TABLE 1.

Oligonucleotide probes used in this study and their corresponding Tds

SeriesProbeaSequenceeDNARNA
Td MeanSDΔTbCVcTd MeanSDΔTCV
S0spmTCGCACATCAGCGTCAGTT45.1±1.20.02.744.8±1.80.04.0
S1s1aaACGCACATCAGCGTCAGTT41.4±1.5−3.73.740.0±1.6−4.84.0
S2s1gaGCGCACATCAGCGTCAGTT43.7±1.5−1.43.342.0±2.5−2.85.9
S3s1caCCGCACATCAGCGTCAGTT40.8±1.0−4.32.340.4±2.1−4.45.1
S4s2agTAGCACATCAGCGTCAGTT43.1±1.4−2.03.341.3±2.5−3.55.9
S5s2ggTGGCACATCAGCGTCAGTT42.7±0.9−2.42.140.7±1.8−4.14.3
S6s2tgTTGCACATCAGCGTCAGTT41.7±1.0−3.42.540.7±1.2−4.12.9
S7s3ccTCCCACATCAGCGTCAGTT37.8±1.0−7.32.635.6±0.6−9.21.7
S8s3tcTCTCACATCAGCGTCAGTT39.1±0.9−6.02.437.6±0.8−7.22.2
S9s3acTCACACATCAGCGTCAGTT41.5±0.6−3.61.538.5±1.1−6.33.0
S10s4ggTCGGACATCAGCGTCAGTT41.6±0.6−3.51.338.4±1.5−6.44.0
S11s4tgTCGTACATCAGCGTCAGTT41.0±0.9−4.12.239.4±1.6−5.44.0
S12s4agTCGAACATCAGCGTCAGTT40.8±0.5−4.31.136.7±1.2−8.13.2
S13s5gtTCGCGCATCAGCGTCAGTT43.2±1.3−1.93.040.2±1.0−4.62.6
S14s5ctTCGCCCATCAGCGTCAGTT39.6±1.0−5.52.538.0±1.3−6.83.3
S15s5ttTCGCTCATCAGCGTCAGTT39.8±2.0−5.34.939.1±0.9−5.72.2
S16s6tgTCGCATATCAGCGTCAGTT41.0±0.6−4.11.540.1±1.0−4.72.4
S17s6agTCGCAAATCAGCGTCAGTT39.4±0.9−5.72.237.2±0.8−7.62.1
S18s6ggTCGCAGATCAGCGTCAGTT40.2±0.9−4.92.336.1±1.4−8.73.7
S19s7gtTCGCACGTCAGCGTCAGTT35.4±0.4−9.71.136.0±1.8−8.85.0
S20s7ctTCGCACCTCAGCGTCAGTT39.4±0.8−5.72.036.8±1.3−8.03.5
S21s7ttTCGCACTTCAGCGTCAGTT41.3±0.8−3.82.038.5±1.3−6.33.3
S22s8aaTCGCACAACAGCGTCAGTT41.6±1.0−3.52.337.9±0.8−6.92.0
S23s8gaTCGCACAGCAGCGTCAGTT43.7±1.3−1.43.038.8±1.1−6.02.8
S24s8caTCGCACACCAGCGTCAGTT41.1±0.9−4.02.138.5±1.1−6.32.8
S25s9tgTCGCACATTAGCGTCAGTT41.1±0.9−4.02.239.4±1.1−5.42.8
S26s9agTCGCACATAAGCGTCAGTT40.2±0.9−4.92.335.6±2.1−9.25.8
S27s9ggTCGCACATGAGCGTCAGTT39.6±0.8−5.52.036.3±1.5−8.54.2
S28s10gtTCGCACATCGGCGTCAGTT43.1±1.2−2.02.739.9±1.7−4.94.3
S29s10ctTCGCACATCCGCGTCAGTT40.6±0.9−4.52.238.0±1.3−6.83.3
S30s10ttTCGCACATCTGCGTCAGTT42.0±1.1−3.12.538.8±0.9−6.02.2
