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Probe/primer details

Name Bacbae3
Accession no. pB-2356
Taxonomy Bacillus baekryungensis; Bacillus; Bacillaceae; Bacillales; Bacilli; Firmicutes; Bacteria
Specificity Bacillus baekryungensis
Target rRNA 16S rRNA
Position 210-229
Sequence 5'- CCA TCC TGC AGT GTT AGC TC -3'
G+C content [%] 55
Length [nt] 20
Check specificity/coverage
Hybridization efficiency
References

Comparison of rhizobacterial community composition in soil suppressive or conducive to tobacco black root rot disease. Kyselková M, Kopecký J, Frapolli M, Défago G, Ságová-Marecková M, Grundmann GL, Moënne-Loccoz Y. The ISME journal. 2009. Pubmed

Used in Microarray Taxonomic 16S rRNA microarray

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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.