Figure 1

• A - Schematic of conservation vs. disorder in a single protein (no data)
• B - figure_1/disorder_vs_conservation_correlation.ipynb
• C - figure_1/disorder_vs_conservation_correlation.ipynb
• D - figure_1/disorder_vs_conservation_correlation.ipynb
• E - Schematic of plasmid shuffling assay (no data)
• F - Data from dilution plates (see supplementary figures and supplementary tables)
• G - Schematic showing constructs (data from dilution plates)
• H - figure_1/abf1_idr2.fasta - amino acid sequence provided

Figure 2

• A - Schematic of chemical conservation vs. sequence conservation
• B - figures_2/composition_conservation.ipynb
• C - figures_2/alignment_schematic_figure_2c.ipynb
• D - growth data from dilution plates (see supplementary figures and supplementary tables). Tree structure from Feng et al. Scientific Reports 2017.
• E - growth data from dilution plates (see supplementary figures and supplementary tables) with protein function taken from UniProt and/or SGD entries on the proteins listed.

Figure 3

• A - Schematic showing folded domain and IDR; growth data from dilution plates (see supplementary figures and supplementary tables).
• B - Schematic showing what sequence "shuffling" means; growth data from dilution plates (see supplementary figures and supplementary tables).
• C - Schematic showing where subregions are being shuffled (schematic to scale); growth data from dilution plates (see supplementary figures and supplementary tables).
• D - figure_3/linear_analysis.ipynb
• E - Schematic highlighting relative positions of the essential motif, Abf1-G4-like subregion, and $Gal4G4 subregion.
• F - Files in figure_3/em_structural_prediction/
• G - growth data from dilution plates (see supplementary figures and supplementary tables).
• H - Schematic (no data)
• I - growth data from dilution plates (see supplementary figures and supplementary tables).
• J - growth data from dilution plates (see supplementary figures and supplementary tables).
• K - growth data from dilution plates (see supplementary figures and supplementary tables).
• L - growth data from dilution plates (see supplementary figures and supplementary tables).
• M - growth data from dilution plates (see supplementary figures and supplementary tables).

Figure 4

• A - Schematic of motif and context (top) and chemical vs. sequence specificity (bottom)
• B - figure_4/coarse_grained_simulation_analysis.ipynb
• C - growth data from dilution plates (see supplementary figures and supplementary tables).
• D - figure_4/coarse_grained_simulation_analysis.ipynb
• E - growth data from dilution plates (see supplementary figures and supplementary tables).
• F - growth data from dilution plates (see supplementary figures and supplementary tables).
• G - growth data from dilution plates (see supplementary figures and supplementary tables).
• H - growth data from dilution plates (see supplementary figures and supplementary tables).
• I - figure_4/composition_analysis_fig_4.ipynb
• J - growth data from dilution plates (see supplementary figures and supplementary tables).
• K - growth data from dilution plates (see supplementary figures and supplementary tables).

Figure 5

• See readme in figure_5/
• A - Schematic of FINCHES-based analysis
• B - Schematic of in silico evolution, with individual intermaps generated using figure_5/evolution/in_silico_evo.ipynb
• C - figure_5/evolution/signal_vs_noise_final.ipynb
• D - Schematic showing error-prone PCR workflow
• E - Schematic of expected behavior
• F (top) - figure_5/evolution/error_prone_pcr_analysis.ipynb
• F (bottom) - figure_5/evolution/error_prone_pcr_vs_in_silico_final.ipynb

Figure 6

• See readme in figure_6/
• A - Schematic of MNase-seq
• B - figure_6/6B/MNase_coverage_Abf1_fig6B.xlsx
• C - Schematic of Anchor Away (no data)
• D - Schematic of ODM-seq (no data)
• E - figure_6/6E/6E_Kubik_responder_sites.tsv
• F - figure_6/6F/
• G - figure_6/6F/
• H - `Schematic of overall model (no data)

Extended data

Extended Data 1

• A - figure_1/disorder_vs_conservation_correlation.ipynb
• B - extended_data_1/fig_s1_analysis.ipynb
• B inset - extended_data_1/fig_s1_analysis.ipynb
• C - extended_data_1/fig_s1_analysis.ipynb
• D - extended_data_1/fig_s1_analysis.ipynb
• E - extended_data_1/fig_s1_analysis.ipynb
• F - extended_data_1/fig_s1_analysis.ipynb
• G -

