Characteristics of site variation among clones of the 340-base pair, tandemly repeated EcoR1 family of human DNA

Twenty-four clones of EcoR1-restricted, 340-base pair (bp) DNA derived from human DNA have been sequenced and compared to a published consensus sequence for this family. No two clones were found to have identical sequences; the clones studied differed from the consensus sequence in as few as 1 or as many as 41 sites. On the average in these clones, a 5.2% divergence from exact homology was found, with 1 of 10 of the site variations being "nonrandom," i.e., cases in which five or more clones had the same nucleotide substitution at that site (viz., 53, 124, 126, 138, 152, and 157). At site 157, for example, 16 of the 24 clones differed from the reference sequence. Positions and their respective changes, as compared to the consensus sequence, are summarized. Variations are discussed with relation to possible functions for these sequences.