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Probe/primer details

PPx3-1428 Tested for in situ hybridization.
Accession no. pB-1161
Specificity Candidatus Alysiomicrobium bavaricum
Category bacteria of relevance in wastewater treatment
Target rRNA 16S rRNA
Position 1428-1445
Sequence 5'- TGG CCC ACC GGC TTC GGG -3'
G+C content [%] 78
Length [nt] 18
Check specificity/coverage
Formamide [%] 50
Hybridization efficiency

Phylogenetic analysis and in situ identification of "Nostocoida limicola"-like filamentous bacteria in activated sludge from industrial wastewater treatment plants. Snaidr I, Beimfohr C, Levantesi C, Rossetti S, van der Waarde J, Geurkink B, Elkelboom D, Lemaitre M, Tandoi V. Water science and technology : a journal of the International Association on Water Pollution Research. 2002. Pubmed


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.