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Table 5 Signatures predicted not to hit any target organisms

From: Predicting the sensitivity and specificity of published real-time PCR assays

  Target Organism Year Analysis
[15] Japanese encephalitis virus 2007 Too many mismatches in either forward or reverse primer. Several strains have 3 mismatches at 3' end of forward primer in addition to internal mismatches.
[15] Yellow fever virus 2007 Reverse primer only has a blast hit to one strain (Angola71). Forward primer only has blast hits to 3 strains, and there are many mismatches (e.g. for Angola71, the 11 bases at the 3' end of the primer do not match).
[15] Saint Louis encephalitis virus 2007 Too many mismatches in the reverse primer, with 3 mismatches at 3' end as well as at other locations.
[16] Dengue virus 1 2006 Reverse primer does not have any BLAST hits to target.
[16] Dengue virus 2 2006 Forward primer has 3 or 12 mismatches at 3' end for most strains, the probe has BLAST hits to only 7 of the 57 genomes available, and reverse primer only has a BLAST hit to 1 genome but there are 3 mismatches at the 3' end.
[16] Dengue virus 4 2006 Too many mismatches in forward primer and in some cases the probe.
[10] Dengue virus 2002 Too many mismatches in forward primer. However, they are at the 5' end, so assay could still work for some strains with 19 matches at the 3' end of the forward primer.
[12] Pseudomonas aeruginosa 2004 No blast hits of probe to Pseudomonas aeruginosa
[12] Bacteroides spp. 2004 Probe is not between or even in close proximity to the forward and reverse primers
[12] Stenotrophomonas maltophilia 2004 No blast hits of probe to Stenotrophomonas maltophilia
[12] Haemophilus influenzae 2004 Probe only matches in 17 of 22 bases, which is unlikely to give a strong signal, since probe is unlikely to bind prior to the primers as desired for real time TaqMan chemistry.