MKATAISRIVSRIRIVKMISVEGRLMVDIARVALPIRCMSRWPAVMLAVRRTARAIG"
     },
     {
      "id": "orf14",
      "strand": "-",
      "frame": -3,
      "start": 1172,
      "end": 1017,
      "lengthNt": 156,
      "codingLengthNt": 153,
      "lengthAa": 51,
      "startCodon": "ATA",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf13"
      ],
      "protein": "MNRIIPYRRPFWTGGVWWPWYVLSRVTSRHHWYMVSVLVSRPSMRSVMEWK"
     },
     {
      "id": "orf15",
      "strand": "-",
      "frame": -1,
      "start": 1168,
      "end": 1040,
      "lengthNt": 129,
      "codingLengthNt": 126,
      "lengthAa": 42,
      "startCodon": "ATA",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf13",
       "orf14"
      ],
      "protein": "MGLSRIEGLFGQVVCGGLGMCFLVLHRAIIGIWLVCWLVGLV"
     },
     {
      "id": "orf16",
      "strand": "-",
      "frame": -3,
      "start": 1346,
      "end": 1215,
      "lengthNt": 132,
      "codingLengthNt": 129,
      "lengthAa": 43,
      "startCodon": "GTG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf13"
      ],
      "protein": "MIDTPDASNTDVFRSGTSRGFSGVMPVGGQCPPNWGVGARLEW"
     },
     {
      "id": "orf17",
      "strand": "+",
      "frame": 1,
      "start": 1273,
      "end": 1350,
      "lengthNt": 78,
      "codingLengthNt": 75,
      "lengthAa": 25,
      "startCodon": "ATC",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf13"
      ],
      "protein": "MTPLNPLEVPLLNTSVLLASGVSIT"
     },
     {
      "id": "orf19",
      "strand": "+",
      "frame": 2,
      "start": 1427,
      "end": 1510,
      "lengthNt": 84,
      "codingLengthNt": 81,
      "lengthAa": 27,
      "startCodon": "ATT",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf18"
      ],
      "protein": "MLPSYKPQSTSSLPSPFPTASTAQHFL"
     },
     {
      "id": "orf21",
      "strand": "-",
      "frame": -1,
      "start": 1687,
      "end": 1592,
      "lengthNt": 96,
      "codingLengthNt": 93,
      "lengthAa": 31,
      "startCodon": "ATC",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf20"
      ],
      "protein": "MNRWRHTEIVKPHLQNASIRRRLRSQSDVWM"
     }
    ],
    "hiddenCount": 11,
    "noStopBeforeEnd": [
     {
      "id": "orf20",
      "strand": "+",
      "frame": 3,
      "start": 1500,
      "end": 1694,
      "lengthNt": 195,
      "codingLengthNt": 195,
      "lengthAa": 65,
      "startCodon": "ATT",
      "stopCodon": null,
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MFCSHRLPRTSRHYWLNFPHYLLHPPTNISLYIQTSLWLRSRRLILAFCRCGLTISVCLHLLMRV"
     }
    ],
    "mustBeAbsent": [
     {
      "strand": "-",
      "frame": -3,
      "start": 257,
      "end": 183,
      "lengthNt": 75,
      "codingLengthNt": 72
     },
     {
      "strand": "-",
      "frame": -3,
      "start": 1010,
      "end": 936,
      "lengthNt": 75,
      "codingLengthNt": 72
     },
     {
      "strand": "-",
      "frame": -2,
      "start": 1140,
      "end": 1066,
      "lengthNt": 75,
      "codingLengthNt": 72
     },
     {
      "strand": "-",
      "frame": -3,
      "start": 1679,
      "end": 1605,
      "lengthNt": 75,
      "codingLengthNt": 72
     }
    ]
   },
   "crossCheck": {
    "biopythonTranslation": "every ORF is Biopython's translation (same table) of its nucleotides, found at its place in the frame translation; one final stop when stopCodon is set, none otherwise",
    "orffinder": {
     "used": true,
     "tool": "NCBI ORFfinder 0.4.3",
     "files": [
      "pipeline/sequence-toolkit/orffinder/mt-atp8-atp6-cox3.g11.s1.nf.fa",
      "pipeline/sequence-toolkit/orffinder/mt-atp8-atp6-cox3.g11.s1.nt.fa"
     ],
     "commands": [
      "ORFfinder -in <fasta> -g 11 -s 1 -ml 75 -strand both -outfmt 0 -n f -out <out>",
      "ORFfinder -in <fasta> -g 11 -s 1 -ml 75 -strand both -outfmt 0 -n t -out <out>"
     ],
     "allOrfsAgree": true,
     "shownByDefaultAgree": true,
     "compared": "start, end and protein of every ORF (-n f) and of the ORFs shown by default (-n t); ORFfinder's 'partial' equals stopCodon null or startsAtFrameStart"
    }
   },
   "method": "ORF rules of the CSO ruling of 6 October 2026, as about.rules states them",
   "oracle": "independent scan in reference.py (scan_orfs), cross-checked against Biopython translations and NCBI ORFfinder",
   "source": "pipeline/sequence-toolkit/reference.py (orf)",
   "oracleVersion": "reference.py sha256 1bc66633d1a7; Biopython 1.88",
   "recordedOn": "2026-10-06",
   "notes": []
  },
  {
   "id": "ecoli-lacI.t1.atgOnly",
   "input": {
    "sequenceId": "ecoli-lacI",
    "table": 1,
    "startCodons": "atgOnly",
    "startCodonList": [
     "ATG"
    ],
    "defaultSetting": true,
    "minimumCodingLengthNt": 75
   },
   "expected": {
    "main": [
     {
      "id": "orf1",
      "strand": "+",
      "frame": 3,
      "start": 12,
      "end": 329,
      "lengthNt": 318,
      "codingLengthNt": 315,
      "lengthAa": 105,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MAQNLSRYGMIAPGRESIQGGECETSNVIRCRRVCRCLLSDRFPRGEPGQPRFCENAGKSGSGDGGAELHSQPRGTTTGGQTVVADWRCHLQSGPARAVANCRGD"
     },
     {
      "id": "orf2",
      "strand": "+",
      "frame": 1,
      "start": 202,
      "end": 1161,
      "lengthNt": 960,
      "codingLengthNt": 957,
      "lengthAa": 319,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPSTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ"
     },
     {
      "id": "orf9",
      "strand": "+",
      "frame": 3,
      "start": 918,
      "end": 1181,
      "lengthNt": 264,
      "codingLengthNt": 261,
      "lengthAa": 87,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MLYPAVNHHQTGFSPAGANQRGPLAATLSGPGGEGQSAVARLTGEKKNHPGAQYANRLSPRVGRFINAAGTTGFPTGKRAVSATQLM"
     },
     {
      "id": "orf10",
      "strand": "-",
      "frame": -3,
      "start": 1195,
      "end": 944,
      "lengthNt": 252,
      "codingLengthNt": 249,
      "lengthAa": 83,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MSELTHINCVALTARFPVGKPVVPAALMNRPTRGERRFAYWAPGWFFFSPVRRATADCPSPPGPERVAASGPRWFAPAGENPV"
     },
     {
      "id": "orf11",
      "strand": "-",
      "frame": -3,
      "start": 1291,
      "end": 1211,
      "lengthNt": 81,
      "codingLengthNt": 78,
      "lengthAa": 26,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MVIAVSCVKLLSAHNSTQHTSRKHKV"
     }
    ],
    "nestedHidden": [
     {
      "id": "orf3",
      "strand": "-",
      "frame": -2,
      "start": 449,
      "end": 342,
      "lengthNt": 108,
      "codingLengthNt": 105,
      "lengthAa": 35,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MISPLTRCARRLCTAALQASTPLRSTIDTTTLAPS"
