--- Type: Sequence Folding: # Rescale energy parameters to a temperature of temp C. custom_temperature: no temperature: 37 # Do not allow GU pairs. no_GU: no # Do not allow GU pairs at the end of helices. no_close_GU: no Features: nt_proportion: yes dinucleotide_proportion: yes gc_content: yes gc_ratio: yes sequence_length: yes stem_length: no stem_number: no avg_bp_stem: no longest_stem_length: no terminal_loop_length: no bulge_number: no loops_number: no longest_loop_length: no aloops_number: no sloops_number: no nt_aloops: no nt_sloops: no longest_simmetric_region: no avg_length_aloops: no avg_length_sloops: no nloops_length: no nbulge_length: no huang_elements_proportion: no huang_ratios: no loop_potential: no stem5_potential: no stem3_potential: no bp_number: yes dP: yes bp_proportion: yes bp_proportion_stem: yes gc_content_loop: no triplets: yes mfe: yes efe: yes ensemble_frequency: yes diversity: yes mfe_efe_difference: yes dQ: yes dG: yes mfei1: yes mfei2: yes mfei3: no mfei4: yes read_count: execute: yes # minimum read length min_length: 8 # minimum mean quality of the read min_quality: 70 # only count the reads that map on the stem only_stem: true pMFE: execute: no iterations: 1000 shuffle: sequence_dishuffle pEFE: execute: no iterations: 1000 shuffle: sequence_dishuffle zEFE: execute: no iterations: 1000 shuffle: sequence_dishuffle zG: execute: no iterations: 1000 shuffle: sequence_dishuffle zMFE: execute: no iterations: 1000 shuffle: sequence_dishuffle zP: execute: no iterations: 1000 shuffle: sequence_dishuffle zQ: execute: no iterations: 1000 shuffle: sequence_dishuffle PostProcess: normalize_per_feature: no normalize_per_sequence: no normalize_per_column: no # Sequences with MFE higher than this are skipped filter_maximum_mfe: 0