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Probe/primer details

Name PSP-6
Accession no. pB-291
Taxonomy Leptothrix; Burkholderiales Genera incertae sedis; unclassified Burkholderiales; Burkholderiales; Betaproteobacteria; Proteobacteria; Bacteria
Specificity Leptothrix discophora SP-6, L. cholodnii CCM1827, Leptothrix sp. strain NC-1
Category bacteria of relevance in wastewater treatment
Target rRNA 16S rRNA
Sequence 5'- GGC TAT CCC CCA CTA CTG -3'
G+C content [%] 61
Check specificity/coverage
Hybridization efficiency

Development and application of 16S rRNA-targeted probes for detection of iron- and manganese-oxidizing sheathed bacteria in environmental samples. Siering PL, Ghiorse WC. Applied and environmental microbiology. 1997. 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.