{
 "about": {
  "generatedBy": "pipeline/plasmid-map/reference.py",
  "scriptSha256": "627599d78dd7057087719d513da2312f1dfe2a8cee8e05d138f50d84ed22864d",
  "recordedOn": "2026-10-06",
  "oracle": "Biopython 1.88",
  "oracleLicence": "Biopython Licence Agreement or BSD-3-Clause",
  "text": "Synthetic SnapGene .dna files written by make-dna-fixtures.py from NCBI records and their submitters' annotations (no SnapGene-authored annotation), read by Biopython's SnapGene reader. Checked on synthetic files only: they cannot show that real SnapGene files read correctly (the pre-live check with real files). The refusal files' expected refusals are stated by this script, not taken from Biopython."
 },
 "cases": [
  {
   "file": "dna/refuse-length-mismatch.dna",
   "sha256": "f5f349d990e62f21b2445eadc0887897f362cd11ead608a2a04fd8a73cfce352",
   "expected": {
    "refusal": "length-mismatch",
    "why": "the DNA packet declares five bytes more than its sequence, running into the next packet"
   },
   "biopython": "ValueError: Unexpected end of packet"
  },
  {
   "file": "dna/refuse-truncated.dna",
   "sha256": "bb3621e0e800810e2c6d7c14b9ddafd0d25e5f5be6b8c7c7667ea5d7816fc623",
   "expected": {
    "refusal": "truncated",
    "why": "the last 40 bytes cut off, inside the features packet"
   },
   "biopython": "ValueError: Unexpected end of packet"
  },
  {
   "file": "dna/refuse-unknown-packet.dna",
   "sha256": "49f8bf3ec732af6f47aa514ee535bfcd6233417f69e9de343a96173a36873c49",
   "expected": {
    "refusal": "unknown-packet",
    "why": "a packet of type 0x63 after the features"
   },
   "biopython": "read (skips what it does not know)"
  },
  {
   "file": "dna/refuse-unknown-version.dna",
   "sha256": "bead3486a060fcecd2065c2ebd3f3be612f453c4f20c505d46298f3a742738ee",
   "expected": {
    "refusal": "unknown-version",
    "why": "the cookie gives import version 99"
   },
   "biopython": "read (skips what it does not know)"
  },
  {
   "file": "dna/synthetic-2micron-origin.dna",
   "sha256": "e582eab439d9790a7308e6d98d4aae340a19a283f7daf0501267fc3004c84dfa",
   "expected": {
    "length": 6318,
    "sequenceSha256": "529faf85e140fabd399654eb454e51c2d6880e99e4c03095c76c357781010946",
    "topology": "circular",
    "features": [
     {
      "type": "mRNA",
      "label": "Flp mRNA",
      "segments": [
       [
        5549,
        6318
       ],
       [
        1,
        545
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "Flp mRNA"
       ],
       "product": [
        "Flp mRNA"
       ]
      }
     },
     {
      "type": "CDS",
      "label": "recombinase (FLP)",
      "segments": [
       [
        5570,
        6318
       ],
       [
        1,
        523
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "codon_start": [
        "1"
       ],
       "label": [
        "recombinase (FLP)"
       ],
       "product": [
        "recombinase (FLP)"
       ],
       "protein_id": [
        "AAB59340.1"
       ]
      }
     },
     {
      "type": "exon",
      "label": "exon",
      "segments": [
       [
        1,
        545
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "exon"
       ]
      }
     },
     {
      "type": "misc_difference",
      "label": "conflict",
      "segments": [
       [
        157,
        160
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "conflict"
       ],
       "note": [
        "conflict"
       ]
      }
     },
     {
      "type": "misc_difference",
      "label": "conflict",
      "segments": [
       [
        289,
        290
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "conflict"
       ],
       "note": [
        "conflict"
       ]
      }
     },
     {
      "type": "repeat_region",
      "label": "IR2",
      "segments": [
       [
        341,
        939
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "IR2"
       ],
       "note": [
        "IR2"
       ]
      }
     },
     {
      "type": "misc_difference",
      "label": "conflict",
      "segments": [
       [
        464,
        466
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "conflict"
       ],
       "note": [
        "conflict"
       ]
      }
     },
     {
      "type": "misc_difference",
      "label": "conflict",
      "segments": [
       [
        558,
        558
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "conflict"
       ],
       "note": [
        "conflict"
       ]
      }
     },
     {
      "type": "misc_difference",
      "label": "conflict",
      "segments": [
       [
        561,
        561
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "conflict"
       ],
       "note": [
        "conflict"
       ]
      }
     },
     {
      "type": "misc_difference",
      "label": "conflict",
      "segments": [
       [
        622,
        624
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "conflict"
       ],
       "note": [
        "conflict"
       ]
      }
     },
     {
      "type": "misc_difference",
      "label": "conflict",
      "segments": [
       [
        642,
        642
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "conflict"
       ],
       "note": [
        "conflict"
       ]
      }
     },
     {
      "type": "misc_difference",
      "label": "conflict",
      "segments": [
       [
        665,
        666
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "conflict"
       ],
       "note": [
        "conflict"
       ]
      }
     },
     {
      "type": "misc_binding",
      "label": "FLP recombinase binding site A [9]",
      "segments": [
       [
        673,
        722
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "bound_moiety": [
        "FLP recombinase"
       ],
       "label": [
        "FLP recombinase binding site A [9]"
       ],
       "note": [
        "FLP recombinase binding site A [9]"
       ]
      }
     },
     {
      "type": "misc_recomb",
      "label": "misc_recomb",
      "segments": [
       [
        702,
        703
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "misc_recomb"
       ]
      }
     },
     {
      "type": "misc_difference",
      "label": "conflict",
      "segments": [
       [
        793,
        794
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "conflict"
       ],
       "note": [
        "conflict"
       ]
      }
     },
     {
      "type": "mRNA",
      "label": "Rep1 mRNA (alt.)",
      "segments": [
       [
        836,
        2038
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "Rep1 mRNA (alt.)"
