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Table 1 The effect of different repeat-masking methods onto PCR primer design.

From: GENOMEMASKER package for designing unique genomic PCR primers

  PRIMER3 + No masking PRIMER3 + DUST PRIMER3 + Tandem
Repeats Finder
PRIMER3 + repeat library
(ALU+LINE+MIR)
PRIMER3 + Repeat Masker -qq GM_PRIMER3 + Genome
Masker -wl 16
Primer selection
was not possible (no primers)
2% 2% 2% 4% 31% 7%
>10 predicted binding sites for
at least one primer of the primer pair
52% 51% 51% 39% 12% NA*
  1. In this test, 1000 random regions, each 1000 bp long, were selected from the human genome for selection of PCR primers. The PRIMER3 program was used in combination with different masking methods to design PCR primers for amplification for each region. The binding sites were predicted for each designed primer using 16 nucleotides from the primer 3'-end and requiring perfect match with template DNA. *Masking the primers that have >10 predicted binding sites is an intrinsic feature of GenomeMasker and thus not comparable to others.