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Primer3 allows users to specify a library of "mispriming" sequences (repeats). v0.4.0 improved how it handles ambiguity codes (N, R, Y, etc.) within these libraries. This prevents the design of primers that anneal to Alu repeats or LINE elements, a common cause of spurious bands in genomic PCR.

Imagine a researcher in a windowless lab, staring at the classic, somewhat dated interface at bioinfo.ut.ee

SEQUENCE_ID=Test_Amplicon SEQUENCE_TEMPLATE=ATGGCGTACTGACGGTACCTAGCTTAGGC SEQUENCE_TARGET=10,20 PRIMER_TASK=generic PRIMER_PICK_LEFT_PRIMER=1 PRIMER_PICK_RIGHT_PRIMER=1 PRIMER_PICK_INTERNAL_OLIGO=0 PRIMER_OPT_SIZE=20 PRIMER_MIN_SIZE=18 PRIMER_MAX_SIZE=27 PRIMER_OPT_TM=60.0 PRIMER_MIN_TM=57.0 PRIMER_MAX_TM=63.0 PRIMER_PRODUCT_SIZE_RANGE=100-300 =