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Probe/primer details

G Rb Tested for in situ hybridization.
Accession no. pB-610
Taxonomy Rhodobacteraceae; Rhodobacterales; Alphaproteobacteria; Proteobacteria; Bacteria
Specificity Rhodobacter, Roseobacter
Category dinitrogen-fixing bacteria
Target rRNA 16S rRNA
Position 645-664
Sequence 5'- GTC AGT ATC GAG CCA GTG AG -3'
G+C content [%] 55
Length [nt] 20
Check specificity/coverage
Formamide [%] 30
Hybridization efficiency

Identification of Culturable Oligotrophic Bacteria within Naturally Occurring Bacterioplankton Communities of the Ligurian Sea by 16S rRNA Sequencing and Probing. Giuliano L, De Domenico M , De Domenico E , Höfle MG, Yakimov MM. Microbial ecology. 1999. Pubmed

Culturability and In situ abundance of pelagic bacteria from the North Sea. Eilers H, Pernthaler J, Glöckner FO, Amann R. Applied and environmental microbiology. 2000. Pubmed


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.