     },
     {
      "id": "orf4",
      "strand": "-",
      "frame": -2,
      "start": 545,
      "end": 453,
      "lengthNt": 93,
      "codingLengthNt": 90,
      "lengthAa": 30,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MGVWSETSRNNAGTLVQAASTAMASWSSSG"
     },
     {
      "id": "orf5",
      "strand": "+",
      "frame": 2,
      "start": 464,
      "end": 634,
      "lengthNt": 171,
      "codingLengthNt": 168,
      "lengthAa": 56,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MTRMPLLWKLPALMFRRYFLMSLTRHPSTVLFSPMKTVRDWAWSIWSHWVTSKSRC"
     },
     {
      "id": "orf6",
      "strand": "-",
      "frame": -1,
      "start": 597,
      "end": 514,
      "lengthNt": 84,
      "codingLengthNt": 81,
      "lengthAa": 27,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2",
       "orf5"
      ],
      "protein": "MLHAQSRTVFMGENNTVDGCLVRDIKK"
     },
     {
      "id": "orf7",
      "strand": "-",
      "frame": -3,
      "start": 643,
      "end": 554,
      "lengthNt": 90,
      "codingLengthNt": 87,
      "lengthAa": 29,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MGPLTARFAGDPMRPDAPRPVAYRLHGRK"
     },
     {
      "id": "orf8",
      "strand": "+",
      "frame": 2,
      "start": 779,
      "end": 889,
      "lengthNt": 111,
      "codingLengthNt": 108,
      "lengthAa": 36,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MRASFPLRCWLPTIRWRWAQCAPLPSPGCALVRISR"
     }
    ],
    "hiddenCount": 6,
    "noStopBeforeEnd": [
     {
      "id": "orf12",
      "strand": "+",
      "frame": 3,
      "start": 1284,
      "end": 1499,
      "lengthNt": 216,
      "codingLengthNt": 216,
      "lengthAa": 72,
      "startCodon": "ATG",
      "stopCodon": null,
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MTMITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPE"
     }
    ],
    "mustBeAbsent": []
   },
   "crossCheck": {
    "biopythonTranslation": "every ORF is Biopython's translation (same table) of its nucleotides, found at its place in the frame translation; one final stop when stopCodon is set, none otherwise",
    "orffinder": {
     "used": true,
     "tool": "NCBI ORFfinder 0.4.3",
     "files": [
      "pipeline/sequence-toolkit/orffinder/ecoli-lacI.g1.s0.nf.fa",
      "pipeline/sequence-toolkit/orffinder/ecoli-lacI.g1.s0.nt.fa"
     ],
     "commands": [
      "ORFfinder -in <fasta> -g 1 -s 0 -ml 75 -strand both -outfmt 0 -n f -out <out>",
      "ORFfinder -in <fasta> -g 1 -s 0 -ml 75 -strand both -outfmt 0 -n t -out <out>"
     ],
     "allOrfsAgree": true,
     "shownByDefaultAgree": true,
     "compared": "start, end and protein of every ORF (-n f) and of the ORFs shown by default (-n t); ORFfinder's 'partial' equals stopCodon null or startsAtFrameStart"
    }
   },
   "method": "ORF rules of the CSO ruling of 6 October 2026, as about.rules states them",
   "oracle": "independent scan in reference.py (scan_orfs), cross-checked against Biopython translations and NCBI ORFfinder",
   "source": "pipeline/sequence-toolkit/reference.py (orf)",
   "oracleVersion": "reference.py sha256 1bc66633d1a7; Biopython 1.88",
   "recordedOn": "2026-10-06",
   "notes": []
  },
  {
   "id": "ecoli-lacI.t1.alternativeStarts",
   "input": {
    "sequenceId": "ecoli-lacI",
    "table": 1,
    "startCodons": "alternativeStarts",
    "startCodonList": [
     "ATG",
     "CTG",
     "TTG"
    ],
    "defaultSetting": false,
    "minimumCodingLengthNt": 75
   },
   "expected": {
    "main": [
     {
      "id": "orf1",
      "strand": "+",
      "frame": 3,
      "start": 12,
      "end": 329,
      "lengthNt": 318,
      "codingLengthNt": 315,
      "lengthAa": 105,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MAQNLSRYGMIAPGRESIQGGECETSNVIRCRRVCRCLLSDRFPRGEPGQPRFCENAGKSGSGDGGAELHSQPRGTTTGGQTVVADWRCHLQSGPARAVANCRGD"
     },
     {
      "id": "orf2",
      "strand": "-",
      "frame": -1,
      "start": 471,
      "end": 94,
      "lengthNt": 378,
      "codingLengthNt": 375,
      "lengthAa": 125,
      "startCodon": "CTG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MVIQRIVNDQPTDALREKIVHRRFTGFDAASFYHRHHHAGTQLIGARFNRRDNLRRRVQGQTGGGNANQQRLFARQLLCHAVGNVIQLRHRRFHFFPRFRRNVAGLVHHAGNGLIRDTGILCDIV"
     },
     {
      "id": "orf3",
      "strand": "+",
      "frame": 1,
      "start": 202,
      "end": 1161,
      "lengthNt": 960,
      "codingLengthNt": 957,
      "lengthAa": 319,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPSTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ"
     },
     {
      "id": "orf16",
      "strand": "+",
      "frame": 3,
      "start": 918,
      "end": 1181,
      "lengthNt": 264,
      "codingLengthNt": 261,
      "lengthAa": 87,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MLYPAVNHHQTGFSPAGANQRGPLAATLSGPGGEGQSAVARLTGEKKNHPGAQYANRLSPRVGRFINAAGTTGFPTGKRAVSATQLM"
     },
     {
      "id": "orf18",
      "strand": "-",
      "frame": -3,
      "start": 1207,
      "end": 944,
      "lengthNt": 264,
      "codingLengthNt": 261,
      "lengthAa": 87,
      "startCodon": "CTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MGCLMSELTHINCVALTARFPVGKPVVPAALMNRPTRGERRFAYWAPGWFFFSPVRRATADCPSPPGPERVAASGPRWFAPAGENPV"
     },
     {
      "id": "orf20",
      "strand": "-",
      "frame": -3,
      "start": 1444,
      "end": 1211,
      "lengthNt": 234,
      "codingLengthNt": 231,
      "lengthAa": 77,
      "startCodon": "CTG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MRNCWEGRSVRASSLLRQLAKGGCAARRLSWVTPGFSQSRRCKTTASESVIMVIAVSCVKLLSAHNSTQHTSRKHKV"
     }
    ],
    "nestedHidden": [
     {
      "id": "orf4",
      "strand": "+",
      "frame": 2,
      "start": 269,
      "end": 376,
      "lengthNt": 108,
      "codingLengthNt": 105,
      "lengthAa": 35,
      "startCodon": "TTG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2",
       "orf3"
      ],
      "protein": "MALPPPVWPCTRRRKLSRRLNLAPINWVPAWWCRW"
     },
     {
      "id": "orf5",
      "strand": "-",
      "frame": -2,
      "start": 449,
      "end": 342,
      "lengthNt": 108,
      "codingLengthNt": 105,
      "lengthAa": 35,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2",
       "orf3"
      ],
      "protein": "MISPLTRCARRLCTAALQASTPLRSTIDTTTLAPS"
     },
     {
      "id": "orf6",
      "strand": "-",
      "frame": -2,
      "start": 551,
      "end": 453,
      "lengthNt": 99,
      "codingLengthNt": 96,
      "lengthAa": 32,
      "startCodon": "CTG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf3"
      ],
      "protein": "MLMGVWSETSRNNAGTLVQAASTAMASWSSSG"