       ],
       "note": [
        "Rep1 mRNA (alt.)"
       ]
      }
     },
     {
      "type": "mRNA",
      "label": "Rep1 mRNA (alt.)",
      "segments": [
       [
        836,
        2019
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "Rep1 mRNA (alt.)"
       ],
       "note": [
        "Rep1 mRNA (alt.)"
       ]
      }
     },
     {
      "type": "mRNA",
      "label": "Rep1 mRNA (alt.)",
      "segments": [
       [
        836,
        2017
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "Rep1 mRNA (alt.)"
       ],
       "note": [
        "Rep1 mRNA (alt.)"
       ]
      }
     },
     {
      "type": "mRNA",
      "label": "Rep1 mRNA (alt.)",
      "segments": [
       [
        836,
        2010
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "Rep1 mRNA (alt.)"
       ],
       "note": [
        "Rep1 mRNA (alt.)"
       ]
      }
     },
     {
      "type": "mRNA",
      "label": "Rep1 mRNA (alt.)",
      "segments": [
       [
        836,
        2005
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "Rep1 mRNA (alt.)"
       ],
       "note": [
        "Rep1 mRNA (alt.)"
       ]
      }
     },
     {
      "type": "mRNA",
      "label": "Rep1 mRNA (alt.)",
      "segments": [
       [
        836,
        2004
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "Rep1 mRNA (alt.)"
       ],
       "note": [
        "Rep1 mRNA (alt.)"
       ]
      }
     },
     {
      "type": "CDS",
      "label": "Rep 1 protein",
      "segments": [
       [
        887,
        2008
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "codon_start": [
        "1"
       ],
       "label": [
        "Rep 1 protein"
       ],
       "product": [
        "Rep 1 protein"
       ],
       "protein_id": [
        "AAB59341.1"
       ]
      }
     },
     {
      "type": "mRNA",
      "label": "D mRNA (alt.; 5' end +/- 3 bp)",
      "segments": [
       [
        2254,
        2861
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "D mRNA (alt.; 5' end +/- 3 bp)"
       ],
       "note": [
        "D mRNA (alt.; 5' end +/- 3 bp)"
       ]
      }
     },
     {
      "type": "mRNA",
      "label": "D mRNA (alt.; 5' end +/- 3 bp)",
      "segments": [
       [
        2254,
        2841
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "D mRNA (alt.; 5' end +/- 3 bp)"
       ],
       "note": [
        "D mRNA (alt.; 5' end +/- 3 bp)"
       ]
      }
     },
     {
      "type": "CDS",
      "label": "D protein",
      "segments": [
       [
        2271,
        2816
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "codon_start": [
        "1"
       ],
       "label": [
        "D protein"
       ],
       "product": [
        "D protein"
       ],
       "protein_id": [
        "AAB59342.1"
       ]
      }
     },
     {
      "type": "repeat_region",
      "label": "IR1",
      "segments": [
       [
        3714,
        4312
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "IR1"
       ],
       "note": [
        "IR1"
       ]
      }
     },
     {
      "type": "misc_binding",
      "label": "FLP-recombinase binding site B [9]",
      "segments": [
       [
        3930,
        3979
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "bound_moiety": [
        "FLP recombinase"
       ],
       "label": [
        "FLP-recombinase binding site B [9]"
       ],
       "note": [
        "FLP-recombinase binding site B [9]"
       ]
      }
     },
     {
      "type": "misc_recomb",
      "label": "misc_recomb",
      "segments": [
       [
        3941,
        3942
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "misc_recomb"
       ]
      }
     },
     {
      "type": "mRNA",
      "label": "REP2 mRNA (minor alt.)",
      "segments": [
       [
        4108,
        5223
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "REP2 mRNA (minor alt.)"
       ],
       "note": [
        "REP2 mRNA (minor alt.)"
       ]
      }
     },
     {
      "type": "mRNA",
      "label": "REP2 mRNA (minor alt.)",
      "segments": [
       [
        4108,
        5212
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "REP2 mRNA (minor alt.)"
