Patch-Type Nucleotide Sequence Matches Across Genomes Suggest Intrinsic Signals for Illegitimate Recombination

Comparative analyses of nucleotide sequences across diverse taxa — including viruses, bacteria, plants, and mammals — consistently reveal patch-type sequence identities of ~ 45%. These identities consist of short identical stretches interspersed with mismatches and occur independently of phylogenetic relatedness. Strikingly, similar identity patterns emerge in alignments of randomized or scrambled sequences, suggesting that patch-type identities reflect intrinsic statistical properties of the four-letter genetic alphabet. Such patterns likely function as recognition signals for illegitimate recombination - a mechanism that promotes sequence insertion, exchange, and rearrangement without extensive homology. Patch-type identities have been observed at integration sites of foreign DNA and may play a role in genome plasticity, facilitating evolutionary innovation and the rapid diversification of RNA viruses such as SARS-CoV-2 . Our results support the view that the statistical architecture of the four-letter genetic alphabet itself may encode not only biological information, but also the potential for genome remodeling and adaptation during evolution.