Probe/primer details

Name	NITROSO4E
Accession no.	pB-958
Taxonomy	Nitrosomonadaceae; Nitrosomonadales; Betaproteobacteria; Proteobacteria; Bacteria
Specificity	Betaproteobacterial ammonia-oxidizing bacteria
Category	ammonia-oxidizing bacteria bacteria of relevance in wastewater treatment
Target rRNA	16S rRNA
Position	639-658
Sequence	5'- CAC TCT AGC YTT GTA GTT TC -3'
G+C content [%]	40
Length [nt]	20
Check specificity/coverage
Hybridization efficiency
References	Comparative analysis of nitrifying bacteria associated with freshwater and marine aquaria. Hovanec TA, DeLong EF. Applied and environmental microbiology. 1996. Pubmed

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Glossary
Name (Alm et al., 1996). Probe designation according to Alm, E. W., Oerther, D. B., Larsen, N., Stahl, D. A., Raskin, L. (1996). The oligonucleotide probe database. Appl Environ Microbiol 62: 3557-9. Abstract (PUBMED).
Position. Probe position according to the E. coli gene numbering.
Sequence. Sequence in IUPAC code: R=G/A, Y=T/C, M=A/C, K=G/T, S=G/C, W=A/T, H=A/C/T, B=G/T/C, V=G/C/A, D=G/A/T, N=G/A/T/C
Tm. Dissoziation temperature according to: Tm=64.9 + 41 x ((G + C - 16.4)/length).
Hybridization efficiency. Use this tool to assess in silico sensitivity (i.e. the hybridization efficiency of the oligonucleotide with its fully complementary target sequence, calculated with ProbeMelt.
Formamide. Percent formamide in the hybridization buffer for optimal hybridization conditions in FISH experiments.
Coverage. Coverage of the three domains calculated using the SILVA reference database 106 if no or a single mismatch is allowed. The detailed method is described in Klindworth et al., 2012. Nucleic Acids Res. 10.1093/nar/gks808 Full Text
Check specificity/coverage. Use these options to reveal the in silico specificity (i.e. number of matching rRNA sequences outside the target taxon) and coverage (i.e. percentage of matching rRNA sequences within the target taxon) of an oligonucleotide against the most recent SSU and LSU rRNA sequence databases.