Probe/primer details
| 181_ProLL | Tested for in situ hybridization. |
| Accession no. | pB-764 |
| Taxonomy | Prochlorococcus; Prochlorococcaceae; Prochlorales; Cyanobacteria; Bacteria |
| Specificity | Prochlorococcus LL (Cyanophyceae) |
| Category | phototrophic bacteria |
| Target rRNA | 16S rRNA |
| Sequence | 5'- CAT TTC ACC TCT CGG CAT -3' |
| G+C content [%] | 50 |
| Check specificity/coverage | 
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| Hybridization efficiency |  |
| References | Closely related Prochlorococcus genotypes show remarkably different depth distributions in two oceanic regions as revealed by in situ hybridization using 16S rRNA-targeted oligonucleotides. West NJ, Schönhuber WA, Fuller NJ, Amann RI, Rippka R, Post AF, Scanlan DJ. Microbiology (Reading, England). 2001. Pubmed |
| Remarks | this probe also recognises several Synechococcus sp. and an Oscillatoria sp. |
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.
