8Phytohormones regulate many aspects of plant life by activating transcription factors (TF) that bind 9 sequence-specific response elements (RE) in regulatory regions of target genes. Despite their short 10 length, REs are degenerate with a core of just 3-4bps. This degeneracy is paradoxical, as it reduces 11 specificity, and REs are extremely common in the genome. To study whether RE degeneracy might serve 12 a biological function we developed an algorithm for the detection of regulatory sequence conservation, 13and applied it to phytohormones REs in 45 angiosperms. Surprisingly, we found that specific RE variants 14 are highly conserved in core hormone response genes. Experimental evidence showed that specific 15 variants act to regulate the magnitude and spatial profile of hormonal response in Arabidopsis and 16 tomato. Our results suggest that hormone-regulated TFs bind a spectrum of REs, each coding for a 17 distinct transcriptional response profile. Our approach is applicable for precise editing and rational 18 promoter design. 19