       ],
       "note": [
        "REP2 mRNA (minor alt.)"
       ]
      }
     },
     {
      "type": "mRNA",
      "label": "REP2 mRNA (major alt.)",
      "segments": [
       [
        4108,
        5198
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "REP2 mRNA (major alt.)"
       ],
       "note": [
        "REP2 mRNA (major alt.)"
       ]
      }
     },
     {
      "type": "mRNA",
      "label": "REP2 mRNA (major alt.)",
      "segments": [
       [
        4108,
        5197
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "REP2 mRNA (major alt.)"
       ],
       "note": [
        "REP2 mRNA (major alt.)"
       ]
      }
     },
     {
      "type": "mRNA",
      "label": "REP2 mRNA (major alt.)",
      "segments": [
       [
        4108,
        5196
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "REP2 mRNA (major alt.)"
       ],
       "note": [
        "REP2 mRNA (major alt.)"
       ]
      }
     },
     {
      "type": "mRNA",
      "label": "REP2 mRNA (major alt.)",
      "segments": [
       [
        4108,
        5195
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "REP2 mRNA (major alt.)"
       ],
       "note": [
        "REP2 mRNA (major alt.)"
       ]
      }
     },
     {
      "type": "mRNA",
      "label": "REP2 mRNA (major alt.)",
      "segments": [
       [
        4108,
        5184
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "REP2 mRNA (major alt.)"
       ],
       "note": [
        "REP2 mRNA (major alt.)"
       ]
      }
     },
     {
      "type": "mRNA",
      "label": "REP2 mRNA (major alt.)",
      "segments": [
       [
        4108,
        5183
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "REP2 mRNA (major alt.)"
       ],
       "note": [
        "REP2 mRNA (major alt.)"
       ]
      }
     },
     {
      "type": "mRNA",
      "label": "REP2 mRNA (major alt.)",
      "segments": [
       [
        4108,
        5182
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "REP2 mRNA (major alt.)"
       ],
       "note": [
        "REP2 mRNA (major alt.)"
       ]
      }
     },
     {
      "type": "CDS",
      "label": "Rep 2 protein",
      "segments": [
       [
        4308,
        5198
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "codon_start": [
        "1"
       ],
       "label": [
        "Rep 2 protein"
       ],
       "product": [
        "Rep 2 protein"
       ],
       "protein_id": [
        "AAB59343.1"
       ]
      }
     },
     {
      "type": "exon",
      "label": "exon",
      "segments": [
       [
        5549,
        6318
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "exon"
       ]
      }
     },
     {
      "type": "old_sequence",
      "label": "old_sequence",
      "segments": [
       [
        5583,
        5583
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "old_sequence"
       ]
      }
     }
    ]
   }
  },
  {
   "file": "dna/synthetic-lac-linear.dna",
   "sha256": "13c7bf59fd3e913bd5f74fae493e94f3c7bb30a3f4e9f30f745c62c4e3beed1c",
   "expected": {
    "length": 7477,
    "sequenceSha256": "2e61da9f500f64b1b07aeab99995426fa0c7fb2b08bddd040e91d08cce60acbe",
    "topology": "linear",
    "features": [
     {
      "type": "variation",
      "label": "c in wild-type; t in 'up' promoter mutant I-Q [11]",
      "segments": [
       [
        16,
        16
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "c in wild-type; t in 'up' promoter mutant I-Q [11]"
       ],
       "note": [
        "c in wild-type; t in 'up' promoter mutant I-Q [11]"
       ]
      }
     },
     {
      "type": "CDS",
      "label": "lacI",
      "segments": [
       [
        79,
        1161
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "codon_start": [
        "1"
       ],
       "gene": [
        "lacI"
       ],
       "label": [
        "lacI"
       ],
       "note": [
        "lac repressor protein (gtg start codon)"
       ],
       "protein_id": [
        "AAA24052.1"
       ],
       "transl_table": [
        "11"
       ]
      }
     },
     {
      "type": "regulatory",
      "label": "cap protein binding site",
      "segments": [
       [
        1162,
        1199
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "cap protein binding site"
       ],
       "note": [
        "cap protein binding site"
       ],
       "regulatory_class": [
        "other"
       ]
      }
     },
     {
      "type": "variation",
      "label": "ttag in wild-type; aatt in strain UV5 [26]",
      "segments": [
       [
        1183,
        1186
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "ttag in wild-type; aatt in strain UV5 [26]"
       ],
       "note": [
        "ttag in wild-type; aatt in strain UV5 [26]"
       ]
      }
     },
     {
      "type": "variation",
      "label": "gct in wild-type; gt in mutant l305 [5]",
      "segments": [
       [
        1209,
        1211
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "gct in wild-type; gt in mutant l305 [5]"
       ],
       "note": [
        "gct in wild-type; gt in mutant l305 [5]"
       ]
      }
     },
     {
      "type": "variation",
      "label": "t in wild-type; a in mutant l241 [5]",
      "segments": [
       [
        1212,
        1212
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "t in wild-type; a in mutant l241 [5]"
       ],
       "note": [
        "t in wild-type; a in mutant l241 [5]"
       ]
      }
     },
     {
      "type": "variation",
      "label": "c in wild-type; a in mutant p-r-1a [5]",
      "segments": [
       [
        1230,
        1230
