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Probe/primer details

Nost993 Tested for in situ hybridization.
Full name
(Alm et al. 1996)
Accession no. pB-1327
Taxonomy Alphaproteobacteria; Proteobacteria; Bacteria
Specificity Filamentous Alphaproteobacteria
Category bacteria of relevance in wastewater treatment
Competitor 5'-GAA AGC CGC CGT CTC CGG -3'
Target rRNA 16S rRNA
Position 993-1010
Sequence 5'- CAG CCG AAA CGG GCA TGT -3'
G+C content [%] 61
Length [nt] 18
Check specificity/coverage
Formamide [%] 20
Hybridization efficiency

Ecophysiology of different filamentous Alphaproteobacteria in industrial wastewater treatment plants. Kragelund C, Kong Y, van der Waarde J, Thelen K, Eikelboom D, Tandoi V, Thomsen TR, Nielsen PH. Microbiology (Reading, England). 2006. Pubmed

Remarks The probe targets two filamentous Alphaproteobacteria species AY428764-65. A helper probe was designed to obtain FISH signal.


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.