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Probe/primer details

ParaC-0658 Tested for in situ hybridization.
Full name
(Alm et al. 1996)
Accession no. pB-597
Taxonomy Parachlamydiaceae; Chlamydiales; Chlamydiia; Chlamydiae; Chlamydiae/Verrucomicrobia group; Bacteria
Specificity subgroup of the Parachlamydiaceae including Neochlamydia hartmannellae, endosymbiont of Acanthamoeba sp. UWC22
Category bacteria of medical or hygienical relevance
Target rRNA 16S rRNA
Position 658-675
Sequence 5'- TCC ATT TTC TCC GTC TAC -3'
G+C content [%] 44
Length [nt] 18
Check specificity/coverage
Formamide [%] 10*
Hybridization efficiency

Neochlamydia hartmannellae gen. nov., sp. nov. (Parachlamydiaceae), an endoparasite of the amoeba Hartmannella vermiformis. Horn M, Wagner M, Müller KD, Schmid EN, Fritsche TR, Schleifer KH, Michel R. Microbiology (Reading, England). 2000. Pubmed

Remarks *formamide concentration when probes Bn9-658 and S-*-ParaC-0658-a-A-18 are used simultaneously


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.