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Supplementary Figure 1: Maximum Likelihood Phylogenetic without cnidarian Hox orthologs. Hox and ParaHox genes of acoels indicated in red. Bootstraps (3000) above 60 are indicated in percentage.

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Supplementary Figure 2: Bayesian phylogenetic orthology assignment of the ClSoxB1.

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Supplementary Table 1: Motif comparison of the acoel Hox genes with that of bilaterian and cnidarian sequences.

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