Probe/primer details
| Name | EUB338_V |
| Full name (Alm et al. 1996) |
S-D-Bact-0338-a-A-18 |
| Accession no. | pB-1550 |
| Taxonomy | Candidatus Cyrtobacter comes; Candidatus Cyrtobacter; Candidatus Midichloriaceae; Rickettsiales; Alphaproteobacteria; Proteobacteria; Bacteria |
| Specificity | Candidatus Cyrtobacter comes some Chloroflexi some Firmicutes some Proteobacteria |
| Competitor | 5'-GCT GCC TCC CGT AGG AGT -3' |
| Target rRNA | 16S rRNA |
| Position | 338-355 |
| Sequence | 5'- GCT GCC CCC CGT AGG AGT -3' |
| G+C content [%] | 72 |
| Length [nt] | 18 |
| Check specificity/coverage | 
|
| Formamide [%] | 30 |
| Hybridization efficiency |  |
| References | "Candidatus anadelfobacter veles" and "Candidatus cyrtobacter comes," two new rickettsiales species hosted by the protist ciliate Euplotes harpa (Ciliophora, Spirotrichea). Vannini C, Ferrantini F, Schleifer KH, Ludwig W, Verni F, Petroni G. Applied and environmental microbiology. 2010. Pubmed |
| Remarks | Optimal specificity of this probe is with 30% Formamide and in competition with probe EUB338 |
Glossary
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.