S31s11ccTCGCACATCACCGTCAGTT37.0±0.7−8.11.835.5±0.2−9.30.6
S32s11tcTCGCACATCATCGTCAGTT38.6±0.9−6.52.336.0±0.6−8.81.6
S33s11acTCGCACATCAACGTCAGTT37.8±0.4−7.31.134.5±0.5−10.31.5
S34s12tgTCGCACATCAGTGTCAGTT41.9±1.1−3.22.540.1±1.2−4.73.0
S35s12agTCGCACATCAGAGTCAGTT40.6±0.9−4.52.336.3±1.2−8.53.3
S36s12ggTCGCACATCAGGGTCAGTT41.5±0.8−3.62.038.1±0.8−6.72.1
S37s13ccTCGCACATCAGCCTCAGTT37.1±0.7−8.01.935.8±0.6−9.01.5
S38s13tcTCGCACATCAGCTTCAGTT38.5±0.5−6.61.436.3±0.6−8.51.7
S39s13acTCGCACATCAGCATCAGTT38.9±1.3−6.23.238.0±0.6−6.81.6
S40s14aaTCGCACATCAGCGACAGTT42.1±0.8−3.01.938.4±1.1−6.42.7
S41s14gaTCGCACATCAGCGGCAGTT44.9±0.7−0.21.640.5±1.5−4.33.6
S42s14caTCGCACATCAGCGCCAGTT42.0±0.6−3.11.339.8±1.4−5.03.5
S43s15tgTCGCACATCAGCGTTAGTT41.2±0.8−3.91.839.3±1.3−5.53.2
S44s15agTCGCACATCAGCGTAAGTT40.6±0.8−4.52.136.3±1.5−8.54.1
S45s15ggTCGCACATCAGCGTGAGTT40.6±0.8−4.51.836.8±0.9−8.02.4
S46s16gtTCGCACATCAGCGTCGGTT43.9±1.3−1.22.941.2±0.6−3.61.5
S47s16ctTCGCACATCAGCGTCCGTT41.3±0.8−3.81.938.7±0.6−6.11.6
S48s16ttTCGCACATCAGCGTCTGTT42.7±0.7−2.41.639.2±0.6−5.61.4
S49s17ccTCGCACATCAGCGTCACTT42.2±0.8−2.91.839.8±1.6−5.04.1
S50s17tcTCGCACATCAGCGTCATTT41.6±0.7−3.51.839.0±1.4−5.83.6
S51s17acTCGCACATCAGCGTCAATT41.3±0.8−3.81.938.7±1.7−6.14.3
S52s18aaTCGCACATCAGCGTCAGAT43.8±1.7−1.33.940.0±1.7−4.84.2
S53s18gaTCGCACATCAGCGTCAGGT45.9±1.00.82.243.7±2.2−1.15.1
S54s18caTCGCACATCAGCGTCAGCT41.7±0.6−3.41.437.2±1.2−7.63.3
S55s19aaTCGCACATCAGCGTCAGTA44.6±1.1−0.52.442.8±1.5−2.03.5
S56s19gaTCGCACATCAGCGTCAGTG44.7±1.4−0.43.141.8±1.0−3.02.3
S57s19caTCGCACATCAGCGTCAGTC44.4±1.4−0.73.241.5±0.7−3.31.7
S581aa2ggAGGCACATCAGCGTCAGTT44.2±1.4−0.93.143.5±1.0−1.32.3
S593cc4ggTCCGACATCAGCGTCAGTT38.8±1.1−6.32.736.9±0.8−7.92.2
S603cc4gg11cc12ggTCCGACATCACGGTCAGTTNDdNDNDNDNDNDNDND
S6111cc12ggTCGCACATCACGGTCAGTT34.2±0.8−10.92.337.5±2.1−7.35.5
N0npmCCCCTCTGCTGCACTCTA43.4±1.30.06.544.3±2.90.06.5
N1n1ggGCCCTCTGCTGCACTCTA42.5±0.8−0.92.043.0±2.5−1.35.7
N2n1agACCCTCTGCTGCACTCTA42.9±2.2−0.55.043.7±2.7−0.66.1