Extended Data 2

• A - extended_data_2/chip_figure.ipynb
• B - figure_2/composition_conservation.ipynb
• C - figure_2/composition_conservation.ipynb
• D - figure_2/composition_conservation.ipynb
• E - figure_2/composition_conservation.ipynb
• F - figure_2/composition_conservation.ipynb
• G - figure_2/composition_conservation.ipynb

Extended Data 3

• A - extended_data_3/ortholog_composition.ipynb
• B - figures_2 /compositional_analysis.ipynb
• C - extended_data_3/sequence_analysis_dead_seqs.ipynb
• D - extended_data_3/patterning_analysis.ipynb
• E - extended_data_3/patterning_analysis.ipynb
• F - extended_data_3/patterning_analysis.ipynb
• G - extended_data_3/sequence_alignment.docx (alignment using Needle).

Extended Data 4

• A - Schematic from simulation snapshot
• B - Parameter matrix
• C - figure_4/coarse_grained_simulation_analysis.ipynb
• D - figure_4/coarse_grained_simulation_analysis.ipynb
• E - Amino acid sequences
• F - extended_data_4/rad16_rad7_intermaps.ipynb
• G - extended_data_4/rad16_rad7_intermaps.ipynb
• H - extended_data_4/other_examples/signal_vs_noise_other_examples.ipynb

Extended Data 5

• See readme in extended_data_5/
• A - extended_data_5/MNase_coverage_Abf1_ED5_A_B_C.xlsx
• B - extended_data_5/MNase_coverage_Abf1_ED5_A_B_C.xlsx
• C - extended_data_5/MNase_coverage_Abf1_ED5_A_B_C.xlsx
• D - extended_data_5/ED5_D/ED5_D_Kubik_responder_sites.tsv
• E - extended_data_5/ED5_E/ED5_E_Kubik_responder_sites.tsv
• F - extended_data_5/ED5_F/ED5_F_RNA_seq_boxplot_stat_v2.html

Extended Data 6

• See readme in extended_data_6/
• A - extended_data_6/ED6_A/ED6_A_fixed_plus_one_grid_by_rep.tsv
• B - extended_data_6/ED6_B/ED6_B_spikein.tsv
• C - extended_data_6/ED6_C/ED6_C_k_resp_grid_by_rep.tsv

Extended Data 7

• See readme in extended_data_7/
• A - extended_data_7/ED7_A_B_C/ED7_A_venn_diagram_invivo.tsv
• B - extended_data_7/ED7_A_B_C/ED7_B_venn_diagram_pwm.tsv
• C - extended_data_7/ED7_A_B_C/ED7_C_venn_diagram_pwm_vs_invivo.tsv
• D - extended_data_7/ED7_D_E_F_G/ED7_D_Hahn_bound_only.tsv
• E - extended_data_7/ED7_D_E_F_G/ED7_E_Hahn_resp_only.tsv
• F - extended_data_7/ED7_D_E_F_G/ED7_F_G_Hahn_bound_and_resp.tsv
• G - extended_data_7/ED7_D_E_F_G/ED7_F_G_Hahn_bound_and_resp.tsv

Extended Data 8

• See readme in extended_data_8/
• A - extended_data_8/ED8_A/
• B - extended_data_8/ED8_B/
• C - extended_data_8/ED8_C/
• D - extended_data_8/ED8_D/
• E - extended_data_8/ED8_E/

Extended Data 9

• A - extended_data_9/fus_sequences.fasta
• B - Schematic of a phase diagram
• C - Schematic of solving free energy surface for Flory-Huggins to build temperature-dependent phase diagrams
• D - extended_data_9/flory_huggins_phase_diagrams.ipynb
• E - extended_data_9/flory_huggins_phase_diagrams.ipynb
• F - extended_data_9/flory_huggins_phase_diagrams.ipynb
• G - extended_data_9/flory_huggins_phase_diagrams.ipynb
• H - extended_data_9/AF-Q13148-F1-model_v4.pdb - PDB structure for TDP-43 used to highlight helical residues 321-342
• I - growth data from dilution plates (see supplementary figures and supplementary tables).

Extended Data 10

• A - extended_data_1/fig_s1_analysis.ipynb
• B - extended_data_1/fig_s1_analysis.ipynb
• C - extended_data_10/ED10_C/ED10_C_genome.tsv

Supplementary information

Supplementary figures 1 and 2

Growth data are provided in the viablity_data/ directory, with two large PDFs that report original images for growth plates.

Supplementary tables

For completeness, we also provide all supplementary tables in the supplementary_tables/ directory (supplementary_tables_2025_11_30.xlsx).