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. 2014 Aug;80(16):5116–5123. doi: 10.1128/AEM.01403-14

TABLE 2.

Taxonomic coverage of primers designed by DegePrime as evaluated by the Probe Match tool in RDPa

Taxonomic group No. of sequences Coverage of primer:
341F 341′F 515′F 805R
Bacteria 1,534,872 0.96 0.93 0.93 0.90
    Actinobacteria 204,784 0.97 0.97 0.72 0.71
    Aquificae 1,279 0.97 0.97 0.97 0.95
    Bacteroidetes 182,923 0.97 0.97 0.97 0.96
    Caldiserica 263 0.98 0.98 0.00 0.97
    Chlamydiae 563 0.76 0.01 0.01 0.96
    Chlorobi 1,531 0.95 0.95 0.62 0.95
    Chloroflexi 25,804 0.89 0.76 0.96 0.35
    Chrysiogenetes 13 0.85 0.85 1.00 1.00
    Deferribacteres 734 0.99 0.99 0.98 0.96
    Deinococcus-Thermus 2,556 0.97 0.97 0.98 0.97
    Dictyoglomi 36 1.00 1.00 0.97 1.00
    Elusimicrobia 326 0.97 0.98 0.98 0.94
    Fibrobacteres 462 0.96 0.96 0.98 0.96
    Fusobacteria 10,194 0.95 0.95 0.97 0.97
    Gemmatimonadetes 2,152 0.98 0.98 0.97 0.93
    Lentisphaerae 1,978 0.94 0.00 0.98 0.96
    Nitrospira 2,258 0.98 0.98 0.97 0.95
    Planctomycetes 14,348 0.81 0.01 0.93 0.94
    Proteobacteria 454,358 0.98 0.98 0.97 0.94
    Spirochaetes 10,644 0.92 0.92 0.97 0.86
    Synergistetes 1,649 0.98 0.98 0.97 0.94
    Tenericutes 4,064 0.94 0.94 0.93 0.96
    Thermodesulfobacteria 166 0.96 0.96 0.96 0.99
    Thermotogae 777 0.97 0.97 0.97 0.94
    BRC1 477 0.94 0.94 0.96 0.97
    OD1 411 0.68 0.00 0.00 0.88
    OP11 150 0.21 0.01 0.27 0.00
    SR1 466 0.95 0.96 0.97 0.97
    TM7 2,596 0.97 0.97 0.00 0.88
    WS3 672 0.96 0.98 0.97 0.97
    Armatimonadetes 1,576 0.29 0.05 0.97 0.91
    Verrucomicrobia 12,387 0.98 0.00 0.96 0.93
    Acidobacteria 27,092 0.98 0.97 0.98 0.95
    Firmicutes 483,681 0.97 0.96 0.97 0.96
    Cyanobacteria/Chloroplast 30,775 0.93 0.93 0.98 0.95
    Unclassified_Bacteria 50,727 0.84 0.66 0.88 0.86
Archaea 78,684 0.00 0.90 0.96 0.94
    Crenarchaeota 20,677 0.00 0.89 0.97 0.93
    Euryarchaeota 41,963 0.00 0.93 0.96 0.95
    Korarchaeota 221 0.00 0.93 0.95 0.93
    Nanoarchaeota 138 0.00 0.00 0.00 0.00
    Thaumarchaeota 0 NA NA NA NA
    Unclassified_Archaea 15,685 0.00 0.85 0.96 0.93
a

The search was conducted against release 11, update 1, of RDP, including only sequences with good-quality scores that span E. coli positions 300 to 850. Primer sequences were the following: 341F, CCTACGGGNGGCWGCAG; 341′F, CCTAHGGGRBGCAGCAG; 515′F, GTGBCAGCMGCCGCGGTAA; 805R, GACTACHVGGGTATCTAATCC. NA, not applicable.