N3n1tgTCCCTCTGCTGCACTCTA42.5±2.2−0.95.343.5±3.2−0.87.4/PICK>
N4n2ggCGCCTCTGCTGCACTCTA42.1±2.1−1.35.043.4±3.0−0.96.8
N5n2agCACCTCTGCTGCACTCTA42.1±2.3−1.35.543.2±3.0−1.16.9
N6n2tgCTCCTCTGCTGCACTCTA41.8±2.3−1.65.443.5±2.8−0.86.3
N7n3ggCCGCTCTGCTGCACTCTA41.1±2.0−2.34.843.2±2.3−1.15.3
N8n3agCCACTCTGCTGCACTCTA41.4±2.4−2.05.842.2±1.8−2.14.2
N9n3tgCCTCTCTGCTGCACTCTA40.6±1.9−2.84.842.0±1.3−2.33.1
N10n4ggCCCGTCTGCTGCACTCTA41.0±1.4−2.43.441.9±1.4−2.43.2
N11n4agCCCATCTGCTGCACTCTA40.9±1.2−2.52.942.0±1.0−2.32.4
N12n4tgCCCTTCTGCTGCACTCTA40.6±1.0−2.82.342.8±2.7−1.56.2
N13n5gaCCCCGCTGCTGCACTCTA40.8±1.0−2.62.442.3±1.7−2.03.9
N14n5aaCCCCACTGCTGCACTCTA40.7±1.5−2.73.842.8±2.8−1.56.6
N15n5caCCCCCCTGCTGCACTCTA39.8±1.8−3.64.442.5±3.0−1.87.0
N16ng6gCCCCTTTGCTGCACTCTA38.6±1.5−4.84.040.4±2.8−3.97.0
N17n6agCCCCTATGCTGCACTCTA40.1±2.1−3.35.240.3±2.6−4.06.5
N18n6ggCCCCTGTGCTGCACTCTA39.3±1.3−4.13.440.0±2.3−4.35.8
N19n7aaCCCCTCAGCTGCACTCTA40.1±2.0−3.35.041.1±2.9−3.27.0
N20n7gaCCCCTCGGCTGCACTCTA40.9±2.1−2.55.140.7±2.1−3.65.1
N21n7caCCCCTCCGCTGCACTCTA39.5±1.6−3.94.040.7±1.9−3.64.7
N22n8ccCCCCTCTCCTGCACTCTA34.7±0.6−8.71.640.1±1.3−4.23.3
N23n8tcCCCCTCTTCTGCACTCTA35.6±1.5−7.84.340.8±1.6−3.53.9
N24n8acCCCCTCTACTGCACTCTA37.6±0.6−5.81.741.8±1.5−2.53.5
N25n9tgCCCCTCTGTTGCACTCTA39.4±0.9−4.02.244.6±2.30.35.1
N26n9agCCCCTCTGATGCACTCTA41.0±1.3−2.43.242.3±1.7−2.04.1
N27n9ggCCCCTCTGGTGCACTCTA39.9±1.3−3.53.341.4±2.0−2.94.7
N28n10aaCCCCTCTGCAGCACTCTA39.8±1.4−3.63.541.0±1.7−3.34.2
N29n10gaCCCCTCTGCGGCACTCTA40.4±1.6−3.04.040.6±1.2−3.72.9
N30n10caCCCCTCTGCCGCACTCTA39.0±1.3−4.43.440.1±1.6−4.23.9
N31n11ccCCCCTCTGCTCCACTCTA35.2±0.7−8.21.938.8±1.3−5.53.2
N32n11tcCCCCTCTGCTTCACTCTA36.7±0.9−6.72.538.9±1.6−5.44.1
N33n11acCCCCTCTGCTACACTCTA38.0±1.1−5.42.940.0±2.0−4.35.0
N34n12tgCCCCTCTGCTGTACTCTA39.9±1.3−3.53.240.7±2.2−3.65.4
N35n12agCCCCTCTGCTGAACTCTA39.2±1.4−4.23.641.2±1.7−3.14.1
N36n12ggCCCCTCTGCTGGACTCTA40.8±0.8−2.62.042.2±1.6−2.13.8
