Analysis of the SD in read length for CGG-repeat-containing FMR1 alleles. (A) Mean SD comparison between inter- and intramolecular subreads for the two plasmid- (underlined tick labels) and PCR-generated libraries. Higher intermolecular (versus intramolecular) SDs are apparent only for the repeat region, consistent with the presence of complex populations of repeat sizes. (B,C) Comparisons of CGG-repeat size distributions for plasmid- and PCR-generated CGG-repeat–containing DNA for (B) normal (∼30 CGG repeats) and (C) premutation (∼100 CGG repeats). Broader distributions for PCR-generated fragments reflect errors associated with PCR amplification of CGG-repeat elements.