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Table 2 Results of in silico benchmarking of QuantPrime

From: QuantPrime – a flexible tool for reliable high-throughput primer design for quantitative PCR

     Primer pair specificity ranking1
Species Transcripts Total search time Average search time Acceptable2 Good3 Very good4
Arabidopsis thaliana 5000 20:22:06 15 s 4916 (98%) 4323 (86%) 2534 (50%)
Vitis vinifera 5000 50:45:33 37 s 4765 (95%) 3927 (78%) 2315 (46%)
Drosophila melanogaster 5000 13:48:45 9.9 s 4894 (97%) 4075 (81%) 3096 (61%)
Chlamydomonas reinhardtii 5000 12:11:07 8.8 s 4568 (91%) 3999 (79%) 2349 (46%)
Oryza sativa ssp japonica 5000 83:31:12 60 s 4658 (93%) 3821 (76%) 1984 (39%)
Hordeum vulgare 23078 22:56:59 3.6 s 22145 (95%) 21564 (93%) -
  1. Primer pairs designed for hypothetical high-throughput experiments, for random transcripts of each species. The numbers of successfully designed primer pairs for the different specificity ranks and the search times are reported for each species (percentages refer to the total number of transcripts tested).
  2. 1 Percentages indicate for how many of the transcripts primer pairs of at least the rank given were identified. 2 'Acceptable' amplifies only the specific sequence, but one primer has a high similarity with a non-target sequence and the primer pair might amplify genomic DNA. 3 'Good' amplifies only the target sequence, but one primer has a high similarity with a non-target sequence or the pair might amplify genomic DNA. This is the highest possible rank for primer pairs designed for species without a genome annotation. 4 'Very good' amplifies only the target sequence, both primers are highly specific to this sequence and will not amplify genomic DNA.