Fig. 1

Schematic detailing AutoCloner, a homologue-specific primer design pipeline for polyploids. a The user inputs a DNA sequence which they wish to clone in a variety for which this sequence is unknown. b AutoCloner finds flanking regions and homologues through BLAST, generates a multiple sequence alignment with Muscle and scans the alignment for SNPs. c The best possible combination of primers, whose overlapping products span the entire input sequence, are returned by the pipeline via Primer3