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Probe/primer details

T28-649 Tested for in situ hybridization.
Accession no. pB-994
Taxonomy Novosphingobium capsulatum; Novosphingobium; Sphingomonadaceae; Sphingomonadales; Alphaproteobacteria; Proteobacteria; Bacteria
Specificity clone T28 and T29 of a subgroup within the Alphaproteobacteria, Sphingomonas capsulata
Target rRNA 16S rRNA
Position 649-667
Sequence 5'- CCT CTC CAA GAT TCC AGT C -3'
G+C content [%] 53
Length [nt] 19
Check specificity/coverage
Formamide [%] 20
Hybridization efficiency
References

Phylogenetic analysis and in situ identification of bacteria in activated sludge. Snaidr J, Amann R, Huber I, Ludwig W, Schleifer KH. Applied and environmental microbiology. 1997. Pubmed

Remarks T28, T29 related to Sphingomonas capsulata

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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.