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "c in wild-type; a in mutant p-r-1a [5]"
       ],
       "note": [
        "c in wild-type; a in mutant p-r-1a [5]"
       ]
      }
     },
     {
      "type": "variation",
      "label": "gt in wild-type; aa in strain UV5 [26]",
      "segments": [
       [
        1237,
        1238
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "gt in wild-type; aa in strain UV5 [26]"
       ],
       "note": [
        "gt in wild-type; aa in strain UV5 [26]"
       ]
      }
     },
     {
      "type": "variation",
      "label": "gtgg in wild-type; ttca in synthetic operator [8]",
      "segments": [
       [
        1242,
        1245
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "gtgg in wild-type; ttca in synthetic operator [8]"
       ],
       "note": [
        "gtgg in wild-type; ttca in synthetic operator [8]"
       ]
      }
     },
     {
      "type": "regulatory",
      "label": "lac repressor protein binding site",
      "segments": [
       [
        1246,
        1266
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "lac repressor protein binding site"
       ],
       "note": [
        "lac repressor protein binding site"
       ],
       "regulatory_class": [
        "other"
       ]
      }
     },
     {
      "type": "variation",
      "label": "tc in wild-type; tg in synthetic operator [8]",
      "segments": [
       [
        1267,
        1268
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "tc in wild-type; tg in synthetic operator [8]"
       ],
       "note": [
        "tc in wild-type; tg in synthetic operator [8]"
       ]
      }
     },
     {
      "type": "variation",
      "label": "ctatgaccat in wild-type; gatccggcca in strain UV5 [26]",
      "segments": [
       [
        1282,
        1291
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "ctatgaccat in wild-type; gatccggcca in strain UV5 [26]"
       ],
       "note": [
        "ctatgaccat in wild-type; gatccggcca in strain UV5 [26]"
       ]
      }
     },
     {
      "type": "CDS",
      "label": "lacZ",
      "segments": [
       [
        1284,
        4358
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "codon_start": [
        "1"
       ],
       "gene": [
        "lacZ"
       ],
       "label": [
        "lacZ"
       ],
       "note": [
        "beta-d-galactosidase"
       ],
       "protein_id": [
        "AAA24053.1"
       ],
       "transl_table": [
        "11"
       ]
      }
     },
     {
      "type": "CDS",
      "label": "lacY",
      "segments": [
       [
        4410,
        5663
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "codon_start": [
        "1"
       ],
       "gene": [
        "lacY"
       ],
       "label": [
        "lacY"
       ],
       "note": [
        "lactose permease"
       ],
       "protein_id": [
        "AAA24054.1"
       ],
       "transl_table": [
        "11"
       ]
      }
     },
     {
      "type": "CDS",
      "label": "lacA",
      "segments": [
       [
        5727,
        6338
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "codon_start": [
        "1"
       ],
       "gene": [
        "lacA"
       ],
       "label": [
        "lacA"
       ],
       "note": [
        "thiogalactoside acetyltransferase (ttg start codon)"
       ],
       "protein_id": [
        "AAA24055.1"
       ],
       "transl_table": [
        "11"
       ]
      }
     }
    ]
   }
  },
  {
   "file": "dna/synthetic-pbr322.dna",
   "sha256": "da6912f3e174bcbfb37c8f21e970e1165ec94ce5332c0ff4ccf24496a3dc9848",
   "expected": {
    "length": 4361,
    "sequenceSha256": "536042a7485bdabdf49c4d21a306213a098d77d19bdba57a1c6adc76ce2b8372",
    "topology": "circular",
    "features": [
     {
      "type": "misc_binding",
      "label": "echinomycin",
      "segments": [
       [
        24,
        27
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "bound_moiety": [
        "echinomycin"
       ],
       "label": [
        "echinomycin"
       ]
      }
     },
     {
      "type": "regulatory",
      "label": "promoter P1 (6)",
      "segments": [
       [
        27,
        33
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "promoter P1 (6)"
       ],
       "note": [
        "promoter P1 (6)"
       ],
       "regulatory_class": [
        "promoter"
       ]
      }
     },
     {
      "type": "misc_binding",
      "label": "echinomycin",
      "segments": [
       [
        39,
        42
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "bound_moiety": [
        "echinomycin"
       ],
       "label": [
        "echinomycin"
       ]
      }
     },
     {
      "type": "regulatory",
      "label": "promoter P2 (6)",
      "segments": [
       [
        43,
        49
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "promoter P2 (6)"
       ],
       "note": [
        "promoter P2 (6)"
       ],
       "regulatory_class": [
        "promoter"
       ]
      }
     },
     {
      "type": "misc_binding",
      "label": "echinomycin",
      "segments": [
       [
        53,
        56
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "bound_moiety": [
        "echinomycin"
       ],
       "label": [
        "echinomycin"
       ]
      }
     },
     {
      "type": "misc_binding",
      "label": "echinomycin",
      "segments": [
       [
        67,
        70
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "bound_moiety": [
        "echinomycin"
       ],
       "label": [
        "echinomycin"
       ]
      }
     },
     {
      "type": "misc_binding",
      "label": "echinomycin",