     },
     {
      "id": "orf7",
      "strand": "+",
      "frame": 2,
      "start": 464,
      "end": 634,
      "lengthNt": 171,
      "codingLengthNt": 168,
      "lengthAa": 56,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf3"
      ],
      "protein": "MTRMPLLWKLPALMFRRYFLMSLTRHPSTVLFSPMKTVRDWAWSIWSHWVTSKSRC"
     },
     {
      "id": "orf8",
      "strand": "-",
      "frame": -1,
      "start": 621,
      "end": 514,
      "lengthNt": 108,
      "codingLengthNt": 105,
      "lengthAa": 35,
      "startCodon": "TTG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf3",
       "orf7"
      ],
      "protein": "MLVTQCDQMLHAQSRTVFMGENNTVDGCLVRDIKK"
     },
     {
      "id": "orf9",
      "strand": "-",
      "frame": -3,
      "start": 643,
      "end": 554,
      "lengthNt": 90,
      "codingLengthNt": 87,
      "lengthAa": 29,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf3"
      ],
      "protein": "MGPLTARFAGDPMRPDAPRPVAYRLHGRK"
     },
     {
      "id": "orf10",
      "strand": "-",
      "frame": -2,
      "start": 701,
      "end": 612,
      "lengthNt": 90,
      "codingLengthNt": 87,
      "lengthAa": 29,
      "startCodon": "TTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf3"
      ],
      "protein": "MRVRYLCQPARRRRAETELNGPANSAICW"
     },
     {
      "id": "orf11",
      "strand": "-",
      "frame": -1,
      "start": 822,
      "end": 643,
      "lengthNt": 180,
      "codingLengthNt": 177,
      "lengthAa": 59,
      "startCodon": "CTG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf3"
      ],
      "protein": "MIVGNQHRSGNDALIQHLHGLLKTGHGTPVAFPFRYRLNLIASEIFMPASQTQTRRDRT"
     },
     {
      "id": "orf12",
      "strand": "-",
      "frame": -3,
      "start": 838,
      "end": 692,
      "lengthNt": 147,
      "codingLengthNt": 144,
      "lengthAa": 48,
      "startCodon": "TTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf3"
      ],
      "protein": "MRPAPSDRWQPASQWERCPHSAFAWFVENRTWHSSRLPVPLSAEFDCE"
     },
     {
      "id": "orf13",
      "strand": "+",
      "frame": 2,
      "start": 779,
      "end": 889,
      "lengthNt": 111,
      "codingLengthNt": 108,
      "lengthAa": 36,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf3"
      ],
      "protein": "MRASFPLRCWLPTIRWRWAQCAPLPSPGCALVRISR"
     },
     {
      "id": "orf14",
      "strand": "-",
      "frame": -2,
      "start": 914,
      "end": 819,
      "lengthNt": 96,
      "codingLengthNt": 93,
      "lengthAa": 31,
      "startCodon": "CTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf3"
      ],
      "protein": "MSSVSSYPTTEISAPTRSPDSVMARIAPSAI"
     },
     {
      "id": "orf15",
      "strand": "-",
      "frame": -3,
      "start": 937,
      "end": 848,
      "lengthNt": 90,
      "codingLengthNt": 87,
      "lengthAa": 29,
      "startCodon": "TTG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf3"
      ],
      "protein": "MTAGYNMSCLRYRRIPLPRYPHQRAARTR"
     },
     {
      "id": "orf17",
      "strand": "-",
      "frame": -1,
      "start": 1029,
      "end": 934,
      "lengthNt": 96,
      "codingLengthNt": 93,
      "lengthAa": 31,
      "startCodon": "CTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf3",
       "orf16"
      ],
      "protein": "MIALHRLALRELQQAVHAGLPQQAKILFDGG"
     },
     {
      "id": "orf19",
      "strand": "-",
      "frame": -2,
      "start": 1172,
      "end": 1026,
      "lengthNt": 147,
      "codingLengthNt": 144,
      "lengthAa": 48,
      "startCodon": "TTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf16",
       "orf18"
      ],
      "protein": "MRCAHCPLSSRETCRASCINESANARGEAVCVLGARVVFLFTSETGNS"
     },
     {
      "id": "orf22",
      "strand": "-",
      "frame": -2,
      "start": 1436,
      "end": 1317,
      "lengthNt": 120,
      "codingLengthNt": 117,
      "lengthAa": 39,
      "startCodon": "CTG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf20",
       "orf21"
      ],
      "protein": "MLGRAIGAGLFAITPAGERGMCCKAIKLGNARVFPVTTL"
     },
     {
      "id": "orf23",
      "strand": "+",
      "frame": 1,
      "start": 1342,
      "end": 1449,
      "lengthNt": 108,
      "codingLengthNt": 105,
      "lengthAa": 35,
      "startCodon": "CTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf21"
      ],
      "protein": "MALPNLIALQHIPLSPAGVIAKRPAPIALPNSCAA"
     },
     {
      "id": "orf24",
      "strand": "-",
      "frame": -1,
      "start": 1485,
      "end": 1357,
      "lengthNt": 129,
      "codingLengthNt": 126,
      "lengthAa": 42,
      "startCodon": "CTG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf21"
      ],
      "protein": "MVPETRQSAIRHSGCATVGKGDRCGPLRYYASWRKGDVLQGD"
     }
    ],
    "hiddenCount": 17,
    "noStopBeforeEnd": [
     {
      "id": "orf21",
      "strand": "+",
      "frame": 3,
      "start": 1284,
      "end": 1499,
      "lengthNt": 216,
      "codingLengthNt": 216,
      "lengthAa": 72,
      "startCodon": "ATG",
      "stopCodon": null,
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MTMITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPE"
     }
    ],
    "mustBeAbsent": []
   },
   "crossCheck": {
    "biopythonTranslation": "every ORF is Biopython's translation (same table) of its nucleotides, found at its place in the frame translation; one final stop when stopCodon is set, none otherwise",
    "orffinder": {
     "used": true,
     "tool": "NCBI ORFfinder 0.4.3",
     "files": [
      "pipeline/sequence-toolkit/orffinder/ecoli-lacI.g1.s1.nf.fa",
      "pipeline/sequence-toolkit/orffinder/ecoli-lacI.g1.s1.nt.fa"
     ],
     "commands": [
      "ORFfinder -in <fasta> -g 1 -s 1 -ml 75 -strand both -outfmt 0 -n f -out <out>",
      "ORFfinder -in <fasta> -g 1 -s 1 -ml 75 -strand both -outfmt 0 -n t -out <out>"
     ],
     "allOrfsAgree": true,
     "shownByDefaultAgree": true,
     "compared": "start, end and protein of every ORF (-n f) and of the ORFs shown by default (-n t); ORFfinder's 'partial' equals stopCodon null or startsAtFrameStart"
    }
   },
   "method": "ORF rules of the CSO ruling of 6 October 2026, as about.rules states them",
   "oracle": "independent scan in reference.py (scan_orfs), cross-checked against Biopython translations and NCBI ORFfinder",
   "source": "pipeline/sequence-toolkit/reference.py (orf)",
   "oracleVersion": "reference.py sha256 1bc66633d1a7; Biopython 1.88",
   "recordedOn": "2026-10-06",
   "notes": []
  },
  {
   "id": "ecoli-lacI.t2.atgOnly",
   "input": {
    "sequenceId": "ecoli-lacI",
    "table": 2,
