==============
I/O parameters
==============
input_seeds_file: ./oligos_size_7
evidence_list: evidence_file_list
seq_file_list: sequence_file_list
output_dir: ./out7mers/

==========================
geneset scoring parameters
==========================
fast_mode: no
using regression scoring: no
bootstrap_motif_score: no
strand-specific: yes

degen_threshold:  0.50
fraction_degen_pos_threshold:  0.50
scoring_params.max_gene_set_size_percentage_threshold:  0.99
scoring_params.min_gene_set_size_absolute_threshold: 376
scoring_params.min_gene_set_size_percentage_threshold:  0.05
min_motif_length: 4
max_motif_length: 10

========================
ensemble PSSM parameters
========================
required_core_length: 6
pssm_crop_threshold:  0.33
cluster_pssm_threshold_fraction:  0.50
fraction_of_top_sequences_to_consider:  0.50
species_type: human

===============================================
clustering similar motif predictions parameters
===============================================
cluster_sim_threshold:  0.85
hypegeom_p_val_cutoff: 1.000000e-30

===============
MISC parameters
===============
estimate p-value: no