      "segments": [
       [
        80,
        83
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "bound_moiety": [
        "echinomycin"
       ],
       "label": [
        "echinomycin"
       ]
      }
     },
     {
      "type": "CDS",
      "label": "tet",
      "segments": [
       [
        86,
        1276
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "codon_start": [
        "1"
       ],
       "gene": [
        "tet"
       ],
       "label": [
        "tet"
       ],
       "product": [
        "tetracycline resistance protein"
       ],
       "protein_id": [
        "AAB59735.1"
       ],
       "transl_table": [
        "11"
       ]
      }
     },
     {
      "type": "misc_feature",
      "label": "Endo.Sce I cleavage site coordinated with site at base 146 (",
      "segments": [
       [
        141,
        142
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "Endo.Sce I cleavage site coordinated with site at base 146 ("
       ],
       "note": [
        "Endo.Sce I cleavage site coordinated with site at base 146 (10)"
       ]
      }
     },
     {
      "type": "misc_feature",
      "label": "tet",
      "segments": [
       [
        146,
        147
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "gene": [
        "tet"
       ],
       "label": [
        "tet"
       ],
       "note": [
        "Endo.Sce I cleavage site coordinated with site at base 142 (10)"
       ]
      }
     },
     {
      "type": "misc_binding",
      "label": "tet",
      "segments": [
       [
        411,
        414
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "bound_moiety": [
        "echinomycin"
       ],
       "gene": [
        "tet"
       ],
       "label": [
        "tet"
       ]
      }
     },
     {
      "type": "misc_difference",
      "label": "tet",
      "segments": [
       [
        426,
        426
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "gene": [
        "tet"
       ],
       "label": [
        "tet"
       ],
       "note": [
        "conflict"
       ]
      }
     },
     {
      "type": "misc_binding",
      "label": "tet",
      "segments": [
       [
        469,
        472
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "bound_moiety": [
        "echinomycin"
       ],
       "gene": [
        "tet"
       ],
       "label": [
        "tet"
       ]
      }
     },
     {
      "type": "old_sequence",
      "label": "tet",
      "segments": [
       [
        526,
        528
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "gene": [
        "tet"
       ],
       "label": [
        "tet"
       ]
      }
     },
     {
      "type": "repeat_region",
      "label": "gamma-delta insertion target sequence",
      "segments": [
       [
        1515,
        1519
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "gamma-delta insertion target sequence"
       ],
       "note": [
        "gamma-delta insertion target sequence"
       ]
      }
     },
     {
      "type": "misc_feature",
      "label": "from pSC101 (bp 1860-1986)",
      "segments": [
       [
        1636,
        1762
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "from pSC101 (bp 1860-1986)"
       ],
       "note": [
        "from pSC101 (bp 1860-1986)"
       ]
      }
     },
     {
      "type": "repeat_region",
      "label": "gamma-delta insertion target sequence",
      "segments": [
       [
        1788,
        1792
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "gamma-delta insertion target sequence"
       ],
       "note": [
        "gamma-delta insertion target sequence"
       ]
      }
     },
     {
      "type": "misc_difference",
      "label": "conflict",
      "segments": [
       [
        1891,
        1892
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "conflict"
       ],
       "note": [
        "conflict"
       ]
      }
     },
     {
      "type": "old_sequence",
      "label": "old_sequence",
      "segments": [
       [
        1892,
        1893
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "old_sequence"
       ]
      }
     },
     {
      "type": "regulatory",
      "label": "ribosome_binding_site",
      "segments": [
       [
        1905,
        1910
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "ribosome_binding_site"
       ],
       "regulatory_class": [
        "ribosome_binding_site"
       ]
      }
     },
     {
      "type": "regulatory",
      "label": "Shine-Dalgarno sequence",
      "segments": [
       [
        1905,
        1909
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "Shine-Dalgarno sequence"
       ],
       "note": [
        "Shine-Dalgarno sequence"
       ],
       "regulatory_class": [
        "ribosome_binding_site"
       ]
      }
     },
     {
      "type": "misc_difference",
      "label": "conflict",
      "segments": [
       [
        1913,
        1914
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "conflict"
       ],
       "note": [
        "conflict"
       ]
      }
     },
     {
      "type": "old_sequence",
      "label": "old_sequence",
      "segments": [
       [
        1914,
        1915
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "old_sequence"
       ]
      }
     },
     {
      "type": "CDS",
      "label": "ROP protein",
      "segments": [
       [
        1915,
        2106
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "codon_start": [
        "1"
       ],
       "label": [
        "ROP protein"
       ],
       "product": [
        "ROP protein"
       ],
       "protein_id": [
        "AAB59736.1"
