Overlapping redundant septuplets identical with regulatory elements of HIV-1 and SV40

Overlapping redundant short oligomers in DNA sequences of retroviruses and papovaviruses have been identified. For each sequence, a search procedure determines the 5% short oligomers of the same length with the highest ratios of observed to expected occurrences based on singlet composition of the sequence. These short oligomers are referred to as compositionally-assessed redundant sequence elements (COARSEs). A pair of COARSEs overlapping by at least one base is considered to be a COARSE overlap. Most COARSE overlaps of the 7th order (overlapping septuplets) are found in long terminal repeats of retroviruses and in the regulatory control regions of papovaviruses SV40, BK and JC. Many of the 7th order COARSE overlaps in HIV-1 and SV40 are identical with regulatory elements determined experimentally. On the contrary, very few of the most frequently occurring oligomer overlaps, which are defined differently from COARSE overlaps, are present in the regulatory regions of retroviruses and papovaviruses. Examining DNA sequences of other genomes by the COARSE overlap method may identify putative regulatory regions.