The Shine-Dalgarno sequence AGGAGG was originally identified because it is enriched in front of the open reading frames of E. coli. Similarly, one might expect that AGGAGG or a subsequence might be enriched in front of open reading frames for all the organisms that carry CCUCCU in the tail of the 16S rRNA. However, because these tails have 13 highly-conserved bases, it is also possible that the Shine-Dalgarno sequence shifts 5’ or 3’ with respect to the tail. It is also of interest to ask what, if any, sequences are enriched in front of open reading frames of organisms with a variant or absent antiSD.

We used the approach of Tompa to ask what sequences are enriched in front of open reading frames of various example prokaryotes. We chose 222 examples from diverse phyla for organisms that had a 13 base tail containing CCUCCU. We also examined all 128 organisms that had a variant or absent antiSD. Full results are shown below.