       ],
       "transl_table": [
        "11"
       ]
      }
     },
     {
      "type": "misc_feature",
      "label": "H-strand Y effector site",
      "segments": [
       [
        2011,
        2167
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "H-strand Y effector site"
       ],
       "note": [
        "H-strand Y effector site"
       ]
      }
     },
     {
      "type": "repeat_region",
      "label": "gamma-delta insertion target sequence",
      "segments": [
       [
        2245,
        2249
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "gamma-delta insertion target sequence"
       ],
       "note": [
        "gamma-delta insertion target sequence"
       ]
      }
     },
     {
      "type": "misc_feature",
      "label": "L-strand Y effector site",
      "segments": [
       [
        2351,
        2414
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "L-strand Y effector site"
       ],
       "note": [
        "L-strand Y effector site"
       ]
      }
     },
     {
      "type": "misc_binding",
      "label": "dnaA",
      "segments": [
       [
        2439,
        2447
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "bound_moiety": [
        "dnaA"
       ],
       "label": [
        "dnaA"
       ]
      }
     },
     {
      "type": "rep_origin",
      "label": "rep_origin",
      "segments": [
       [
        2535,
        2535
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "rep_origin"
       ]
      }
     },
     {
      "type": "old_sequence",
      "label": "revision according to (17)",
      "segments": [
       [
        2729,
        2730
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "revision according to (17)"
       ],
       "note": [
        "revision according to (17)"
       ]
      }
     },
     {
      "type": "old_sequence",
      "label": "old_sequence",
      "segments": [
       [
        2729,
        2729
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "old_sequence"
       ]
      }
     },
     {
      "type": "old_sequence",
      "label": "revision according to (16)",
      "segments": [
       [
        2730,
        2730
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "revision according to (16)"
       ],
       "note": [
        "revision according to (16)"
       ]
      }
     },
     {
      "type": "mobile_element",
      "label": "mobile_element",
      "segments": [
       [
        3148,
        4361
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "mobile_element"
       ]
      }
     },
     {
      "type": "repeat_region",
      "label": "corresponds to one of the 38bp repeats found in Tn3 (bp 1-38",
      "segments": [
       [
        3148,
        3185
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "corresponds to one of the 38bp repeats found in Tn3 (bp 1-38"
       ],
       "note": [
        "corresponds to one of the 38bp repeats found in Tn3 (bp 1-38 and complement (4920-4957))"
       ]
      }
     },
     {
      "type": "CDS",
      "label": "bla",
      "segments": [
       [
        3293,
        4153
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "codon_start": [
        "1"
       ],
       "gene": [
        "bla"
       ],
       "label": [
        "bla"
       ],
       "note": [
        "E-286"
       ],
       "product": [
        "beta-lactamase"
       ],
       "protein_id": [
        "AAB59737.1"
       ],
       "transl_table": [
        "11"
       ]
      }
     },
     {
      "type": "sig_peptide",
      "label": "bla",
      "segments": [
       [
        4085,
        4153
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "gene": [
        "bla"
       ],
       "label": [
        "bla"
       ]
      }
     },
     {
      "type": "mat_peptide",
      "label": "bla",
      "segments": [
       [
        3296,
        4084
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "gene": [
        "bla"
       ],
       "label": [
        "bla"
       ],
       "product": [
        "beta-lactamase"
       ]
      }
     },
     {
      "type": "regulatory",
      "label": "Shine-Dalgarno sequence",
      "segments": [
       [
        4161,
        4165
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "Shine-Dalgarno sequence"
       ],
       "note": [
        "Shine-Dalgarno sequence"
       ],
       "regulatory_class": [
        "ribosome_binding_site"
       ]
      }
     },
     {
      "type": "regulatory",
      "label": "promoter P3 (6)",
      "segments": [
       [
        4188,
        4194
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "promoter P3 (6)"
       ],
       "note": [
        "promoter P3 (6)"
       ],
       "regulatory_class": [
        "promoter"
       ]
      }
     },
     {
      "type": "misc_binding",
      "label": "echinomycin",
      "segments": [
       [
        4268,
        4271
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "bound_moiety": [
        "echinomycin"
       ],
       "label": [
        "echinomycin"
       ]
      }
     },
     {
      "type": "misc_binding",
      "label": "echinomycin",
      "segments": [
       [
        4280,
        4283
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "bound_moiety": [
        "echinomycin"
       ],
       "label": [
        "echinomycin"
       ]
      }
     },
     {
      "type": "misc_binding",
      "label": "echinomycin",
      "segments": [
       [
        4285,
        4288
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "bound_moiety": [
        "echinomycin"
       ],
       "label": [
        "echinomycin"
       ]
