Probe/primer details

PSE227	Tested for in situ hybridization.
Accession no.	pB-2539
Taxonomy	Pseudomonas; Pseudomonadaceae; Pseudomonadales; Gammaproteobacteria; Proteobacteria; Bacteria
Specificity	Pseudomonas spp.
Target rRNA	16S rRNA
Position	227-245
Sequence	5'- AAT CCG ACC TAG GCT CAT C -3'
G+C content [%]	53
Length [nt]	19
Check specificity/coverage
Formamide [%]	30
Hybridization efficiency
References	Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH). Watt M, Hugenholtz P, White R, Vinall K. Environmental microbiology. 2006. Pubmed

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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.