Probe/primer details

Name	Mmb1121
Accession no.	pB-586
Taxonomy	Methylomicrobium; Methylococcaceae; Methylococcales; Gammaproteobacteria; Proteobacteria; Bacteria
Specificity	Methylomicrobium album BG8, M. agile A30
Category	methylotrophic bacteria
Target rRNA	16S rRNA
Position	1121-1140
Sequence	5'- CAT CAC GTG TTG GCA ACT AA -3'
G+C content [%]	45
Length [nt]	20
Check specificity/coverage
Hybridization efficiency
References	Fluorescent oligonucleotide rDNA probes for specific detection of methane oxidising bacteria. Bourne DG, Holmes AJ, Iversen N, Murrell JC. FEMS microbiology ecology. 2000. Pubmed

Print

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.