      }
     },
     {
      "type": "misc_binding",
      "label": "echinomycin",
      "segments": [
       [
        4296,
        4299
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "bound_moiety": [
        "echinomycin"
       ],
       "label": [
        "echinomycin"
       ]
      }
     },
     {
      "type": "misc_binding",
      "label": "echinomycin",
      "segments": [
       [
        4311,
        4314
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "bound_moiety": [
        "echinomycin"
       ],
       "label": [
        "echinomycin"
       ]
      }
     },
     {
      "type": "misc_binding",
      "label": "echinomycin",
      "segments": [
       [
        4317,
        4320
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "bound_moiety": [
        "echinomycin"
       ],
       "label": [
        "echinomycin"
       ]
      }
     },
     {
      "type": "misc_binding",
      "label": "echinomycin",
      "segments": [
       [
        4331,
        4334
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "bound_moiety": [
        "echinomycin"
       ],
       "label": [
        "echinomycin"
       ]
      }
     }
    ]
   }
  },
  {
   "file": "dna/synthetic-pcineo.dna",
   "sha256": "79bd56a92dc05581cef5da8e8533158c78095b7cb018e135f44ce0fb3396d326",
   "expected": {
    "length": 5472,
    "sequenceSha256": "01a9d3c456ed72050e1d56f3ff970ea8aa26def2647b9d2c36cf11c9e9df47ce",
    "topology": "circular",
    "features": [
     {
      "type": "regulatory",
      "label": "Cytomegalovirus immediate-early enhancer",
      "segments": [
       [
        1,
        659
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "Cytomegalovirus immediate-early enhancer"
       ],
       "note": [
        "Non-ASCII: β-lactamase, 5′ to 3′, 37 °C, µg"
       ],
       "regulatory_class": [
        "enhancer"
       ]
      }
     },
     {
      "type": "regulatory",
      "label": "Cytomegalovirus immediate-early promoter",
      "segments": [
       [
        669,
        750
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "Cytomegalovirus immediate-early promoter"
       ],
       "note": [
        "Cytomegalovirus immediate-early promoter"
       ],
       "regulatory_class": [
        "promoter"
       ]
      }
     },
     {
      "type": "intron",
      "label": "chimeric intron",
      "segments": [
       [
        890,
        1022
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "chimeric intron"
       ],
       "note": [
        "chimeric intron"
       ]
      }
     },
     {
      "type": "regulatory",
      "label": "T7 promoter",
      "segments": [
       [
        1067,
        1085
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "T7 promoter"
       ],
       "note": [
        "T7 promoter"
       ],
       "regulatory_class": [
        "promoter"
       ]
      }
     },
     {
      "type": "misc_feature",
      "label": "multiple cloning sites",
      "segments": [
       [
        1085,
        1137
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "multiple cloning sites"
       ],
       "note": [
        "multiple cloning sites"
       ]
      }
     },
     {
      "type": "regulatory",
      "label": "T3 promoter",
      "segments": [
       [
        1140,
        1158
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "T3 promoter"
       ],
       "note": [
        "T3 promoter"
       ],
       "regulatory_class": [
        "promoter"
       ]
      }
     },
     {
      "type": "regulatory",
      "label": "SV40 late polyadenylation signal",
      "segments": [
       [
        1167,
        1388
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "SV40 late polyadenylation signal"
       ],
       "note": [
        "SV40 late polyadenylation signal"
       ],
       "regulatory_class": [
        "polyA_signal_sequence"
       ]
      }
     },
     {
      "type": "rep_origin",
      "label": "phage f1 region",
      "segments": [
       [
        1483,
        1938
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "phage f1 region"
       ],
       "note": [
        "phage f1 region"
       ]
      }
     },
     {
      "type": "regulatory",
      "label": "SV40 enhancer and early promoter - neomycin selectable marke",
      "segments": [
       [
        2002,
        2418
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "SV40 enhancer and early promoter - neomycin selectable marke"
       ],
       "note": [
        "SV40 enhancer and early promoter - neomycin selectable marker"
       ],
       "regulatory_class": [
        "promoter"
       ]
      }
     },
     {
      "type": "rep_origin",
      "label": "SV40 minimum origin of replication - neomycin selectable mar",
      "segments": [
       [
        2316,
        2381
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "SV40 minimum origin of replication - neomycin selectable mar"
       ],
       "note": [
        "SV40 minimum origin of replication - neomycin selectable marker"
       ]
      }
     },
     {
      "type": "CDS",
      "label": "NeoR",
      "segments": [
       [
        2463,
        3257
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "codon_start": [
        "1"
       ],
       "gene": [
        "NeoR"
       ],
       "label": [
        "NeoR"
       ],
       "product": [
        "neomycin phosphotransferase"
       ],
       "protein_id": [
        "AAA88781.1"
       ]
      }
     },
     {
      "type": "regulatory",
      "label": "synthetic polyadenylation signal - neomycin selectable marke",
      "segments": [
