Probe/primer details

CFX223	Tested for in situ hybridization.
Full name (Alm et al. 1996)	S-*-Bact-0223-a-A-18
Accession no.	pB-2657
Taxonomy	Chloroflexi; Bacteria
Specificity	Eikelboom type 0092 Chloroflexi
Target rRNA	16S rRNA
Position	223-240
Sequence	5'- GGT GCT GGC TCC TCC CAG -3'
G+C content [%]	72
Length [nt]	18
Check specificity/coverage
Formamide [%]	35
Hybridization efficiency
References	Filamentous bacterium Eikelboom type 0092 in activated sludge plants in Australia is a member of the phylum Chloroflexi. Speirs L, Nittami T, McIlroy S, Schroeder S, Seviour RJ. Applied and environmental microbiology. 2009. Pubmed

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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.