Output fields

TSV and JSON contain the same logical fields. Empty pair-specific fields on a no_candidates row are expected.

Target and run

Field	Meaning
target_id	Stable target label
source	Input adapter, such as fasta, bed, or snapgene
reference_name	Source reference identifier
feature_strand	Strand of the source annotation when available
target_start, target_end	Required interval on the source reference
status, message	Design outcome and explanation
rank	Primer3 pair rank, starting at 1
workflow, context, converted_strand	Chemistry settings
design_engine	primer3
metadata, parameters	JSON objects describing source and design settings

Amplicon

Field	Meaning
amplicon_start, amplicon_end, amplicon_length	Complete product coordinates and size
amplicon_reference_sequence	Original top-reference product sequence
amplicon_unconverted_sequence	Product in converted-strand orientation before conversion
amplicon_converted_sequence	Predicted conversion-aware product

Primers

Forward and reverse fields use the same suffixes:

Suffix	Meaning
_start, _end	Binding-site coordinates on the top reference
_unconverted_sequence	Binding sequence before conversion, in primer orientation
_order_sequence	Final 5′→3′ IUPAC sequence to review for ordering
_tm	Primer3 Tm for the concrete expected converted allele
_gc_fraction	Primer3 GC percentage divided by 100
_degeneracies	Number of non-ACGT bases in the order sequence

pair_score is Primer3's pair penalty; lower ranks are preferred within the same run.

Specificity

Specificity fields are populated only when a Bowtie index is supplied:

• specificity_status
• specificity_index
• specificity_mismatches
• specificity_forward_hits
• specificity_reverse_hits
• specificity_intended_amplicons
• specificity_off_target_amplicons
• specificity_off_target_loci

The GenBank companion stores the same design context as feature qualifiers and retains source annotations when the input supplies them.