       [
        3321,
        3369
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "synthetic polyadenylation signal - neomycin selectable marke"
       ],
       "note": [
        "synthetic polyadenylation signal - neomycin selectable marker"
       ],
       "regulatory_class": [
        "polyA_signal_sequence"
       ]
      }
     },
     {
      "type": "CDS",
      "label": "ampR",
      "segments": [
       [
        3780,
        4640
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "codon_start": [
        "1"
       ],
       "gene": [
        "ampR"
       ],
       "label": [
        "ampR"
       ],
       "product": [
        "beta-lactamase"
       ],
       "protein_id": [
        "AAA88782.1"
       ]
      }
     }
    ]
   }
  },
  {
   "file": "dna/synthetic-pgem3z-origin.dna",
   "sha256": "845d1e2c7e231c58866834bb7cdbc649e32f893eebb114cf7d8f0ac963bed889",
   "expected": {
    "length": 2743,
    "sequenceSha256": "4f560f61d69429fe294d5d5218159d1e5c69a7025ce66fc439c680ef7ffb6b9a",
    "topology": "circular",
    "features": [
     {
      "type": "misc_feature",
      "label": "lac operon sequence",
      "segments": [
       [
        2564,
        2724
       ],
       [
        94,
        323
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "lac operon sequence"
       ],
       "note": [
        "lac operon sequence"
       ]
      }
     },
     {
      "type": "regulatory",
      "label": "T7 promoter",
      "segments": [
       [
        2727,
        2743
       ],
       [
        1,
        3
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "T7 promoter"
       ],
       "note": [
        "T7 promoter"
       ],
       "regulatory_class": [
        "promoter"
       ]
      }
     },
     {
      "type": "misc_feature",
      "label": "T7 transcription initiation site",
      "segments": [
       [
        1,
        1
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "T7 transcription initiation site"
       ],
       "note": [
        "T7 transcription initiation site"
       ]
      }
     },
     {
      "type": "misc_feature",
      "label": "multiple cloning sites",
      "segments": [
       [
        5,
        61
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "multiple cloning sites"
       ],
       "note": [
        "multiple cloning sites"
       ]
      }
     },
     {
      "type": "regulatory",
      "label": "SP6 promoter",
      "segments": [
       [
        67,
        86
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "SP6 promoter"
       ],
       "note": [
        "SP6 promoter"
       ],
       "regulatory_class": [
        "promoter"
       ]
      }
     },
     {
      "type": "misc_feature",
      "label": "SP6 transcription initiation site",
      "segments": [
       [
        69,
        69
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "SP6 transcription initiation site"
       ],
       "note": [
        "SP6 transcription initiation site"
       ]
      }
     },
     {
      "type": "primer_bind",
      "label": "pUC/M13 reverse sequencing primer",
      "segments": [
       [
        104,
        125
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "pUC/M13 reverse sequencing primer"
       ],
       "note": [
        "pUC/M13 reverse sequencing primer"
       ]
      }
     },
     {
      "type": "misc_feature",
      "label": "lacZ",
      "segments": [
       [
        106,
        108
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "gene": [
        "lacZ"
       ],
       "label": [
        "lacZ"
       ],
       "note": [
        "lacZ start codon"
       ]
      }
     },
     {
      "type": "misc_feature",
      "label": "lac operator",
      "segments": [
       [
        128,
        144
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "lac operator"
       ],
       "note": [
        "lac operator"
       ]
      }
     },
     {
      "type": "CDS",
      "label": "bla",
      "segments": [
       [
        1265,
        2125
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "codon_start": [
        "1"
       ],
       "gene": [
        "bla"
       ],
       "label": [
        "bla"
       ],
       "product": [
        "beta-lactamase"
       ],
       "protein_id": [
        "CAA46396.2"
       ],
       "transl_table": [
        "11"
       ]
      }
     },
     {
      "type": "primer_bind",
      "label": "pUC/M13 forward sequencing primer",
      "segments": [
       [
        2677,
        2700
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "pUC/M13 forward sequencing primer"
       ],
       "note": [
        "pUC/M13 forward sequencing primer"
       ]
      }
     },
     {
      "type": "primer_bind",
      "label": "pUC/M13 forward sequencing primer",
      "segments": [
       [
        2677,
        2700
       ]
      ],
      "strand": "+",
      "qualifiers": {
       "label": [
        "pUC/M13 forward sequencing primer"
       ]
      }
     },
     {
      "type": "primer_bind",
      "label": "pUC/M13 reverse sequencing primer",
      "segments": [
       [
        104,
        125
       ]
      ],
      "strand": "-",
      "qualifiers": {
       "label": [
        "pUC/M13 reverse sequencing primer"
       ]
      }
     }
    ]
   }
  },
  {
   "file": "dna/synthetic-puc19-linear.dna",
   "sha256": "3ddbfcfbfe034e3a5214a102357f95843b23558a769151c1498b62d5d1c1eed6",
   "expected": {
    "length": 2686,
    "sequenceSha256": "8a205af08518dae1b0045c7b098986dca18824ef654e75233603602ab89cad04",
    "topology": "linear",
    "features": []
   }
  }
 ]
}
