Probe/primer details
| Name | Rint623 |
| Full name (Alm et al. 1996) |
S-*-Rint-0623-a-A-18 |
| Accession no. | pB-735 |
| Taxonomy | Roseburia; Lachnospiraceae; Clostridiales; Clostridia; Firmicutes; Bacteria |
| Specificity | Roseburia cecicola, Roseburia intestinalis, human gut isolates L1-81, L1-83, L1-8151, L1-82, L1-952, L1-810, L1-93, A2-194, and A1-86, bacterium clones adhufec8, adhufec225, adhufec150, and adhufec75.25 rumen clones 4C28d-8, 4C3d-14, and 3C3d-8 |
| Category | animal and human associated microbiota intestinal microbiota |
| Target rRNA | 16S rRNA |
| Position | 623-640 |
| Sequence | 5'- TTC CAA TGC AGT ACC GGG -3' |
| G+C content [%] | 56 |
| Length [nt] | 18 |
| Check specificity/coverage | 
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| Hybridization efficiency |  |
| References | Oligonucleotide probes that detect quantitatively significant groups of butyrate-producing bacteria in human feces. Hold GL, Schwiertz A, Aminov RI, Blaut M, Flint HJ. Applied and environmental microbiology. 2003. Pubmed Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale. Aminov RI, Walker AW, Duncan SH, Harmsen HJ, Welling GW, Flint HJ. Applied and environmental microbiology. 2006. Pubmed |
| Remarks | No formamide used hybridization temperature: 54° C. Helper probe available: GTTGAGCCCCGGGCTTT. |
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.
