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Probe/primer details

Amx820 Tested for in situ hybridization.
Full name
(Alm et al. 1996)
Accession no. pB-409
Taxonomy Candidatus Brocadiaceae; Candidatus Brocadiales; Planctomycetia; Planctomycetes; Bacteria
Specificity anaerobic ammonium-oxidizing bacteria, Candidatus `Brocadia anammoxidansapos and Candidatus `Kuenenia stuttgartiensisapos
Category anaerobic ammonium-oxidizing bacteria
bacteria of relevance in wastewater treatment
Target rRNA 16S rRNA
Position 820-841
Sequence 5'- AAA ACC CCT CTA CTT AGT GCC C -3'
G+C content [%] 50
Length [nt] 22
Check specificity/coverage
Formamide [%] 40
Hybridization efficiency

16S-23S rDNA intergenic spacer and 23S rDNA of anaerobic ammonium-oxidizing bacteria: implications for phylogeny and in situ detection. Schmid M, Schmitz-Esser S, Jetten M, Wagner M. Environmental microbiology. 2001. Pubmed

Used in Microarray Freshwater Sediment-Microarray


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.