├── .github └── workflows │ ├── docs.yml │ ├── release.yml │ └── test.yml ├── .gitignore ├── .pre-commit-config.yaml ├── AUTHORS ├── CHANGES ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── api │ ├── bindings.md │ ├── index.md │ ├── p3helpers.md │ └── thermoanalysis.md ├── changes_link.md ├── conf.py ├── cython_help.md ├── development.md ├── index.md ├── make.bat ├── miscellany.md └── quickstart.md ├── examples ├── basicprimerdesign.py └── orthogonalprimers.py ├── primer3 ├── __init__.py ├── argdefaults.py ├── bindings.py ├── p3helpers.h ├── p3helpers.pxd ├── p3helpers.pyx ├── src │ └── libprimer3 │ │ ├── ABOUT.txt │ │ ├── LICENSE.txt │ │ ├── Makefile │ │ ├── Makefile.OSX │ │ ├── amplicontm.c │ │ ├── amplicontm.h │ │ ├── amplicontm_main.c │ │ ├── dpal.c │ │ ├── dpal.h │ │ ├── format_output.c │ │ ├── format_output.h │ │ ├── gpl-2.0.txt │ │ ├── humrep_and_simple.txt │ │ ├── klib │ │ ├── .gitignore │ │ ├── README.md │ │ ├── khash.h │ │ └── test │ │ │ ├── Makefile │ │ │ ├── khash_keith.c │ │ │ ├── khash_keith2.c │ │ │ └── khash_test.c │ │ ├── libprimer3.c │ │ ├── libprimer3.h │ │ ├── libprimer3flex.c │ │ ├── libprimer3flex.h │ │ ├── long_seq_tm_test_main.c │ │ ├── masker.c │ │ ├── masker.h │ │ ├── masker_main.c │ │ ├── ntdpal_main.c │ │ ├── oligotm.c │ │ ├── oligotm.h │ │ ├── oligotm_main.c │ │ ├── p3_seq_lib.c │ │ ├── p3_seq_lib.h │ │ ├── paranoid_tests.sh │ │ ├── primer3_boulder_main.c │ │ ├── primer3_config │ │ ├── dangle.dh │ │ ├── dangle.ds │ │ ├── interpretations │ │ │ ├── dangle_i.dh │ │ │ ├── dangle_i.ds │ │ │ ├── loops_i.dh │ │ │ ├── loops_i.ds │ │ │ ├── stack_i.dh │ │ │ ├── stack_i.ds │ │ │ ├── stackmm_i_mm.dh │ │ │ ├── stackmm_i_mm.ds │ │ │ ├── tetraloop_i.dh │ │ │ ├── tetraloop_i.ds │ │ │ ├── triloop_i.dh │ │ │ ├── triloop_i.ds │ │ │ ├── tstack2_i.dh │ │ │ ├── tstack2_i.ds │ │ │ ├── tstack_i.dh │ │ │ ├── tstack_i.ds │ │ │ ├── tstack_tm_inf_i.dh │ │ │ └── tstack_tm_inf_i.ds │ │ ├── loops.dh │ │ ├── loops.ds │ │ ├── stack.dh │ │ ├── stack.ds │ │ ├── stackmm.dh │ │ ├── stackmm.ds │ │ ├── tetraloop.dh │ │ ├── tetraloop.ds │ │ ├── triloop.dh │ │ ├── triloop.ds │ │ ├── tstack.dh │ │ ├── tstack2.dh │ │ ├── tstack2.ds │ │ └── tstack_tm_inf.ds │ │ ├── print_boulder.c │ │ ├── print_boulder.h │ │ ├── read_boulder.c │ │ ├── read_boulder.h │ │ ├── release_notes.txt │ │ ├── thal.c │ │ ├── thal.h │ │ ├── thal_main.c │ │ ├── thal_parameters.c │ │ ├── thal_parameters.h │ │ ├── thalflex.c │ │ ├── thalflex.h │ │ └── thalflexsignatures.h ├── thermoanalysis.pxd ├── thermoanalysis.pxi └── thermoanalysis.pyx ├── pyproject.toml ├── setup.cfg ├── setup.py ├── tests ├── __init__.py ├── _simulatedbindings.py ├── checkdatasets.py ├── input_files │ ├── dv_conc_vs_dntp_conc_input │ ├── long_seq_input │ ├── p3-tmpl-mispriming_input │ ├── p3_3_prime_0_input │ ├── p3_3_prime_n_input │ ├── primer1_input │ ├── primer1_th_input │ ├── primer3_v1_1_4_default_settings_input │ ├── primer3web_v0_4_0_default_settings_input │ ├── primer3web_v3_0_0_default_settings_input │ ├── primer3web_v4_0_0_default_settings_input │ ├── primer_all_settingsfiles_input │ ├── primer_annealing_temp_input │ ├── primer_boundary1_input │ ├── primer_boundary_input │ ├── primer_check_input │ ├── primer_dmso_formamide_input │ ├── primer_end_pathology_input │ ├── primer_first_base_index_input │ ├── primer_gc_end_input │ ├── primer_high_gc_load_set_input │ ├── primer_high_tm_load_set_input │ ├── primer_human_input │ ├── primer_input │ ├── primer_internal1_input │ ├── primer_internal_input │ ├── primer_internal_position_input │ ├── primer_lib_amb_codes_input │ ├── primer_masker_input │ ├── primer_mispriming_boundary1_input │ ├── primer_mispriming_boundary2_input │ ├── primer_mispriming_input │ ├── primer_mispriming_long_lib_input │ ├── primer_mispriming_th_input │ ├── primer_must_match_input │ ├── primer_must_overlap_point_input │ ├── primer_must_use_input │ ├── primer_must_use_op_input │ ├── primer_must_use_th_input │ ├── primer_new_tasks_input │ ├── primer_new_tasks_th_input │ ├── primer_num_best_input │ ├── primer_obj_fn_input │ ├── primer_ok_regions2_input │ ├── primer_ok_regions_input │ ├── primer_overhang_input │ ├── primer_overhang_th_input │ ├── primer_overlap_junction_input │ ├── primer_poly_x_input │ ├── primer_position_penalty_input │ ├── primer_quality_boundary_input │ ├── primer_rat_input │ ├── primer_renewed_tasks_input │ ├── primer_sec_struct_dpal_input │ ├── primer_sec_struct_thal_input │ ├── primer_start_codon_input │ ├── primer_syntax_input │ ├── primer_task_input │ ├── primer_task_th_input │ ├── primer_thal_args_input │ ├── primer_thal_max_seq_error_input │ ├── primer_thermod_align_input │ ├── primer_three_prime_distance_input │ ├── primer_tm_lc_masking_input │ ├── primer_windows_newlines_input │ ├── test_compl_error_input │ ├── test_left_to_right_of_right_input │ ├── th-w-other-tasks_input │ ├── thal_input │ └── thal_output ├── 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