Probe/primer details
| EUB338 (Bact338) (bacterial) | Tested for in situ hybridization. |
| Full name (Alm et al. 1996) |
S-D-Bact-0338-a-A-18 |
| Accession no. | pB-159 |
| Taxonomy | Bacteria |
| Specificity | most Bacteria |
| Category | higher taxonomic levels |
| Target rRNA | 16S rRNA |
| Modified version(s) | EUB338 III (SBACT V 338) EUB338 II (SBACT P 338) |
| Position | 338-355 |
| Sequence | 5'- GCT GCC TCC CGT AGG AGT -3' |
| G+C content [%] | 67 |
| Length [nt] | 18 |
| Check specificity/coverage | 
|
| Formamide [%] | 0-50 |
| Hybridization efficiency |  |
| References | Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA. Applied and environmental microbiology. 1990. Pubmed |
| Remarks | Use probe in equimolar mixture together with probes EUB338II and EUB338III to detect all bacteria. |
| Used in Microarray | Bacillus-PhyloChip SRP-PhyloChip RHC-PhyloChip ECC-PhyloChip Nitrifier-Microarray Freshwater Sediment-Microarray Burkholderia-Phylochip |
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.