    "startCodons": "atgOnly",
    "startCodonList": [
     "ATG"
    ],
    "defaultSetting": true,
    "minimumCodingLengthNt": 75
   },
   "expected": {
    "main": [
     {
      "id": "orf1",
      "strand": "+",
      "frame": 1,
      "start": 202,
      "end": 1056,
      "lengthNt": 855,
      "codingLengthNt": 852,
      "lengthAa": 284,
      "startCodon": "ATG",
      "stopCodon": "AGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPMAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPSTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVK"
     },
     {
      "id": "orf4",
      "strand": "+",
      "frame": 3,
      "start": 918,
      "end": 1199,
      "lengthNt": 282,
      "codingLengthNt": 279,
      "lengthAa": 93,
      "startCodon": "ATG",
      "stopCodon": "AGG",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MLYPAVNHHQTGFSPAGANQRGPLAATLSGPGGEGQSAVARLTGEKKNHPGAQYANRLSPRVGRFINAAGTTGFPTGKRAVSATQLMWVSSLI"
     },
     {
      "id": "orf6",
      "strand": "-",
      "frame": -3,
      "start": 1291,
      "end": 1211,
      "lengthNt": 81,
      "codingLengthNt": 78,
      "lengthAa": 26,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MVMAVSCVKLLSAHNSTQHTSRKHKV"
     }
    ],
    "nestedHidden": [
     {
      "id": "orf2",
      "strand": "-",
      "frame": -3,
      "start": 643,
      "end": 560,
      "lengthNt": 84,
      "codingLengthNt": 81,
      "lengthAa": 27,
      "startCodon": "ATG",
      "stopCodon": "AGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf1"
      ],
      "protein": "MGPLTARFAGDPMRPDAPRPVAYRLHG"
     },
     {
      "id": "orf3",
      "strand": "-",
      "frame": -2,
      "start": 848,
      "end": 690,
      "lengthNt": 159,
      "codingLengthNt": 156,
      "lengthAa": 52,
      "startCodon": "ATG",
      "stopCodon": "AGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf1"
      ],
      "protein": "MARIAPSAIWSLATSIAVGTMPSFSICMVCWKPDMALQSPSRSAIGWIWLRV"
     },
     {
      "id": "orf5",
      "strand": "-",
      "frame": -3,
      "start": 1195,
      "end": 1088,
      "lengthNt": 108,
      "codingLengthNt": 105,
      "lengthAa": 35,
      "startCodon": "ATG",
      "stopCodon": "AGG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4"
      ],
      "protein": "MSELTHINCVALTARFPVGKPVVPAALMNRPTRGE"
     }
    ],
    "hiddenCount": 3,
    "noStopBeforeEnd": [
     {
      "id": "orf7",
      "strand": "+",
      "frame": 3,
      "start": 1284,
      "end": 1499,
      "lengthNt": 216,
      "codingLengthNt": 216,
      "lengthAa": 72,
      "startCodon": "ATG",
      "stopCodon": null,
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MTMITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPE"
     }
    ],
    "mustBeAbsent": []
   },
   "crossCheck": {
    "biopythonTranslation": "every ORF is Biopython's translation (same table) of its nucleotides, found at its place in the frame translation; one final stop when stopCodon is set, none otherwise",
    "orffinder": {
     "used": true,
     "tool": "NCBI ORFfinder 0.4.3",
     "files": [
      "pipeline/sequence-toolkit/orffinder/ecoli-lacI.g2.s0.nf.fa",
      "pipeline/sequence-toolkit/orffinder/ecoli-lacI.g2.s0.nt.fa"
     ],
     "commands": [
      "ORFfinder -in <fasta> -g 2 -s 0 -ml 75 -strand both -outfmt 0 -n f -out <out>",
      "ORFfinder -in <fasta> -g 2 -s 0 -ml 75 -strand both -outfmt 0 -n t -out <out>"
     ],
     "allOrfsAgree": true,
     "shownByDefaultAgree": true,
     "compared": "start, end and protein of every ORF (-n f) and of the ORFs shown by default (-n t); ORFfinder's 'partial' equals stopCodon null or startsAtFrameStart"
    }
   },
   "method": "ORF rules of the CSO ruling of 6 October 2026, as about.rules states them",
   "oracle": "independent scan in reference.py (scan_orfs), cross-checked against Biopython translations and NCBI ORFfinder",
   "source": "pipeline/sequence-toolkit/reference.py (orf)",
   "oracleVersion": "reference.py sha256 1bc66633d1a7; Biopython 1.88",
   "recordedOn": "2026-10-06",
   "notes": []
  },
  {
   "id": "ecoli-lacI.t2.alternativeStarts",
   "input": {
    "sequenceId": "ecoli-lacI",
    "table": 2,
    "startCodons": "alternativeStarts",
    "startCodonList": [
     "ATA",
     "ATC",
     "ATG",
     "ATT",
     "GTG"
    ],
    "defaultSetting": false,
    "minimumCodingLengthNt": 75
   },
   "expected": {
    "main": [
     {
      "id": "orf2",
      "strand": "+",
      "frame": 1,
      "start": 70,
      "end": 1056,
      "lengthNt": 987,
      "codingLengthNt": 984,
      "lengthAa": 328,
      "startCodon": "GTG",
      "stopCodon": "AGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MVNVKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPMAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPSTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVK"
     },
     {
      "id": "orf14",
      "strand": "+",
      "frame": 3,
      "start": 918,
      "end": 1199,
      "lengthNt": 282,
      "codingLengthNt": 279,
      "lengthAa": 93,
      "startCodon": "ATG",
      "stopCodon": "AGG",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MLYPAVNHHQTGFSPAGANQRGPLAATLSGPGGEGQSAVARLTGEKKNHPGAQYANRLSPRVGRFINAAGTTGFPTGKRAVSATQLMWVSSLI"
     },
     {
      "id": "orf19",
      "strand": "-",
      "frame": -1,
      "start": 1272,
      "end": 1195,
      "lengthNt": 78,
      "codingLengthNt": 75,
      "lengthAa": 25,
      "startCodon": "GTG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MWNCYPLTIPHNMRAGSMKCKAWGA"
     },
     {
      "id": "orf20",
      "strand": "-",
      "frame": -3,
      "start": 1294,
      "end": 1211,
      "lengthNt": 84,
      "codingLengthNt": 81,
      "lengthAa": 27,
      "startCodon": "ATC",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MMVMAVSCVKLLSAHNSTQHTSRKHKV"
     },
     {
      "id": "orf21",
      "strand": "-",
      "frame": -2,
      "start": 1301,
      "end": 1218,
      "lengthNt": 84,
      "codingLengthNt": 81,
      "lengthAa": 27,
      "startCodon": "ATC",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MRNHGHSCFLCEIVIRSQFHTTYEPEA"
     }
    ],
    "nestedHidden": [
     {
      "id": "orf3",
      "strand": "-",
      "frame": -3,
      "start": 238,
      "end": 122,
      "lengthNt": 117,
      "codingLengthNt": 114,
      "lengthAa": 38,
      "startCodon": "GTG",
      "stopCodon": "AGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MPRGWECNSAPPSPLPLFPAFSQKRGWPGSPRGKRSDK"
     },
     {
      "id": "orf4",
      "strand": "-",
      "frame": -2,
