Probe/primer details
| Rfla729 | Tested for in situ hybridization. |
| Full name (Alm et al. 1996) |
S-*-Rfla-0729-a-A-18 |
| Accession no. | pB-557 |
| Taxonomy | Ruminococcus; Ruminococcaceae; Clostridiales; Clostridia; Firmicutes; Bacteria |
| Specificity | Ruminococcus albus, R. flavefaciens |
| Competitor | 5'-AAA GCC CAG TAG GCC GCC -3' 5'-AAG GCC CAG TAA GCC GCC -3' |
| Target rRNA | 16S rRNA |
| Position | 729-746 |
| Sequence | 5'- AAA GCC CAG TAA GCC GCC -3' |
| G+C content [%] | 61 |
| Length [nt] | 18 |
| Check specificity/coverage | 
|
| Formamide [%] | 20 |
| Hybridization efficiency |  |
| References | Extensive set of 16S rRNA-based probes for detection of bacteria in human feces. Harmsen HJ, Raangs GC, He T, Degener JE, Welling GW. Applied and environmental microbiology. 2002. Pubmed Design and validation of 16S rRNA probes to enumerate members of the Clostridium leptum subgroup in human faecal microbiota. Lay C, Sutren M, Rochet V, Saunier K, Doré J, Rigottier-Gois L. Environmental microbiology. 2005. Pubmed |
| Remarks | 15 min treatment with 10 µl of 1 mg lysozyme per ml in 100 mM Tris-HCl (pH 8.5). More competitors: 3. AAAGCCCAGCAAGCCGCC and 4. TCAGTCCAGTAAGCCGCC. |
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.
