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Probe/primer details

LSPotu11021-1127 Tested for in situ hybridization.
Full name
(Alm et al. 1996)
S-*-Lsp-1127-a-A-20
Accession no. pB-36
Taxonomy Lachnospiraceae; Clostridiales; Clostridia; Firmicutes; Bacteria
Specificity Lachnospiraceae OTU_11021
Category animal and human associated microbiota
intestinal microbiota
Target rRNA 16S rRNA
Position 1127-1146
Sequence 5'- TTC CCA TCT TTC TTG CTG GC -3'
G+C content [%] 50
Length [nt] 20
Check specificity/coverage
Formamide [%] 30
Hybridization efficiency
References

Phylotype-level 16S rRNA analysis reveals new bacterial indicators of health state in acute murine colitis. Berry D, Schwab C, Milinovich G, Reichert J, Ben Mahfoudh K, Decker T, Engel M, Hai B, Hainzl E, Heider S, Kenner L, Müller M, Rauch I, Strobl B, Wagner M, Schleper C, Urich T, Loy A. The ISME journal. 2012. Pubmed

Remarks Specific use together with probe LSPotu11021-1448.

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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.