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Table 1 Comparison of selected features among different primer design tools

From: Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

  Primer-BLAST QuantPrime PRIMEGENS
General    
  Scope of primer design task General purpose Real time PCR only General purpose
  Alignment algorithm for specificity checking Local and global Local only Local only
Specificity checking options    
  Specify a range for the number of nucleotide mismatches   required between primer and unintended targets Yes No No
  Define a custom region at 3’ end where certain number of nucleotide   mismatches must exist between primer and unintended target Yes No No
  Number of organisms covered by mRNA and genome databases 7546 333 18
Exon/intron requirement settings    
  Place primers across exon/exon junction Yes Yes No
  Place primer pairs that span an intron Yes No No
  Set custom nucleotide match on either side of exon/exon junction Yes No No
Other primer design options    
  Allow custom PCR template sequence in FASTA format Yes No Yes
  Avoid SNP in primers Yes Yes No
  Allow specificity checking for pre-existing primers Yes No No
Result presentation    
  Graphic overview of primers found Yes No No
  Detailed nucleotide alignments between primers and targets Yes No No