      "start": 203,
      "end": 126,
      "lengthNt": 78,
      "codingLengthNt": 75,
      "lengthAa": 25,
      "startCodon": "ATC",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2",
       "orf3"
      ],
      "protein": "MAASTFSRVFAETWLAWFTTRETVW"
     },
     {
      "id": "orf5",
      "strand": "-",
      "frame": -1,
      "start": 300,
      "end": 169,
      "lengthNt": 132,
      "codingLengthNt": 129,
      "lengthAa": 43,
      "startCodon": "GTG",
      "stopCodon": "AGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MQGQTGGGNANQQRLFARQLLCHAVGNVIQLRHRRFHFFPRFR"
     },
     {
      "id": "orf6",
      "strand": "+",
      "frame": 2,
      "start": 215,
      "end": 376,
      "lengthNt": 162,
      "codingLengthNt": 159,
      "lengthAa": 53,
      "startCodon": "ATT",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MTFPTAWHNNWRANSRCWLALPPPVWPCTRRRKLSRRLNLAPINWVPAWWCRW"
     },
     {
      "id": "orf7",
      "strand": "-",
      "frame": -2,
      "start": 371,
      "end": 294,
      "lengthNt": 78,
      "codingLengthNt": 75,
      "lengthAa": 25,
      "startCodon": "ATC",
      "stopCodon": "AGG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2",
       "orf6"
      ],
      "protein": "MDTTTLAPSWSARDLIAATICDGAC"
     },
     {
      "id": "orf8",
      "strand": "-",
      "frame": -1,
      "start": 504,
      "end": 331,
      "lengthNt": 174,
      "codingLengthNt": 171,
      "lengthAa": 57,
      "startCodon": "ATT",
      "stopCodon": "AGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MSAGSFHSNGILVIQRMVNDQPTDALREKIVHRRFTGFDAASFYHRHHHAGTQLIGA"
     },
     {
      "id": "orf9",
      "strand": "-",
      "frame": -1,
      "start": 615,
      "end": 529,
      "lengthNt": 87,
      "codingLengthNt": 84,
      "lengthAa": 28,
      "startCodon": "GTG",
      "stopCodon": "AGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MTQCDQMLHAQSRTVFMGENNTVDGCLV"
     },
     {
      "id": "orf10",
      "strand": "-",
      "frame": -3,
      "start": 643,
      "end": 560,
      "lengthNt": 84,
      "codingLengthNt": 81,
      "lengthAa": 27,
      "startCodon": "ATG",
      "stopCodon": "AGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MGPLTARFAGDPMRPDAPRPVAYRLHG"
     },
     {
      "id": "orf11",
      "strand": "+",
      "frame": 3,
      "start": 606,
      "end": 686,
      "lengthNt": 81,
      "codingLengthNt": 78,
      "lengthAa": 26,
      "startCodon": "ATT",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MGSPANRAVSGPIKFCLGASASGWLA"
     },
     {
      "id": "orf12",
      "strand": "-",
      "frame": -1,
      "start": 954,
      "end": 649,
      "lengthNt": 306,
      "codingLengthNt": 303,
      "lengthAa": 101,
      "startCodon": "ATC",
      "stopCodon": "AGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MLFDGGWRRDMTWAVFGIVVSHYRDIRTNAQPGLGNGAHCAQRHLIVGNQHRSGNDALIQHLHGLLKTGHGTPVAFPFRYRLNLIASEMFMPASQTQTRRD"
     },
     {
      "id": "orf13",
      "strand": "-",
      "frame": -2,
      "start": 881,
      "end": 690,
      "lengthNt": 192,
      "codingLengthNt": 189,
      "lengthAa": 63,
      "startCodon": "ATA",
      "stopCodon": "AGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2",
       "orf12"
      ],
      "protein": "MSAPTRSPDSVMARIAPSAIWSLATSIAVGTMPSFSICMVCWKPDMALQSPSRSAIGWIWLRV"
     },
     {
      "id": "orf15",
      "strand": "-",
      "frame": -2,
      "start": 1064,
      "end": 960,
      "lengthNt": 105,
      "codingLengthNt": 102,
      "lengthAa": 34,
      "startCodon": "GTG",
      "stopCodon": "AGG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf14"
      ],
      "protein": "MVFLFTSETGNSWLPFTAWPWESCSKRSTLVCPS"
     },
     {
      "id": "orf16",
      "strand": "-",
      "frame": -1,
      "start": 1077,
      "end": 1000,
      "lengthNt": 78,
      "codingLengthNt": 75,
      "lengthAa": 25,
      "startCodon": "ATT",
      "stopCodon": "AGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf14"
      ],
      "protein": "MGRQGGFSFHQWDGQQLIALHRLAL"
     },
     {
      "id": "orf17",
      "strand": "+",
      "frame": 2,
      "start": 1025,
      "end": 1117,
      "lengthNt": 93,
      "codingLengthNt": 90,
      "lengthAa": 30,
      "startCodon": "ATC",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf14"
      ],
      "protein": "MSCCPSHWWKEKPPWRPMRKPPLPARWPIH"
     },
     {
      "id": "orf18",
      "strand": "-",
      "frame": -3,
      "start": 1195,
      "end": 1088,
      "lengthNt": 108,
      "codingLengthNt": 105,
      "lengthAa": 35,
      "startCodon": "ATG",
      "stopCodon": "AGG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf14"
      ],
      "protein": "MSELTHINCVALTARFPVGKPVVPAALMNRPTRGE"
     },
     {
      "id": "orf23",
      "strand": "+",
      "frame": 1,
      "start": 1300,
      "end": 1410,
      "lengthNt": 111,
      "codingLengthNt": 108,
      "lengthAa": 36,
      "startCodon": "ATT",
      "stopCodon": "AGG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf22"
      ],
      "protein": "MHWPSFYNVVTGKTLALPNLIALQHIPLSPAGVMAK"
     },
     {
      "id": "orf24",
      "strand": "-",
      "frame": -1,
      "start": 1458,
      "end": 1357,
      "lengthNt": 102,
      "codingLengthNt": 99,
      "lengthAa": 33,
      "startCodon": "ATT",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf22"
      ],
      "protein": "MRHSGCATVGKGDRCGPLRYYASWRKGDVLQGD"
     }
    ],
    "hiddenCount": 17,
    "noStopBeforeEnd": [
     {
      "id": "orf1",
      "strand": "-",
      "frame": -1,
      "start": 78,
      "end": 1,
      "lengthNt": 78,
      "codingLengthNt": 78,
      "lengthAa": 26,
      "startCodon": "ATT",
      "stopCodon": null,
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MHHPELTLFRALSCHTAKGFAPFDGV"
     },
     {
      "id": "orf22",
      "strand": "+",
      "frame": 3,
      "start": 1242,
      "end": 1499,
      "lengthNt": 258,
      "codingLengthNt": 258,
      "lengthAa": 86,
      "startCodon": "GTG",
      "stopCodon": null,
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MELWADNNFTQETAMTMITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPE"
     },
     {
      "id": "orf25",
      "strand": "+",
      "frame": 1,
      "start": 1420,
      "end": 1500,
      "lengthNt": 81,
      "codingLengthNt": 81,
      "lengthAa": 27,
      "startCodon": "ATC",
      "stopCodon": null,
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MALPNSCAAWMANGALPGFRHQKRCRK"
     }
    ],
    "mustBeAbsent": [
     {
      "strand": "-",
