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Probe/primer details

CST440 Tested for in situ hybridization.
Accession no. pB-1198
Taxonomy [Clostridium] stercorarium; Ruminiclostridium; Ruminococcaceae; Clostridiales; Clostridia; Firmicutes; Bacteria
Specificity Group 1 clones (AC044 and AC051), closely related to Clostridium stercorarium
Category cellulose-decomposing bacteria
Target rRNA 16S rRNA
Position 440-459
Sequence 5'- CGT CTA TTT CGT CCC CGA TC -3'
G+C content [%] 55
Length [nt] 20
Check specificity/coverage
Formamide [%] 30
Hybridization efficiency
References

Identification, detection, and spatial resolution of Clostridium populations responsible for cellulose degradation in a methanogenic landfill leachate bioreactor. Burrell PC, O'Sullivan C, Song H, Clarke WP, Blackall LL. Applied and environmental microbiology. 2004. Pubmed

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Glossary
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.