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Probe/primer details

GNSB-941 Tested for in situ hybridization.
Accession no. pB-718
Taxonomy Chloroflexi; Bacteria
Specificity phylum Chloroflexi (green nonsulfur bacteria)
Category phototrophic bacteria
higher taxonomic levels
Target rRNA 16S rRNA
Position 941-957
Sequence 5'- AAA CCA CAC GCT CCG CT -3'
G+C content [%] 59
Length [nt] 17
Check specificity/coverage
Formamide [%] 35
Hybridization efficiency

Previously unknown and phylogenetically diverse members of the green nonsulfur bacteria are indigenous to freshwater lakes. Gich F, Garcia-Gil J, Overmann J. Archives of microbiology. 2001. Pubmed

Remarks Use probes GNSB-941 and CFX1223 in equimolar mixture to detect all Chloroflexi


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.