scieee AI-readable full text Open interactive document viewer

A Structure-Guided Kinase–Transcription Factor Interactome Atlas Reveals Docking Landscapes of the Kinome

Kim, Ah-Ram; Huang, Kerui; Johnson, Jared L.; Yaron-Barir, Tomer M.; Wang, Keven; Cantley, Lewis C.; Hu, Yanhui; Perrimon, Norbert

Publisher
Zenodo
DOI
10.5281/zenodo.17314335
Repository
zenodo.org
Language
en

Abstract

This repository contains the complete supplementary data tables associated with the manuscript, "A Structure-Guided Kinase–Transcription Factor Interactome Atlas Reveals Docking Landscapes of the Kinome" by Kim et al. 2025. The full preprint is available on bioRxiv (DOI: https://doi.org/10.1101/2025.10.10.681672). The study presents a structure-guided atlas of the human and Drosophila kinome, built by applying a new interface-aware scoring framework (iLIS) to AlphaFold-Multimer predictions to map kinase-transcription factor interactions. This resource provides residue-level structural insight into partner recognition across the kinome. This repository contains the following data files, along with a README.txt file that describes the content of each file and its columns: Supplementary Data 1: The complete human Serine/Threonine kinase–transcription factor interactome, including iLIS scores and predicted residue-level interface data. Supplementary Data 2: The complete set of computationally derived Position Weight Matrices (PWMs) for the human S/T kinase screen. Supplementary Data 3: The complete Drosophila kinome–transcription factor interactome, including iLIS scores and predicted residue-level interface data. Supplementary Data 4: The complete set of computationally derived Position Weight Matrices (PWMs) for the Drosophila kinome screen. Supplementary Data 5: A comprehensive catalog of all predicted interaction hotspots for the human and Drosophila kinomes. Supplementary Figure 8: Sequence logos displaying the computed position weight matrices (PWMs) for all high-confidence kinase clusters identified in the Drosophila kinome screen, showing enrichment patterns for all 20 amino acids across the ±10 residue window. Code Availability The Python code for iLIS analysis and benchmarking is publicly available on GitHub: https://github.com/flyark/AFM-LIS Please refer to the README.txt file for detailed descriptions and the associated manuscript for full methodological details.