      "frame": -3,
      "start": 97,
      "end": 23,
      "lengthNt": 75,
      "codingLengthNt": 72
     }
    ]
   },
   "crossCheck": {
    "biopythonTranslation": "every ORF is Biopython's translation (same table) of its nucleotides, found at its place in the frame translation; one final stop when stopCodon is set, none otherwise",
    "orffinder": {
     "used": true,
     "tool": "NCBI ORFfinder 0.4.3",
     "files": [
      "pipeline/sequence-toolkit/orffinder/ecoli-lacI.g2.s1.nf.fa",
      "pipeline/sequence-toolkit/orffinder/ecoli-lacI.g2.s1.nt.fa"
     ],
     "commands": [
      "ORFfinder -in <fasta> -g 2 -s 1 -ml 75 -strand both -outfmt 0 -n f -out <out>",
      "ORFfinder -in <fasta> -g 2 -s 1 -ml 75 -strand both -outfmt 0 -n t -out <out>"
     ],
     "allOrfsAgree": true,
     "shownByDefaultAgree": true,
     "compared": "start, end and protein of every ORF (-n f) and of the ORFs shown by default (-n t); ORFfinder's 'partial' equals stopCodon null or startsAtFrameStart"
    }
   },
   "method": "ORF rules of the CSO ruling of 6 October 2026, as about.rules states them",
   "oracle": "independent scan in reference.py (scan_orfs), cross-checked against Biopython translations and NCBI ORFfinder",
   "source": "pipeline/sequence-toolkit/reference.py (orf)",
   "oracleVersion": "reference.py sha256 1bc66633d1a7; Biopython 1.88",
   "recordedOn": "2026-10-06",
   "notes": []
  },
  {
   "id": "ecoli-lacI.t11.atgOnly",
   "input": {
    "sequenceId": "ecoli-lacI",
    "table": 11,
    "startCodons": "atgOnly",
    "startCodonList": [
     "ATG"
    ],
    "defaultSetting": true,
    "minimumCodingLengthNt": 75
   },
   "expected": {
    "main": [
     {
      "id": "orf1",
      "strand": "+",
      "frame": 3,
      "start": 12,
      "end": 329,
      "lengthNt": 318,
      "codingLengthNt": 315,
      "lengthAa": 105,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MAQNLSRYGMIAPGRESIQGGECETSNVIRCRRVCRCLLSDRFPRGEPGQPRFCENAGKSGSGDGGAELHSQPRGTTTGGQTVVADWRCHLQSGPARAVANCRGD"
     },
     {
      "id": "orf2",
      "strand": "+",
      "frame": 1,
      "start": 202,
      "end": 1161,
      "lengthNt": 960,
      "codingLengthNt": 957,
      "lengthAa": 319,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPSTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ"
     },
     {
      "id": "orf9",
      "strand": "+",
      "frame": 3,
      "start": 918,
      "end": 1181,
      "lengthNt": 264,
      "codingLengthNt": 261,
      "lengthAa": 87,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MLYPAVNHHQTGFSPAGANQRGPLAATLSGPGGEGQSAVARLTGEKKNHPGAQYANRLSPRVGRFINAAGTTGFPTGKRAVSATQLM"
     },
     {
      "id": "orf10",
      "strand": "-",
      "frame": -3,
      "start": 1195,
      "end": 944,
      "lengthNt": 252,
      "codingLengthNt": 249,
      "lengthAa": 83,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MSELTHINCVALTARFPVGKPVVPAALMNRPTRGERRFAYWAPGWFFFSPVRRATADCPSPPGPERVAASGPRWFAPAGENPV"
     },
     {
      "id": "orf11",
      "strand": "-",
      "frame": -3,
      "start": 1291,
      "end": 1211,
      "lengthNt": 81,
      "codingLengthNt": 78,
      "lengthAa": 26,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MVIAVSCVKLLSAHNSTQHTSRKHKV"
     }
    ],
    "nestedHidden": [
     {
      "id": "orf3",
      "strand": "-",
      "frame": -2,
      "start": 449,
      "end": 342,
      "lengthNt": 108,
      "codingLengthNt": 105,
      "lengthAa": 35,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MISPLTRCARRLCTAALQASTPLRSTIDTTTLAPS"
     },
     {
      "id": "orf4",
      "strand": "-",
      "frame": -2,
      "start": 545,
      "end": 453,
      "lengthNt": 93,
      "codingLengthNt": 90,
      "lengthAa": 30,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MGVWSETSRNNAGTLVQAASTAMASWSSSG"
     },
     {
      "id": "orf5",
      "strand": "+",
      "frame": 2,
      "start": 464,
      "end": 634,
      "lengthNt": 171,
      "codingLengthNt": 168,
      "lengthAa": 56,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MTRMPLLWKLPALMFRRYFLMSLTRHPSTVLFSPMKTVRDWAWSIWSHWVTSKSRC"
     },
     {
      "id": "orf6",
      "strand": "-",
      "frame": -1,
      "start": 597,
      "end": 514,
      "lengthNt": 84,
      "codingLengthNt": 81,
      "lengthAa": 27,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2",
       "orf5"
      ],
      "protein": "MLHAQSRTVFMGENNTVDGCLVRDIKK"
     },
     {
      "id": "orf7",
      "strand": "-",
      "frame": -3,
      "start": 643,
      "end": 554,
      "lengthNt": 90,
      "codingLengthNt": 87,
      "lengthAa": 29,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MGPLTARFAGDPMRPDAPRPVAYRLHGRK"
     },
     {
      "id": "orf8",
      "strand": "+",
      "frame": 2,
      "start": 779,
      "end": 889,
      "lengthNt": 111,
      "codingLengthNt": 108,
      "lengthAa": 36,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MRASFPLRCWLPTIRWRWAQCAPLPSPGCALVRISR"
     }
    ],
    "hiddenCount": 6,
    "noStopBeforeEnd": [
     {
      "id": "orf12",
      "strand": "+",
      "frame": 3,
      "start": 1284,
      "end": 1499,
      "lengthNt": 216,
      "codingLengthNt": 216,
      "lengthAa": 72,
      "startCodon": "ATG",
      "stopCodon": null,
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MTMITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPE"
     }
    ],
    "mustBeAbsent": []
   },
   "crossCheck": {
    "biopythonTranslation": "every ORF is Biopython's translation (same table) of its nucleotides, found at its place in the frame translation; one final stop when stopCodon is set, none otherwise",
    "orffinder": {
     "used": true,
     "tool": "NCBI ORFfinder 0.4.3",
     "files": [
      "pipeline/sequence-toolkit/orffinder/ecoli-lacI.g11.s0.nf.fa",
      "pipeline/sequence-toolkit/orffinder/ecoli-lacI.g11.s0.nt.fa"
     ],
     "commands": [
      "ORFfinder -in <fasta> -g 11 -s 0 -ml 75 -strand both -outfmt 0 -n f -out <out>",
      "ORFfinder -in <fasta> -g 11 -s 0 -ml 75 -strand both -outfmt 0 -n t -out <out>"
     ],
     "allOrfsAgree": true,
     "shownByDefaultAgree": true,
     "compared": "start, end and protein of every ORF (-n f) and of the ORFs shown by default (-n t); ORFfinder's 'partial' equals stopCodon null or startsAtFrameStart"
    }
   },
   "method": "ORF rules of the CSO ruling of 6 October 2026, as about.rules states them",
   "oracle": "independent scan in reference.py (scan_orfs), cross-checked against Biopython translations and NCBI ORFfinder",
   "source": "pipeline/sequence-toolkit/reference.py (orf)",
