This category includes some of the first repeated sequences that were recognized in bacteria, including Chi sites (8-nt sites in E. coli used by the mechanism of DNA recombination), and HIP (Highly Iterated Palindromes) sequences (8-nt sequences that may also be related to recombination), DNA uptake signals (9-nt sites important for certain bacteria to recognize exogenous DNA as self). 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: Where do they occur in the genome? In genes? Downstream from genes? Upstream? Are their sequences conserved between different related bacteria? How fast do their sequences change in evolutionary time? How fast do their positions change in evolutionary time? ...and so forth.

Articles of possible interest: Smith HO, Gwinn ML, Salzberg SL (1999). DNA uptake signal sequences in naturally transformable bacteria. Res Microbiol 150:603-616.   Stahl F (2005). Chi: A little sequence controls a big enzyme. Genetics 170:487-493.   Robinson NJ, Robinson PJ, Gupta A, Bleasby AJ, Whitton BA, Morby, AP (1995). Singular over-representation of an octameric palindrome, HIP1, in DNA from many cyanobacteria. Nucl Acids Res 23:729-735 Notes of possible interest: Computational detection of origins of replication Small dispersed repeats (for overlap with HIP1 sequences)