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If DUSs are associated with recombination, either by selection or molecular drive, then one would expect there to be a close association between their spacing and the sizes of conversion fragments. We then computed the distribution of the distances between consecutive DUSs. To control for the selection of close inverted DUSs in transcription terminators, we clustered pairs of DUS in each such element into a composite DUS (cDUS). Regions containing a complementary DUS pair separated by 21 nucleotides or less were regarded as a single cDUS. Thus, the term cDUS stands for a single isolated DUS or a pair of DUSs in close inverse configuration in a rho-independent terminator. The average inter-cDUS distance among meningococci is approximately 1,500 nucleotides, which corresponds to the average size of conversion fragments (Additional data files 2 and 5). It should be noted that not controlling for pairs of DUSs in transcription terminators did not radically change this number (average distance between DUS about 1,150 nucleotides), emphasizing the close concordance between conversion fragments and DUS distribution. When all neisserial genomes were analyzed, the distance between cDUS decreased to 1,128 nucleotides because DUS density is higher in N. lactamica (Table 1). This higher density of DUSs in N. lactamica is in remarkable agreement with the conversion fragment data, which shows much shorter conversion fragments in this species than in N. meningitidis Z2491 (573 versus 1,734 nucleotides; P


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