Output Format

Each optimized sequence includes:

Field	Description
Optimized CDS	Synonymous codon replacements only — AA identity 100%
CAI score	Codon adaptation index for the selected host codon table
GC content	Global and first-region (first 90 nt)
Scan report	PolyA signals, CpG/TpA hotspots, homopolymers, rare codon runs, restriction sites
Domestication report	BsaI/BsmBI and custom restriction sites removed, edit count
Construct ID	Reproducible hash for tracking and reproducibility

FASTA Output

Profile-engine CLI --output FASTA uses self-describing metadata headers:

>target_optimized|engine=profile|profile=balanced|cai=0.810|gc=52.40|score=0.730
ATGAAACAGTTGGTCCTGGGG...

Profile output does not emit an objective field. objective is reserved for the DP feasibility engine, where objective=feasibility_best identifies the DP objective; profile-engine output is identified by engine=profile and profile=<profile>.

GenBank Output

GenBank format includes all metadata as FEATURES annotations, suitable for review in sequence editing tools (Benchling, SnapGene, etc.).

Validator Contract

The design pipeline emits an output only after the hard-fail validator passes:

Check	Requirement
Amino acid identity	100%
Internal stop codons	0
Invalid codons	0
Sequence length	Correct (input AA × 3)

If any check fails, no output is produced.