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Probe/primer details

EUK1209 Tested for in situ hybridization.
Accession no. pB-771
Taxonomy Eukaryota
Specificity Eukarya
Category eukaryotes
higher taxonomic levels
Target rRNA 18S rRNA
Position 1431-1446
Sequence 5'- GGG CAT CAC AGA CCT G -3'
G+C content [%] 63
Length [nt] 16
Check specificity/coverage
Hybridization efficiency

Application of rRNA-based probes for observing marine nanoplanktonic protists. Lim EL, Amaral LA, Caron DA, DeLong EF. Applied and environmental microbiology. 1993. Pubmed

Remarks also validated for Dot Blot and flow cytometry, target position refers to Phaeocystis globosa


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.