Probe/primer details

Name	VASA
Accession no.	pB-2581
Taxonomy	Vagococcus salmoninarum; Vagococcus; Enterococcaceae; Lactobacillales; Bacilli; Firmicutes; Bacteria
Specificity	Vagococcus salmoninarum
Target rRNA	16S rRNA
Sequence	5'- GTG GGA GAG TAA CTG TTC CCA CC -3'
G+C content [%]	57
Check specificity/coverage
Hybridization efficiency
References	Simultaneous discrimination between 15 fish pathogens by using 16S ribosomal DNA PCR and DNA microarrays. Warsen AE, Krug MJ, LaFrentz S, Stanek DR, Loge FJ, Call DR. Applied and environmental microbiology. 2004. Pubmed
Used in Microarray	Fish Pathogen 16S Microarray

Print

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.