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Probe/primer details

Name DCC868
Full name
(Alm et al. 1996)
Accession no. pB-64
Taxonomy Desulfobacteraceae; Desulfobacterales; Deltaproteobacteria; delta/epsilon subdivisions; Proteobacteria; Bacteria
Specificity Desulfosarcina sp., Desulfonema spp., Desulfococcus sp., Desulfobacterium spp., Desulfobotulus sp., Desulfostipes sp., Desulfomusa sp.
Category sulfate-reducing microbes
Target rRNA 16S rRNA
Position 868-885
Sequence 5'- CAG GCG GAT CAC TTA ATG -3'
G+C content [%] 50
Length [nt] 18
Check specificity/coverage
Hybridization efficiency

Development of oligonucleotide probes and PCR primers for detecting phylogenetic subgroups of sulfate-reducing bacteria. Daly K, Sharp RJ, McCarthy AJ. Microbiology (Reading, England). 2000. Pubmed

Used in Microarray SRP-PhyloChip


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.