   "oracleVersion": "reference.py sha256 1bc66633d1a7; Biopython 1.88",
   "recordedOn": "2026-10-06",
   "notes": []
  },
  {
   "id": "ecoli-lacI.t11.alternativeStarts",
   "input": {
    "sequenceId": "ecoli-lacI",
    "table": 11,
    "startCodons": "alternativeStarts",
    "startCodonList": [
     "ATA",
     "ATC",
     "ATG",
     "ATT",
     "CTG",
     "GTG",
     "TTG"
    ],
    "defaultSetting": false,
    "minimumCodingLengthNt": 75
   },
   "expected": {
    "main": [
     {
      "id": "orf2",
      "strand": "+",
      "frame": 3,
      "start": 12,
      "end": 329,
      "lengthNt": 318,
      "codingLengthNt": 315,
      "lengthAa": 105,
      "startCodon": "ATG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MAQNLSRYGMIAPGRESIQGGECETSNVIRCRRVCRCLLSDRFPRGEPGQPRFCENAGKSGSGDGGAELHSQPRGTTTGGQTVVADWRCHLQSGPARAVANCRGD"
     },
     {
      "id": "orf4",
      "strand": "+",
      "frame": 1,
      "start": 70,
      "end": 1161,
      "lengthNt": 1092,
      "codingLengthNt": 1089,
      "lengthAa": 363,
      "startCodon": "GTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MVNVKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPSTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ"
     },
     {
      "id": "orf21",
      "strand": "+",
      "frame": 3,
      "start": 894,
      "end": 1181,
      "lengthNt": 288,
      "codingLengthNt": 285,
      "lengthAa": 95,
      "startCodon": "ATA",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MRRYRRQLMLYPAVNHHQTGFSPAGANQRGPLAATLSGPGGEGQSAVARLTGEKKNHPGAQYANRLSPRVGRFINAAGTTGFPTGKRAVSATQLM"
     },
     {
      "id": "orf24",
      "strand": "-",
      "frame": -3,
      "start": 1207,
      "end": 944,
      "lengthNt": 264,
      "codingLengthNt": 261,
      "lengthAa": 87,
      "startCodon": "CTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MGCLMSELTHINCVALTARFPVGKPVVPAALMNRPTRGERRFAYWAPGWFFFSPVRRATADCPSPPGPERVAASGPRWFAPAGENPV"
     },
     {
      "id": "orf26",
      "strand": "-",
      "frame": -3,
      "start": 1444,
      "end": 1211,
      "lengthNt": 234,
      "codingLengthNt": 231,
      "lengthAa": 77,
      "startCodon": "CTG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MRNCWEGRSVRASSLLRQLAKGGCAARRLSWVTPGFSQSRRCKTTASESVIMVIAVSCVKLLSAHNSTQHTSRKHKV"
     }
    ],
    "nestedHidden": [
     {
      "id": "orf3",
      "strand": "-",
      "frame": -3,
      "start": 238,
      "end": 65,
      "lengthNt": 174,
      "codingLengthNt": 171,
      "lengthAa": 57,
      "startCodon": "GTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2"
      ],
      "protein": "MPRGWECNSAPPSPLPLFPAFSQKRGWPGSPRGKRSDKRHRHTLRHRITLLVSHSPP"
     },
     {
      "id": "orf5",
      "strand": "-",
      "frame": -1,
      "start": 504,
      "end": 94,
      "lengthNt": 411,
      "codingLengthNt": 408,
      "lengthAa": 136,
      "startCodon": "ATT",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4"
      ],
      "protein": "MSAGSFHSNGILVIQRIVNDQPTDALREKIVHRRFTGFDAASFYHRHHHAGTQLIGARFNRRDNLRRRVQGQTGGGNANQQRLFARQLLCHAVGNVIQLRHRRFHFFPRFRRNVAGLVHHAGNGLIRDTGILCDIV"
     },
     {
      "id": "orf6",
      "strand": "-",
      "frame": -2,
      "start": 326,
      "end": 216,
      "lengthNt": 111,
      "codingLengthNt": 108,
      "lengthAa": 36,
      "startCodon": "ATC",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf2",
       "orf4",
       "orf5"
      ],
      "protein": "MAATICDGACRARLEVATPISNDCLPASCCATRLGM"
     },
     {
      "id": "orf7",
      "strand": "+",
      "frame": 2,
      "start": 269,
      "end": 376,
      "lengthNt": 108,
      "codingLengthNt": 105,
      "lengthAa": 35,
      "startCodon": "TTG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4",
       "orf5"
      ],
      "protein": "MALPPPVWPCTRRRKLSRRLNLAPINWVPAWWCRW"
     },
     {
      "id": "orf8",
      "strand": "-",
      "frame": -2,
      "start": 449,
      "end": 342,
      "lengthNt": 108,
      "codingLengthNt": 105,
      "lengthAa": 35,
      "startCodon": "ATG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4",
       "orf5"
      ],
      "protein": "MISPLTRCARRLCTAALQASTPLRSTIDTTTLAPS"
     },
     {
      "id": "orf9",
      "strand": "-",
      "frame": -2,
      "start": 557,
      "end": 453,
      "lengthNt": 105,
      "codingLengthNt": 102,
      "lengthAa": 34,
      "startCodon": "ATA",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4"
      ],
      "protein": "MILLMGVWSETSRNNAGTLVQAASTAMASWSSSG"
     },
     {
      "id": "orf10",
      "strand": "+",
      "frame": 2,
      "start": 455,
      "end": 634,
      "lengthNt": 180,
      "codingLengthNt": 177,
      "lengthAa": 59,
      "startCodon": "ATC",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4"
      ],
      "protein": "MRWMTRMPLLWKLPALMFRRYFLMSLTRHPSTVLFSPMKTVRDWAWSIWSHWVTSKSRC"
     },
     {
      "id": "orf11",
      "strand": "-",
      "frame": -1,
      "start": 621,
      "end": 514,
      "lengthNt": 108,
      "codingLengthNt": 105,
      "lengthAa": 35,
      "startCodon": "TTG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4",
       "orf10"
      ],
      "protein": "MLVTQCDQMLHAQSRTVFMGENNTVDGCLVRDIKK"
     },
     {
      "id": "orf12",
      "strand": "-",
      "frame": -3,
      "start": 688,
      "end": 554,
      "lengthNt": 135,
      "codingLengthNt": 132,
      "lengthAa": 44,
      "startCodon": "ATT",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4"
      ],
      "protein": "MYASQPDADAPRQNLMGPLTARFAGDPMRPDAPRPVAYRLHGRK"
     },
     {
      "id": "orf13",
      "strand": "+",
      "frame": 3,
      "start": 606,
      "end": 686,
      "lengthNt": 81,
      "codingLengthNt": 78,
      "lengthAa": 26,
      "startCodon": "ATT",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4",
       "orf12"
      ],
      "protein": "MGSPANRAVSGPIKFCLGASASGWLA"
     },
     {
      "id": "orf14",
      "strand": "-",
      "frame": -2,
      "start": 701,
      "end": 612,
      "lengthNt": 90,
      "codingLengthNt": 87,
      "lengthAa": 29,
      "startCodon": "TTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4"
      ],
      "protein": "MRVRYLCQPARRRRAETELNGPANSAICW"
     },
     {
      "id": "orf15",
      "strand": "-",
      "frame": -1,
      "start": 903,
      "end": 643,
      "lengthNt": 261,
      "codingLengthNt": 258,
      "lengthAa": 86,
      "startCodon": "ATC",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4"
      ],
      "protein": "MVVSHYRDIRTNAQPGLGNGAHCAQRHLIVGNQHRSGNDALIQHLHGLLKTGHGTPVAFPFRYRLNLIASEIFMPASQTQTRRDRT"
