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Probe/primer details

Sita-649 Tested for in situ hybridization.
Accession no. pB-1164
Taxonomy Sphaeronema; Tylenchulinae; Tylenchulidae; Criconematoidea; Tylenchina; Tylenchida; Chromadorea; Nematoda; Ecdysozoa; Protostomia; Bilateria; Eumetazoa; Metazoa; Opisthokonta; Eukaryota
Specificity Candidatus Sphaeronema italicum
Category bacteria of relevance in wastewater treatment
Competitor 5'-CCT CTC CCG GTC TCC AGC C -3'
Target rRNA 16S rRNA
Position 649-666
Sequence 5'- CCW CTC CCG GAC YCC AGC -3'
G+C content [%] 72
Length [nt] 18
Check specificity/coverage
Formamide [%] 50
Hybridization efficiency

Filamentous Alphaproteobacteria associated with bulking in industrial wastewater treatment plants. Levantesi C, Beimfohr C, Geurkink B, Rossetti S, Thelen K, Krooneman J, Snaidr J, van der Waarde J, Tandoi V. Systematic and applied microbiology. 2004. Pubmed

Remarks Competitor to exclude PPx3-1428


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.