Calculating ...

Press ESC to cancel.

Probe/primer details

EPSY549 Tested for in situ hybridization.
Full name
(Alm et al. 1996)
S-C-eProt-0549-a-A-18
Accession no. pB-1321
Taxonomy Epsilonproteobacteria; delta/epsilon subdivisions; Proteobacteria; Bacteria
Specificity Epsilonproteobacteria
Category higher taxonomic levels
Target rRNA 16S rRNA
Position 549-566
Sequence 5'- CAG TGA TTC CGA GTA ACG -3'
G+C content [%] 50
Length [nt] 18
Check specificity/coverage
Hybridization efficiency
References

Comparison of vertical distributions of prokaryotic assemblages in the anoxic Cariaco Basin and Black Sea by use of fluorescence in situ hybridization. Lin X, Wakeham SG, Putnam IF, Astor YM, Scranton MI, Chistoserdov AY, Taylor GT. Applied and environmental microbiology. 2006. Pubmed

Remarks 55 % FA for CARD-FISH

Print

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.