     },
     {
      "id": "orf16",
      "strand": "+",
      "frame": 3,
      "start": 687,
      "end": 782,
      "lengthNt": 96,
      "codingLengthNt": 93,
      "lengthAa": 31,
      "startCodon": "ATA",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4",
       "orf15"
      ],
      "protein": "MSHSQSNSADSGTGRRLECHVRFSTNHANAE"
     },
     {
      "id": "orf17",
      "strand": "-",
      "frame": -3,
      "start": 838,
      "end": 692,
      "lengthNt": 147,
      "codingLengthNt": 144,
      "lengthAa": 48,
      "startCodon": "TTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4",
       "orf15"
      ],
      "protein": "MRPAPSDRWQPASQWERCPHSAFAWFVENRTWHSSRLPVPLSAEFDCE"
     },
     {
      "id": "orf18",
      "strand": "+",
      "frame": 2,
      "start": 779,
      "end": 889,
      "lengthNt": 111,
      "codingLengthNt": 108,
      "lengthAa": 36,
      "startCodon": "ATG",
      "stopCodon": "TAG",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4",
       "orf15"
      ],
      "protein": "MRASFPLRCWLPTIRWRWAQCAPLPSPGCALVRISR"
     },
     {
      "id": "orf19",
      "strand": "-",
      "frame": -2,
      "start": 914,
      "end": 819,
      "lengthNt": 96,
      "codingLengthNt": 93,
      "lengthAa": 31,
      "startCodon": "CTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4"
      ],
      "protein": "MSSVSSYPTTEISAPTRSPDSVMARIAPSAI"
     },
     {
      "id": "orf20",
      "strand": "-",
      "frame": -3,
      "start": 937,
      "end": 848,
      "lengthNt": 90,
      "codingLengthNt": 87,
      "lengthAa": 29,
      "startCodon": "TTG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4"
      ],
      "protein": "MTAGYNMSCLRYRRIPLPRYPHQRAARTR"
     },
     {
      "id": "orf22",
      "strand": "+",
      "frame": 2,
      "start": 902,
      "end": 1018,
      "lengthNt": 117,
      "codingLengthNt": 114,
      "lengthAa": 38,
      "startCodon": "ATA",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4",
       "orf21"
      ],
      "protein": "MPKTAHVISRRQPPSNRIFACWGKPAWTACCNSLRARR"
     },
     {
      "id": "orf23",
      "strand": "-",
      "frame": -1,
      "start": 1029,
      "end": 934,
      "lengthNt": 96,
      "codingLengthNt": 93,
      "lengthAa": 31,
      "startCodon": "CTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf4",
       "orf21"
      ],
      "protein": "MIALHRLALRELQQAVHAGLPQQAKILFDGG"
     },
     {
      "id": "orf25",
      "strand": "-",
      "frame": -2,
      "start": 1172,
      "end": 1026,
      "lengthNt": 147,
      "codingLengthNt": 144,
      "lengthAa": 48,
      "startCodon": "TTG",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf21",
       "orf24"
      ],
      "protein": "MRCAHCPLSSRETCRASCINESANARGEAVCVLGARVVFLFTSETGNS"
     },
     {
      "id": "orf27",
      "strand": "-",
      "frame": -2,
      "start": 1301,
      "end": 1218,
      "lengthNt": 84,
      "codingLengthNt": 81,
      "lengthAa": 27,
      "startCodon": "ATC",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf26"
      ],
      "protein": "MRNHGHSCFLCEIVIRSQFHTTYEPEA"
     },
     {
      "id": "orf29",
      "strand": "+",
      "frame": 1,
      "start": 1300,
      "end": 1449,
      "lengthNt": 150,
      "codingLengthNt": 147,
      "lengthAa": 49,
      "startCodon": "ATT",
      "stopCodon": "TGA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf28"
      ],
      "protein": "MHWPSFYNVVTGKTLALPNLIALQHIPLSPAGVIAKRPAPIALPNSCAA"
     },
     {
      "id": "orf30",
      "strand": "-",
      "frame": -2,
      "start": 1451,
      "end": 1317,
      "lengthNt": 135,
      "codingLengthNt": 132,
      "lengthAa": 44,
      "startCodon": "ATT",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf28"
      ],
      "protein": "MQAAQLLGRAIGAGLFAITPAGERGMCCKAIKLGNARVFPVTTL"
     },
     {
      "id": "orf31",
      "strand": "-",
      "frame": -1,
      "start": 1485,
      "end": 1357,
      "lengthNt": 129,
      "codingLengthNt": 126,
      "lengthAa": 42,
      "startCodon": "CTG",
      "stopCodon": "TAA",
      "startsAtFrameStart": false,
      "nested": true,
      "containedIn": [
       "orf28"
      ],
      "protein": "MVPETRQSAIRHSGCATVGKGDRCGPLRYYASWRKGDVLQGD"
     }
    ],
    "hiddenCount": 24,
    "noStopBeforeEnd": [
     {
      "id": "orf1",
      "strand": "-",
      "frame": -1,
      "start": 78,
      "end": 1,
      "lengthNt": 78,
      "codingLengthNt": 78,
      "lengthAa": 26,
      "startCodon": "ATT",
      "stopCodon": null,
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MHHPELTLFRALSCHTAKGFAPFDGV"
     },
     {
      "id": "orf28",
      "strand": "+",
      "frame": 3,
      "start": 1284,
      "end": 1499,
      "lengthNt": 216,
      "codingLengthNt": 216,
      "lengthAa": 72,
      "startCodon": "ATG",
      "stopCodon": null,
      "startsAtFrameStart": false,
      "nested": false,
      "containedIn": [],
      "protein": "MTMITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPE"
     }
    ],
    "mustBeAbsent": [
     {
      "strand": "-",
      "frame": -2,
      "start": 203,
      "end": 129,
      "lengthNt": 75,
      "codingLengthNt": 72
     }
    ]
   },
   "crossCheck": {
    "biopythonTranslation": "every ORF is Biopython's translation (same table) of its nucleotides, found at its place in the frame translation; one final stop when stopCodon is set, none otherwise",
    "orffinder": {
     "used": true,
     "tool": "NCBI ORFfinder 0.4.3",
     "files": [
      "pipeline/sequence-toolkit/orffinder/ecoli-lacI.g11.s1.nf.fa",
      "pipeline/sequence-toolkit/orffinder/ecoli-lacI.g11.s1.nt.fa"
     ],
     "commands": [
      "ORFfinder -in <fasta> -g 11 -s 1 -ml 75 -strand both -outfmt 0 -n f -out <out>",
      "ORFfinder -in <fasta> -g 11 -s 1 -ml 75 -strand both -outfmt 0 -n t -out <out>"
     ],
     "allOrfsAgree": true,
     "shownByDefaultAgree": true,
     "compared": "start, end and protein of every ORF (-n f) and of the ORFs shown by default (-n t); ORFfinder's 'partial' equals stopCodon null or startsAtFrameStart"
    }
   },
   "method": "ORF rules of the CSO ruling of 6 October 2026, as about.rules states them",
   "oracle": "independent scan in reference.py (scan_orfs), cross-checked against Biopython translations and NCBI ORFfinder",
   "source": "pipeline/sequence-toolkit/reference.py (orf)",
   "oracleVersion": "reference.py sha256 1bc66633d1a7; Biopython 1.88",
   "recordedOn": "2026-10-06",
   "notes": []
  }
 ]
}