Full text

-10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around S in Cluster 1 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around T in Cluster 1 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around Y in Cluster 1 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around P in Cluster 1 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around D in Cluster 1 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around E in Cluster 1 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around K in Cluster 1 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around R in Cluster 1 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around H in Cluster 1 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 5 0 5 Log Ratio (Prediction / background) Sequence Preferences around W in Cluster 1 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around F in Cluster 1 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around Q in Cluster 1 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around N in Cluster 1 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around C in Cluster 1 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around G in Cluster 1 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around A in Cluster 1 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around V in Cluster 1 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around L in Cluster 1 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around I in Cluster 1 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around M in Cluster 1 Cluster 1 (14 members): CG6800, Cdk1, Cdk12, Cdk2, Cdk4, Cdk5, Cdk7, Cdk8, Cdk9, Eip63E, Pitslre, Sdr, cdc2rk, msn Supplementary Figure 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around S in Cluster 2 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around T in Cluster 2 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around Y in Cluster 2 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around P in Cluster 2 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around D in Cluster 2 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 0.5 0.0 0.5 1.0 Log Ratio (Prediction / background) Sequence Preferences around E in Cluster 2 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around K in Cluster 2 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around R in Cluster 2 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around H in Cluster 2 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around W in Cluster 2 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around F in Cluster 2 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around Q in Cluster 2 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around N in Cluster 2 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around C in Cluster 2 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around G in Cluster 2 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around A in Cluster 2 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around V in Cluster 2 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 0.5 0.0 0.5 1.0 Log Ratio (Prediction / background) Sequence Preferences around L in Cluster 2 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around I in Cluster 2 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around M in Cluster 2 Cluster 2 (6 members): Erk7, bsk, p38a, p38b, p38c, rl Supplementary Figure 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around S in Cluster 3 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around T in Cluster 3 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around Y in Cluster 3 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around P in Cluster 3 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around D in Cluster 3 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around E in Cluster 3 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around K in Cluster 3 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around R in Cluster 3 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around H in Cluster 3 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around W in Cluster 3 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around F in Cluster 3 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around Q in Cluster 3 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around N in Cluster 3 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around C in Cluster 3 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around G in Cluster 3 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around A in Cluster 3 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around V in Cluster 3 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around L in Cluster 3 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around I in Cluster 3 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around M in Cluster 3 Cluster 3 (7 members): CG1227, Drak, S6k, Takl1, bon, sqa, trc Supplementary Figure 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around S in Cluster 4 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around T in Cluster 4 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around Y in Cluster 4 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around P in Cluster 4 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around D in Cluster 4 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around E in Cluster 4 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around K in Cluster 4 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around R in Cluster 4 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around H in Cluster 4 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around W in Cluster 4 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around F in Cluster 4 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around Q in Cluster 4 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around N in Cluster 4 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around C in Cluster 4 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around G in Cluster 4 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around A in Cluster 4 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around V in Cluster 4 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around L in Cluster 4 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around I in Cluster 4 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around M in Cluster 4 Cluster 4 (11 members): CG8173, Doa, GckIII, Madm, PKD, Pkc53E, Pkc98E, Pkcdelta, Pkn, aPKC, inaC Supplementary Figure 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 0.5 0.0 0.5 1.0 Log Ratio (Prediction / background) Sequence Preferences around S in Cluster 5 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around T in Cluster 5 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around Y in Cluster 5 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around P in Cluster 5 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around D in Cluster 5 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around E in Cluster 5 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around K in Cluster 5 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around R in Cluster 5 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around H in Cluster 5 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around W in Cluster 5 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around F in Cluster 5 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around Q in Cluster 5 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around N in Cluster 5 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around C in Cluster 5 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around G in Cluster 5 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 0.5 0.0 0.5 1.0 Log Ratio (Prediction / background) Sequence Preferences around A in Cluster 5 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around V in Cluster 5 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 0.5 0.0 0.5 1.0 Log Ratio (Prediction / background) Sequence Preferences around L in Cluster 5 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around I in Cluster 5 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around M in Cluster 5 Cluster 5 (14 members): Akt1, Bub1, CG12069, CG4839, CG8565, JIL-1, Pdk, Pka-C1, Pka-C2, Pka-C3, SRPK, aurA, aurB, srpk79D Supplementary Figure 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around S in Cluster 6 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around T in Cluster 6 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around Y in Cluster 6 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around P in Cluster 6 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around D in Cluster 6 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around E in Cluster 6 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around K in Cluster 6 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around R in Cluster 6 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around H in Cluster 6 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around W in Cluster 6 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around F in Cluster 6 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around Q in Cluster 6 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around N in Cluster 6 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around C in Cluster 6 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around G in Cluster 6 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around A in Cluster 6 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around V in Cluster 6 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around L in Cluster 6 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around I in Cluster 6 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around M in Cluster 6 Cluster 6 (5 members): AMPKalpha, CG7236, CaMKI, fray, sff Supplementary Figure 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around S in Cluster 7 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around T in Cluster 7 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around Y in Cluster 7 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around P in Cluster 7 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around D in Cluster 7 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around E in Cluster 7 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around K in Cluster 7 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around