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Probe/primer details

Name MB1
Accession no. pB-200
Taxonomy Methanosarcina; Methanosarcinaceae; Methanosarcinales; Methanomicrobia; Euryarchaeota; Archaea
Specificity Methanosarcina frisius, Methanosarcina sp., Methanosarcina acidovorans, Methanosarcina thermophila, Methanosarcina barkeri
Category methanogenic archaea
Target rRNA 16S rRNA
Sequence 5'- CCG GAG GAC TGA CCA AA -3'
G+C content [%] 59
Check specificity/coverage
Hybridization efficiency

Differentiation of methanosaeta concilii and methanosarcina barkeri in anaerobic mesophilic granular sludge by fluorescent In situ hybridization and confocal scanning laser microscopy Rocheleau S, Greer CW, Lawrence JR, Cantin C, Laramee L, Guiot SR. Applied and environmental microbiology. 1999. Pubmed

Remarks wrong sequence in reference (should be reverse complementary)


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.