We show that the number of G...G (in CGG repeat) or C...C (in CCG repeat) mismatches (other than A...T, T...A, C...G and G...C canonical base pairs) dictates the secondary structural choice of the sense and antisense strands of the FMR1 gene and their corresponding transcripts in fragile X-associated tremor/ataxia syndrome (FXTAS). The gene discussed is FMR1; the disease is fragile X-associated tremor/ataxia syndrome.