R in Cluster 7 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around H in Cluster 7 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around W in Cluster 7 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around F in Cluster 7 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around Q in Cluster 7 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around N in Cluster 7 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around C in Cluster 7 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around G in Cluster 7 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around A in Cluster 7 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around V in Cluster 7 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 0.5 0.0 0.5 1.0 Log Ratio (Prediction / background) Sequence Preferences around L in Cluster 7 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around I in Cluster 7 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around M in Cluster 7 Cluster 7 (12 members): CG4041, Haspin, Pak, Pak3, Pask, PhKgamma, Rok, S6kII, gek, hppy, mbt, sti Supplementary Figure 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around S in Cluster 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around T in Cluster 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around Y in Cluster 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around P in Cluster 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around D in Cluster 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around E in Cluster 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around K in Cluster 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around R in Cluster 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around H in Cluster 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 5 0 5 Log Ratio (Prediction / background) Sequence Preferences around W in Cluster 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around F in Cluster 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around Q in Cluster 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around N in Cluster 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around C in Cluster 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around G in Cluster 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around A in Cluster 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around V in Cluster 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around L in Cluster 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around I in Cluster 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 5 0 5 Log Ratio (Prediction / background) Sequence Preferences around M in Cluster 8 Cluster 8 (4 members): Cad96Ca, Eph, Myt1, ninaC Supplementary Figure 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around S in Cluster 9 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around T in Cluster 9 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around Y in Cluster 9 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around P in Cluster 9 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around D in Cluster 9 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around E in Cluster 9 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around K in Cluster 9 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around R in Cluster 9 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around H in Cluster 9 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 5 0 5 Log Ratio (Prediction / background) Sequence Preferences around W in Cluster 9 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around F in Cluster 9 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around Q in Cluster 9 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around N in Cluster 9 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around C in Cluster 9 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around G in Cluster 9 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around A in Cluster 9 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around V in Cluster 9 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around L in Cluster 9 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around I in Cluster 9 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around M in Cluster 9 Cluster 9 (16 members): CG11486, CG3008, CG31097, CG7616, CG8726, Ddr, Gcn2, Ilk, Prpk, RIOK2, Stlk, Takl2, babo, pll, sax, tkv Supplementary Figure 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around S in Cluster 16 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 5 0 5 Log Ratio (Prediction / background) Sequence Preferences around T in Cluster 16 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 5 0 5 Log Ratio (Prediction / background) Sequence Preferences around Y in Cluster 16 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 5 0 5 Log Ratio (Prediction / background) Sequence Preferences around P in Cluster 16 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around D in Cluster 16 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around E in Cluster 16 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 5 0 5 10 Log Ratio (Prediction / background) Sequence Preferences around K in Cluster 16 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 5 0 5 10 Log Ratio (Prediction / background) Sequence Preferences around R in Cluster 16 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 5 0 5 Log Ratio (Prediction / background) Sequence Preferences around H in Cluster 16 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 5 0 5 10 Log Ratio (Prediction / background) Sequence Preferences around W in Cluster 16 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around F in Cluster 16 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 5 0 5 10 Log Ratio (Prediction / background) Sequence Preferences around Q in Cluster 16 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around N in Cluster 16 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 5 0 5 Log Ratio (Prediction / background) Sequence Preferences around C in Cluster 16 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around G in Cluster 16 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around A in Cluster 16 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around V in Cluster 16 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around L in Cluster 16 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 5 0 5 Log Ratio (Prediction / background) Sequence Preferences around I in Cluster 16 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 5 0 5 Log Ratio (Prediction / background) Sequence Preferences around M in Cluster 16 Cluster 16 (5 members): CG10738, CG31183, CG3216, CG34357, Gyc32E Supplementary Figure 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around S in Cluster 17 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around T in Cluster 17 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around Y in Cluster 17 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around P in Cluster 17 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around D in Cluster 17 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around E in Cluster 17 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around K in Cluster 17 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around R in Cluster 17 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around H in Cluster 17 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 5 0 5 Log Ratio (Prediction / background) Sequence Preferences around W in Cluster 17 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around F in Cluster 17 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around Q in Cluster 17 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around N in Cluster 17 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around C in Cluster 17 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around G in Cluster 17 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around A in Cluster 17 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around V in Cluster 17 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around L in Cluster 17 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around I in Cluster 17 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around M in Cluster 17 Cluster 17 (8 members): Ask1, Nek2, Pkg21D, Tak1, Wee1, for, ik2, tlk Supplementary Figure 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 0.5 0.0 0.5 1.0 Log Ratio (Prediction / background) Sequence Preferences around S in Cluster 18 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around T in Cluster 18 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around Y in Cluster 18 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around P in Cluster 18 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 0.5 0.0 0.5 1.0 Log Ratio (Prediction / background) Sequence Preferences around D in Cluster 18 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 0.5 0.0 0.5 1.0 Log Ratio (Prediction / background) Sequence Preferences around E in Cluster 18 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around K in Cluster 18 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around R in Cluster 18 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around H in Cluster 18 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around W in Cluster 18 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around F in Cluster 18 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around Q in Cluster 18 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around N in Cluster 18 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around C in Cluster 18 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 0.5 0.0 0.5 1.0 Log Ratio (Prediction / background) Sequence Preferences around G in Cluster 18 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around A in Cluster 18 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around V in Cluster 18 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 0.5 0.0 0.5 Log Ratio (Prediction / background) Sequence Preferences around L in Cluster 18 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around I in Cluster 18 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around M in Cluster 18 Cluster 18 (10 members): CG10702, CG7028, Dyrk2, Pk34A, aux, gskt, gwl, hipk, hpo, mnb Supplementary Figure 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around S in Cluster 19 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around T in Cluster 19 