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assay-report-template.md
56 lines · skills/primer-design/assets/assay-report-template.md at 5f2bc03
Primer design evidence report
Raw lines 1 to 23## Assay and intended conclusion
5- Purpose, template type, organism, and intended target/isoforms:
6- Intended and explicitly excluded products:
7- Product-size requirement and reason:
8- Current evidence level: computational candidate / experimental results available:
Assay and intended conclusion
- Purpose, template type, organism, and intended target/isoforms:
- Intended and explicitly excluded products:
- Product-size requirement and reason:
- Current evidence level: computational candidate / experimental results available:
10## Reference manifest
12| File | Source URL/accession.version | Assembly/transcript release | Retrieval date | SHA-256 | Scope and limitations |
13| --- | --- | --- | --- | --- | --- |
15Record local-to-reference coordinate mapping, strand, circularity, and annotation source.
16Record variant/repeat mask source, release, thresholds, and coordinate transformation.
Reference manifest
| File | Source URL/accession.version | Assembly/transcript release | Retrieval date | SHA-256 | Scope and limitations |
|---|
Record local-to-reference coordinate mapping, strand, circularity, and annotation source. Record variant/repeat mask source, release, thresholds, and coordinate transformation.
Raw lines 10 to 1718## Reaction and design assumptions
20- Polymerase and buffer formulation:
21- Monovalent / total divalent / total dNTP concentrations (mM):
22- Initial reaction primer concentration (nM):
23- Primer3 effective annealing-oligo concentration (nM) and rationale:
24- Design constraints, engine versions, and report paths:
25- Assumptions requiring confirmation:
Reaction and design assumptions
- Polymerase and buffer formulation:
- Monovalent / total divalent / total dNTP concentrations (mM):
- Initial reaction primer concentration (nM):
- Primer3 effective annealing-oligo concentration (nM) and rationale:
- Design constraints, engine versions, and report paths:
- Assumptions requiring confirmation:
27## Candidate oligos
29| Pair | Role | Annealing core 5′→3′ | 5′ tail | Full order sequence 5′→3′ | Core Tm / conditions | Binding interval |
30| --- | --- | --- | --- | --- | --- | --- |
32State coordinate convention and reference ID. Do not reverse-complement a returned
33reverse-primer ordering sequence again. Include intended product sequence/length and,
34for tailed assays, the separately reconstructed final product.
Candidate oligos
| Pair | Role | Annealing core 5′→3′ | 5′ tail | Full order sequence 5′→3′ | Core Tm / conditions | Binding interval |
|---|
State coordinate convention and reference ID. Do not reverse-complement a returned reverse-primer ordering sequence again. Include intended product sequence/length and, for tailed assays, the separately reconstructed final product.
Raw lines 27 to 3536## Specificity evidence
38| Pair | Intended products recovered | Potential unintended products | Search engine/reference | Search limits/completeness | Decision and reason |
39| --- | --- | --- | --- | --- | --- |
41Include FF/RR as well as FR products, 3′ mismatch positions, unknown-base regions,
42cap saturation, and heuristic limitations. For multiplex, include cross-pair products.
Specificity evidence
| Pair | Intended products recovered | Potential unintended products | Search engine/reference | Search limits/completeness | Decision and reason |
|---|
Include FF/RR as well as FR products, 3′ mismatch positions, unknown-base regions, cap saturation, and heuristic limitations. For multiplex, include cross-pair products.
Raw lines 36 to 4344## Thermodynamic evidence
46Record core Tm, full-oligo hairpins and dimers, directional 3′ interactions, chemistry,
47temperature for delta-G, unsupported calculations, and relevant panel interactions.
48Explain assay-specific ranking; do not invent universal pass thresholds.
Thermodynamic evidence
Record core Tm, full-oligo hairpins and dimers, directional 3′ interactions, chemistry, temperature for delta-G, unsupported calculations, and relevant panel interactions. Explain assay-specific ranking; do not invent universal pass thresholds.
Raw lines 44 to 4950## Experimental checks and final recommendation
52- Product identity/size evidence and relevant controls:
53- Quantitative assay efficiency, dynamic range, and precision when applicable:
54- Findings supporting each selected candidate:
55- Unresolved questions and next validation steps:
56- Output files, hashes, and upstream method citations:
Experimental checks and final recommendation
- Product identity/size evidence and relevant controls:
- Quantitative assay efficiency, dynamic range, and precision when applicable:
- Findings supporting each selected candidate:
- Unresolved questions and next validation steps:
- Output files, hashes, and upstream method citations: