Calculating ...

Press ESC to cancel.

Probe/primer details

Caal Tested for in situ hybridization.
Accession no. pB-353
Taxonomy Candida albicans; Candida; Candida/Lodderomyces clade; Debaryomycetaceae; Saccharomycetales; Saccharomycetes; Saccharomycotina; saccharomyceta; Ascomycota; Dikarya; Fungi; Opisthokonta; Eukaryota
Specificity Candida albicans
Category bacteria of medical or hygienical relevance
eukaryotes
Target rRNA 18S rRNA
Position 1249-1267
Sequence 5'- GCC AAG GCT TAT ACT CGC T -3'
G+C content [%] 53
Length [nt] 19
Check specificity/coverage
Formamide [%] 30
Hybridization efficiency
References

Fluorescent In situ hybridization allows rapid identification of microorganisms in blood cultures. Kempf VA, Trebesius K, Autenrieth IB. Journal of clinical microbiology. 2000. Pubmed

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.