Emitted products

{% if product_groups %}

Exact products written by this run. Antigen positions are zero-based, end-exclusive amino-acid positions in the peptide or encoded protein.

{% for group in product_groups %}

{{ group.modality }}

Constructs: {{ group.counts.constructs }} ({{ group.counts.unique_construct_sequences }} unique sequences). Antigen slots: {{ group.counts.antigen_slots }}. Unique antigen sequences: {{ group.counts.unique_antigen_sequences if group.counts.unique_antigen_sequences is not none else 'unavailable in this historical design' }}.

{% if selection_policy and group.modality in selection_policy.modalities %}{% set settings = selection_policy.modalities[group.modality] %}

{{ settings.origin | e }}

{% for label, value in settings.rows %}{% endfor %}
{{ label | e }}{{ value | e }}
{% endif %} {% if group.counts.source_candidates %}

Recorded source events: {{ group.counts.source_events }}. Candidate mappings without a recorded event: {{ group.counts.source_candidates_without_event }}. Related alternative sequences do not establish independent target coverage.

{% endif %} {% if group.assembly_decisions is defined %} {% if group.assembly_decisions is not none %}

Assembly order: {{ group.assembly_decisions.order | replace('_', ' ') }}. Identical final amino-acid sequences share one antigen slot, retaining all source mappings. Distinct overlapping sequences remain separate; their source-event count is reported above.

{% for decision in group.assembly_decisions.rows %}{% endfor %}
Order / sourcesFinal antigen sequencePacking outcome
{{ decision.order }}: {% for source in decision.sources %}{{ source }}{% if not loop.last %}, {% endif %}{% endfor %}
{{ decision.mapping_count }} candidate mappings		 {{ decision.sequence }}{{ decision.outcome | replace('_', ' ') }}{% if decision.products %}: {{ decision.products | join(', ') }}{% endif %}
{% else %}

Historical assembly ordering, deduplication and capacity decisions were not recorded. Product mappings below describe the saved result.

{% endif %}{% endif %} {% if group.files %}

Product files (relative to the run output directory): {% for file in group.files %}{{ file }}{% if not loop.last %}; {% endif %}{% endfor %}.

{% endif %} {% for product in group.products %}

{{ product.display_name | e }} · {{ product.length }} {{ product.unit }}

Product ID: {{ product.name | e }}

{% if product.window_decisions %}

Recorded window rationale: {% for decision in product.window_decisions %}{{ decision }}{% if not loop.last %}, {% endif %}{% endfor %}.

{% else %}

A window-selection rationale was not recorded for this product.

{% endif %} {% if product.junction %}
Linker decisions

{{ product.junction.status | e }}.

{% if product.junction.rows %}{% for label, value in product.junction.rows %}{% endfor %}
{{ label | e }}{{ value | e }}
{% if not product.junction.decisions %}

The recorded comparison is for the complete construct. Independent per-junction benefit was not recorded.

{% endif %}{% endif %} {% for linker in product.junction.linkers %}

Junction {{ linker.junction_index }}: {{ linker.name | e }}; {{ linker.aa }}. Encoded protein [{{ linker.start_aa }}, {{ linker.end_aa }}).

{% endfor %}{% endif %} {% if product.junction and product.junction.decisions %}

Per-junction preference minimizes strong count, mild count, then negative minimum rank; exact ties retain candidate order. The complete construct comparison above determines whether the preferred linkers or the shared default are emitted.

{% for decision in product.junction.decisions %}{% endfor %}
JunctionPreferred / emittedCandidate ordering keys
{{ decision.junction_index }}{{ decision.preferred_linker | e }} / {{ decision.emitted_linker | e }}{% for alternative in decision.candidates %}{{ alternative.linker | e }}: {{ alternative.key | tojson | e }}, order {{ alternative.candidate_order }}{% if not loop.last %}
{% endif %}{% endfor %}
{% endif %} {% if product.unit == 'aa' %}

N-terminal acetylation: {{ 'yes' if product.n_terminal_acetylation else 'no' }}; C-terminal amidation: {{ 'yes' if product.c_terminal_amidation else 'no' }}.

{% endif %}

{{ 'Full nucleotide sequence, including polyA' if product.unit == 'nt' else 'Manufactured amino-acid sequence' }}:

{% if product.sequence_html %}
{{ product.sequence_html }}
{% else %}
{{ product.sequence | wordwrap(70, break_long_words=True) }}
{% endif %} {% if product.protein %}

Encoded protein:

{{ product.protein_html }}
{% endif %} {% if product.antigens %} {% for antigen in product.antigens %} {% endfor %}
Antigen / source genesExact antigen sequencePosition [start, end)Source mappings
{{ antigen.display_name }}
Antigen {{ loop.index }} label {% for label in antigen.context_labels %}
{{ label }}{% endfor %}		 {{ antigen.sequence_html }}{% if not antigen.target_coordinates_known %}
Target coordinates unavailable or differ across sources.{% endif %}		[{{ antigen.start }}, {{ antigen.end }})
{{ antigen.length }} aa		 {{ antigen.sources if antigen.sources is not none else "unavailable" }} candidate mapping{{ "" if antigen.sources == 1 else "s" }}; {{ antigen.transcripts if antigen.transcripts is not none else "unavailable" }} transcript{{ "" if antigen.transcripts == 1 else "s" }} {% if antigen.source_ids %}
Report sources: {% for source in antigen.source_ids %}{{ source }}{% if not loop.last %}, {% endif %}{% endfor %}{% endif %}

Full antigen labels and source identities are in Methods and provenance. Exact evidence mappings remain in the manifest and native dataset.

{% for antigen in product.antigens %}{% if antigen.target_intervals %}

Antigen {{ loop.index }} targetable regions within its sequence: {% for start, end in antigen.target_intervals %}[{{ start }}, {{ end }}){% if not loop.last %}, {% endif %}{% endfor %}.

{% endif %}{% endfor %} {% else %}

Historical product: antigen placement/source mappings were not recorded. Labels: {{ product.antigen_names | join(', ') }}.

{% endif %} {% if include_manufacturability and product.manufacturability %}
Manufacturability metrics
{% for key, value in product.manufacturability.items() %} {% endfor %}
{{ key | replace('_', ' ') }}{{ value }}
{% endif %}
{% else %}

No {{ group.modality }} products were emitted.

{% endfor %}
{% endfor %} {% else %}

No construct files were emitted. Use --output-dir to request product assembly. Candidate windows are analysis results.

{% endif %}