Calculating ...

Press ESC to cancel.

Probe/primer details

Pchl454 Tested for in situ hybridization.
Accession no. pB-740
Taxonomy Pseudomonas chlororaphis; Pseudomonas chlororaphis group; Pseudomonas; Pseudomonadaceae; Pseudomonadales; Gammaproteobacteria; Proteobacteria; Bacteria
Specificity Pseudomonas chlororaphis
Target rRNA 16S rRNA
Position 454-470
Sequence 5'- GTA CTT ACC TAA TAC GT -3'
G+C content [%] 35
Length [nt] 17
Check specificity/coverage
Hybridization efficiency

Biomonitoring of pJP4-carrying Pseudomonas chlororaphis with Trb protein-specific antisera. Schmidt-Eisenlohr H, Rittig M, Preithner S, Baron C. Environmental microbiology. 2001. Pubmed

Remarks The probe sequence given in the paper is 6 nucleotides longer (5apos-GTACTTACCTAATACGTGAGTAT-3apos).


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.