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around Y in Cluster 19 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around P in Cluster 19 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around D in Cluster 19 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around E in Cluster 19 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around K in Cluster 19 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 0.5 0.0 0.5 1.0 Log Ratio (Prediction / background) Sequence Preferences around R in Cluster 19 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around H in Cluster 19 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around W in Cluster 19 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around F in Cluster 19 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 0.5 0.0 0.5 1.0 Log Ratio (Prediction / background) Sequence Preferences around Q in Cluster 19 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around N in Cluster 19 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around C in Cluster 19 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around G in Cluster 19 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around A in Cluster 19 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around V in Cluster 19 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 0.5 0.0 0.5 Log Ratio (Prediction / background) Sequence Preferences around L in Cluster 19 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around I in Cluster 19 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around M in Cluster 19 Cluster 19 (14 members): CG13850, CG2124, CG8866, Cdc7, Dyrk3, Ire1, MAPk-Ak2, Tao, fu, grp, hop, ird5, nmo, wts Supplementary Figure 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around S in Cluster 20 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around T in Cluster 20 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around Y in Cluster 20 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around P in Cluster 20 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around D in Cluster 20 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around E in Cluster 20 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around K in Cluster 20 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around R in Cluster 20 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around H in Cluster 20 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 5 0 5 Log Ratio (Prediction / background) Sequence Preferences around W in Cluster 20 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around F in Cluster 20 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around Q in Cluster 20 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around N in Cluster 20 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around C in Cluster 20 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around G in Cluster 20 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around A in Cluster 20 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around V in Cluster 20 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 0.5 0.0 0.5 1.0 Log Ratio (Prediction / background) Sequence Preferences around L in Cluster 20 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around I in Cluster 20 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around M in Cluster 20 Cluster 20 (5 members): CG10177, CaMKII, Lk6, SAK, lkb1 Supplementary Figure 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 0.5 0.0 0.5 1.0 Log Ratio (Prediction / background) Sequence Preferences around S in Cluster 21 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around T in Cluster 21 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around Y in Cluster 21 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around P in Cluster 21 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around D in Cluster 21 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 0.5 0.0 0.5 1.0 Log Ratio (Prediction / background) Sequence Preferences around E in Cluster 21 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around K in Cluster 21 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around R in Cluster 21 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around H in Cluster 21 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around W in Cluster 21 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around F in Cluster 21 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around Q in Cluster 21 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around N in Cluster 21 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around C in Cluster 21 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around G in Cluster 21 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 0.5 0.0 0.5 1.0 Log Ratio (Prediction / background) Sequence Preferences around A in Cluster 21 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around V in Cluster 21 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 0.5 0.0 0.5 1.0 Log Ratio (Prediction / background) Sequence Preferences around L in Cluster 21 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around I in Cluster 21 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around M in Cluster 21 Cluster 21 (12 members): CG14305, CG17528, CG42366, CG4629, CG9222, KP78a, KP78b, Ror, Sik2, Sik3, ird1, lok Supplementary Figure 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around S in Cluster 22 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around T in Cluster 22 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around Y in Cluster 22 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around P in Cluster 22 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around D in Cluster 22 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around E in Cluster 22 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around K in Cluster 22 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around R in Cluster 22 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around H in Cluster 22 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around W in Cluster 22 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around F in Cluster 22 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around Q in Cluster 22 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around N in Cluster 22 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around C in Cluster 22 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around G in Cluster 22 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around A in Cluster 22 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around V in Cluster 22 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around L in Cluster 22 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around I in Cluster 22 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around M in Cluster 22 Cluster 22 (4 members): CG4945, Drl-2, dnt, drl Supplementary Figure 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around S in Cluster 23 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around T in Cluster 23 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around Y in Cluster 23 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around P in Cluster 23 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around D in Cluster 23 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around E in Cluster 23 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around K in Cluster 23 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around R in Cluster 23 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around H in Cluster 23 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around W in Cluster 23 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around F in Cluster 23 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around Q in Cluster 23 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around N in Cluster 23 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around C in Cluster 23 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around G in Cluster 23 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around A in Cluster 23 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around V in Cluster 23 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 Log Ratio (Prediction / background) Sequence Preferences around L in Cluster 23 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around I in Cluster 23 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around M in Cluster 23 Cluster 23 (5 members): Atg1, CG3608, CG8485, S6KL, par-1 Supplementary Figure 8 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around S in Cluster 24 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around T in Cluster 24 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around Y in Cluster 24 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around P in Cluster 24 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around D in Cluster 24 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around E in Cluster 24 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around K in Cluster 24 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around R in Cluster 24 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around H in Cluster 24 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2.5 0.0 2.5 5.0 Log Ratio (Prediction / background) Sequence Preferences around W in Cluster 24 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around F in Cluster 24 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around Q in Cluster 24 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around N in Cluster 24 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around C in Cluster 24 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around G in Cluster 24 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around A in Cluster 24 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 Log Ratio (Prediction / background) Sequence Preferences around V in Cluster 24 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 0.5 0.0 0.5 1.0 Log Ratio (Prediction / background) Sequence Preferences around L in Cluster 24 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 1 0 1 2 Log Ratio (Prediction / background) Sequence Preferences around I in Cluster 24 -10-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 2 0 2 4 Log Ratio (Prediction / background) Sequence Preferences around M in Cluster 24 Cluster 24 (20 members): Asator, CG11221, CG17698, CG31751, CG3277, CG34356, LIMK1, Mekk1, PEK, Pdk1, Raf, ball, cdi, dop, fs(1)h, ksr, otk, slik, slpr, wnd Supplementary Figure 8