Mode 3: FASTA + MISA + GFF + Annotation

Complete SSR primer design with full genomic annotation. This mode combines SSR detection, genomic feature annotation (exon/intron/UTR), and functional annotations to provide comprehensive primer design results.

DNA sequences in FASTA format
SSR catalog from MISA (TSV)
GFF file with gene structure (e.g., from AUGUSTUS)
Functional annotation table (TSV)
Download Sample File (.tsv) — view required column format
Example: 500-900 or 400-1000
Primer pairs per SSR region (1-10)
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Input: FASTA + MISA + GFF + Annotation
Output: TSV
Classifies: Exon / Intron / UTR / Intergenic
Includes: GO terms, gene descriptions, Tm, GC%