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Probe/primer details

Name 28
Accession no. pB-403
Taxonomy Bacillus subtilis group; Bacillus; Bacillaceae; Bacillales; Bacilli; Firmicutes; Bacteria
Specificity Subtilis group including Bacillus subtilis, B. amyloliquefaciens, B. polilliae, B. pumilus, B. licheniformis
Target rRNA 16S rRNA
Position 1281-1300
Sequence 5'- ACA GAT TTG TGG GAT TGG CT -3'
G+C content [%] 45
Length [nt] 20
Check specificity/coverage
Hybridization efficiency
2.4x) was achieved between PM and 1-MM duplexes at the dissociation temperature at which 50% of the probe-target duplexes remained intact. This provided excellent differentiation among representatives of different Bacillus species, both individually and in mixtures of two or three. The overall pattern of hybridization derived from this hierarchical probe set also provided a clear 'chip fingerprint' for each of these closely related Bacillus species.'>

Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach. Liu WT, Mirzabekov AD, Stahl DA. Environmental microbiology. 2001. Pubmed

Used in Microarray Bacillus-PhyloChip


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.