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Probe/primer details

DSC213 Tested for in situ hybridization.
Full name
(Alm et al. 1996)
Accession no. pB-1111
Taxonomy Desulfocapsa thiozymogenes; Desulfocapsa; Desulfobulbaceae; Desulfobacterales; Deltaproteobacteria; delta/epsilon subdivisions; Proteobacteria; Bacteria
Specificity Desulfocapsa thiozymogenes
Category sulfate-reducing microbes
Target rRNA 16S rRNA
Position 213-230
Sequence 5'- CCT CCC TGT ACG ATA GCT -3'
G+C content [%] 56
Length [nt] 18
Check specificity/coverage
Formamide [%] 30
Hybridization efficiency

In situ analysis of sulfate-reducing bacteria related to Desulfocapsa thiozymogenes in the chemocline of meromictic Lake Cadagno (Switzerland). Tonolla M, Demarta A, Peduzzi S, Hahn D, Peduzzi 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.