{
  "analysis_date_WIB": "2026-10-01",
  "execution": "external local Python run, not Kernel",
  "software_versions": {
    "dnachisel": "3.2.16",
    "python_codon_tables": "0.1.18",
    "biopython": "1.88",
    "numpy": "2.5.3"
  },
  "seed": 20261001,
  "intended_host": "Bacillus subtilis; production strain not selected",
  "table": "b_subtilis_1423; package species-level Kazusa/NCBI-derived snapshot; not a curated highly expressed-gene set",
  "method": "CodonOptimize(method=match_codon_usage) over 261 sense codons",
  "constraints": [
    "same 261-aa bacterial-code protein",
    "native ATG retained",
    "native TAA retained"
  ],
  "not_constrained_or_predicted": [
    "GC target",
    "restriction-site avoidance",
    "mRNA folding",
    "secretion efficiency",
    "vendor synthesis acceptance"
  ],
  "native": {
    "length_bp": 786,
    "gc_percent": 37.659033078880405,
    "max_homopolymer_nt": 6,
    "sha256": "f39e94ef48fbfd98c320cae57cdd859fac1ca239c2e995a340013afe59f24a3a"
  },
  "candidate": {
    "length_bp": 786,
    "gc_percent": 42.49363867684478,
    "max_homopolymer_nt": 7,
    "sha256": "1c6160793711da702eae16da1fa266116ddf5b88cbc25268418c0bba4921159c"
  },
  "nucleotide_substitutions": 52,
  "synonymous_codons_changed": 47,
  "protein_length_aa_without_stop": 261,
  "match_codon_usage_objective_score_before": -88.17999999999998,
  "match_codon_usage_objective_score_after": -12.360000000000003,
  "objective_interpretation": "Closer to zero is better for this discrepancy objective; this is not CAI and not measured expression. Rounding/discrete codon counts can prevent a perfect profile match.",
  "CAI": "Not computed/reported; avoid claiming that this codon-profile objective is a CAI result.",
  "checks": {
    "length_786_bp": true,
    "only_acgt": true,
    "start_atg_preserved": true,
    "terminal_taa_preserved": true,
    "protein_identical_261_aa": true,
    "no_internal_in_frame_stops": true,
    "native_matches_verified_v2": true,
    "optimizer_constraints_pass": true
  },
  "candidate_not_imported_or_screened_in_Kernel": true,
  "native_v2_unchanged": true,
  "assignment_acceptance": "External alternative; instructor acceptance of replacing the requested Kernel optimization step has not been confirmed.",
  "sources": [
    "https://edinburgh-genome-foundry.github.io/DnaChisel/ref/builtin_specifications.html",
    "https://github.com/Edinburgh-Genome-Foundry/python_codon_tables",
    "https://www.kazusa.or.jp/codon/"
  ]
}