This category includes a variety of important short dispersed repeats, generally sequences that interact with proteins. We've seen these as clusters of very short sequences -- DnaA-binding sites and repressor-binding sites. In addition, you've encountered gapped palindromes that serve as a certain class of transcriptional terminator. Identifying these sites is certainly of interest, but greater insights can come from comparing them, either within a single genome or amongst several genomes. For example: What other sequence features surround DnaA-binding sites from different organisms? What is the genetic context of such sites? Where are gapped palindromes found in certain phages? How distant are they from gene ends? How are common intergenic motifs preserved from one phage to the next? ...and so forth.

Articles of possible interest: Petrillo M, Silvestro G, Paolo Di Nocera P, Boccia A, Paolella G (2006). Stem-loop structures in prokaryotic genomes. BMC Genomics 7:170   Friedman DI, Court DL (2001). Bacteriophage lambda: Alive and well and still doing its thing. Curr Opin Microbiol 4:201-207.   van Helden J, André B, Collado-Vides, J (1998). Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J Molec Biol 281:827-842. Notes of possible interest: Gene regulation and bacteriophage Search for regulatory sequences Companion to Fuller RS et al (1984): The dnaA protein complex with... oriC... Computational detection of origins of replication