Probe/primer details
| Curvi997 | Tested for in situ hybridization. |
| Accession no. | pB-2587 |
| Taxonomy | Curvibacter; Comamonadaceae; Burkholderiales; Betaproteobacteria; Proteobacteria; Bacteria |
| Specificity | Genus Curvibacter |
| Competitor | 5'-CTC TGG CAA CTT CCG TAC -3' 5'-CTC TGG TCA CTT CCG TAC -3' |
| Target rRNA | 16S rRNA |
| Position | 997-1014 |
| Sequence | 5'- CTC TGG TAA CTT CCG TAC -3' |
| G+C content [%] | 50 |
| Length [nt] | 18 |
| Check specificity/coverage | 
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| Formamide [%] | 35 |
| Hybridization efficiency |  |
| References | Micromanipulation and further identification of FISH-labelled microcolonies of a dominant denitrifying bacterium in activated sludge. Thomsen TR, Nielsen JL, Ramsing NB, Nielsen PH. Environmental microbiology. 2004. Pubmed Nielsen JL and Hansen AA. 2009 Identification of denitrifying microorganisms in activated sludge by FISH. In: FISH handbook for Biological Wastewater Treatment: Identification and quantification of microorganisms in activated sludge and biofilms by FISH (Nielsen, P., Daims, H. Lemmer, H. ed) IWA Publishing, London, UK, p. 19-24. |
| Remarks | The probe was formerly published under the name Aqs997 (S-*-Aquaspi-997-a-A-18). |
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.
