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Table S1 Polymorphic sites in CG3223. Dots represent same nucleotide as in Drosophila virilis and hyphens represent indels

Table S2 Polymorphic sites in ebony

Table S3 Polymorphic sites in CG13444

Table S4 Polymorphic sites in transformer

Table S5 Polymorphic sites in period

Table S6 Polymorphic sites in elav

Table S7 Polymorphic sites in yp1

Table S8 Polymorphic sites in fused1

Table S9 Polymorphic sites in timeless

Table S10 Polymorphic sites in lim3

Table S11 Polymorphic sites in bib

Table S12 Polymorphic sites in CG18397

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