N37n13gtCCCCTCTGCTGCGCTCTA41.9±1.0−1.52.344.9±3.50.67.8
N38n13ctCCCCTCTGCTGCCCTCTA38.3±0.5−5.11.243.4±1.9−0.94.4
N39n13ttCCCCTCTGCTGCTCTCTA39.3±0.8−4.12.141.2±1.6−3.13.8
N40n14tgCCCCTCTGCTGCATTCTA38.8±1.2−4.63.140.9±2.2−3.45.4
N41n14agCCCCTCTGCTGCAATCTA39.0±0.9−4.42.340.3±1.8−4.04.5
N42n14ggCCCCTCTGCTGCAGTCTA39.8±0.9−3.62.240.2±1.6−4.14.0
N43n15aaCCCCTCTGCTGCACACTA39.8±0.4−3.61.040.1±1.4−4.23.4
N44n15gaCCCCTCTGCTGCACGCTA40.8±0.8−2.61.840.0±1.4−4.33.5
N45n15caCCCCTCTGCTGCACCCTA39.0±1.2−4.43.140.7±1.5−3.63.6
N46n16tgCCCCTCTGCTGCACTTTA40.6±0.9−2.82.340.7±1.3−3.63.2
N47n16agCCCCTCTGCTGCACTATA41.9±0.6−1.51.440.9±1.8−3.44.3
N48n16ggCCCCTCTGCTGCACTGTA42.6±0.3−0.80.743.8±1.8−0.54.1
N49n17aaCCCCTCTGCTGCACTCAA42.3±1.3−1.13.143.7±1.8−0.64.1
N50n17gaCCCCTCTGCTGCACTCGA44.6±1.51.23.444.5±1.40.23.2
N51n17caCCCCTCTGCTGCACTCCA42.0±1.1−1.42.641.8±1.7−2.54.0
N52n18gtCCCCTCTGCTGCACTCTG42.9±1.7−0.53.943.0±1.3−1.33.0
N53n18ctCCCCTCTGCTGCACTCTC42.7±1.7−0.73.942.9±1.4−1.43.3
N54n18ttCCCCTCTGCTGCACTCTT43.5±1.40.13.243.8±1.4−0.53.2
N551gg2ggGGCCTCTGCTGCACTCTA41.1±1.0−2.32.543.0±1.8−1.34.1
N563gg4ggCCGGTCTGCTGCACTCTA37.0±0.9−6.42.439.3±0.8−5.01.9
N578cc9gg14ggCCCCTCTCGTGCACTCTA33.6±1.5−9.84.539.4±1.1−4.92.8
N588cc9gg11cc12ggCCCCTCTCGTCGACTCTANDNDNDND32.7±2.1−11.66.3
N596gg8cc9gg11cc12ggCCCCTGTCGTCGACTCTANDNDNDNDNDNDNDND
N608cc9gg14ggCCCCTCTCGTCGAGTCTANDNDNDNDNDNDNDND
N616gg8cc9gg11cc12ggCCCCTGTCGTCGAGTCTANDNDNDNDNDNDNDND
  • a Probe names incorporate the type of target (s, Staphylococcus; n, Nitrosomonas), position of the mismatch from the 5′ terminus, and the type of mismatch (probe-target). spm and npm, perfect-match probes for Staphylococcus and Nitrosomonas targets, respectively.

  • b ΔT, difference of the Td between the perfect-match probe and each mismatch probe.

  • c CV, coefficient of variation.

  • d ND, not determined due to faint fluorescence signal.

  • e Mismatches are underlined.