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Table S1. Regulatory regions examined (see Supp. Bibliography for full reference)

Table S2. Divergence values for alternate outgroups

Table S3. Test statistic significance values within S. purpuratus

Table S4. Test statistic significance values against outgroup A. fragilis

Table S5. Test statistic significance values against outgroup S. droebachiensis

Table S6. Test statistic significance values against outgroup S. franciscanus

Table S7. Comparisons of polymorphism and divergence for binding sites and non-binding sites

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