Extended Data Fig. 7: Evidence of winner-take-all in flag experiments.

a, An example flag pattern (A flag 12), and uniform 50 nM concentration ‘no flag’ pattern. b, Fluorescence normalized to maximum readings, from the temperature ramp experiment (Extended Data Fig. 6 and Supplementary Information section 5). The fluorescence at the end of the experiment, F_p,s,f, of fluorophore f in sample s of pattern p is used along with the corresponding fluorescence value for the no flag pattern, F_{no flag,s,f}, to calculate the ratio M_p,s,f. This ratio corresponds to the relative amount of quenching for that fluorophore in the flag pattern compared to the no flag pattern. The ratios are averaged across the 5 on-target fluorophores (circled in b) in samples for the flag pattern to obtain an average on-target ratio, and across the 10 off-target fluorophores to obtain an average off-target ratio. c, The on- and off-target ratios are plotted for each flag pattern. For winner-take-all behavior, on-target quenching is expected to be higher with a flag pattern than with no flag, resulting in \({M}_{p}^{{\rm{on}}\,{\rm{target}}} > 1\), while off-target quenching is expected to be reduced, resulting in \({M}_{p}^{{\rm{off}}\,{\rm{target}}} < 1\).