chemart / rna-folding-ac

{"species": [{"id": "CGUUAAUUACUCCUCCGGAAUUUGUCCUAC", "structure": "CGUUAAUUACUCCUCCGGAAUUUGUCCUAC ................(((.....)))..."}, {"id": "ACUACCUAGCAUACCCAUGUAGCGUCGACU", "structure": "ACUACCUAGCAUACCCAUGUAGCGUCGACU ........((.(((....)))))......."}, {"id": "CGCACGCUCGUUCAGGUCCACGUUAGUCCU", "structure": "CGCACGCUCGUUCAGGUCCACGUUAGUCCU .(.((...(((........)))...)).)."}, {"id": "GGGGUUAAGUAGUUUAGUCACAAUGUUUCC", "structure": "GGGGUUAAGUAGUUUAGUCACAAUGUUUCC .............................."}, {"id": "GCUAUGCGCUUCCAGGUUUUUAACCUUCGG", "structure": "GCUAUGCGCUUCCAGGUUUUUAACCUUCGG ((.....))....(((((...)))))...."}, {"id": "UACGCUUUCUAGCAGUUAUUCAUUCAACUC", "structure": "UACGCUUUCUAGCAGUUAUUCAUUCAACUC ...(((....)))((((........))))."}, {"id": "AGGAGCGAGCGCGACGUCAGGGACUUCGAU", "structure": "AGGAGCGAGCGCGACGUCAGGGACUUCGAU ...........(((.(((...))).))).."}, {"id": "CCUGUAUUAAACCAUCUUAGUAACACCGGC", "structure": "CCUGUAUUAAACCAUCUUAGUAACACCGGC ((((((((((......))))).)))..))."}, {"id": "CGUUAAU", "structure": "CGUUAAU ......."}, {"id": "UACUCCUCCGGAAUUUGUCCUAC", "structure": "UACUCCUCCGGAAUUUGUCCUAC .........(((.....)))..."}, {"id": "GGGGUUAAGUAGUUUAGUCACAAU", "structure": "GGGGUUAAGUAGUUUAGUCACAAU ........................"}, {"id": "GUUUCC", "structure": "GUUUCC ......"}, {"id": "CGCACGCUCGUUCAGGU", "structure": "CGCACGCUCGUUCAGGU ................."}, {"id": "CCACGUUAGUCCU", "structure": "CCACGUUAGUCCU ............."}, {"id": "GGGGU", "structure": "GGGGU ....."}, {"id": "UAAGUAGUUUAGUCACAAUGUUUCC", "structure": "UAAGUAGUUUAGUCACAAUGUUUCC ........................."}, {"id": "GCUAUGCGCUUCCAGGU", "structure": "GCUAUGCGCUUCCAGGU ((.....))........"}, {"id": "UUUUAACCUUCGG", "structure": "UUUUAACCUUCGG ............."}, {"id": "UACUCCUCCGGAAU", "structure": "UACUCCUCCGGAAU ...(((...))).."}, {"id": "UUGUCCUAC", "structure": "UUGUCCUAC ........."}, {"id": "UAAGUAGUUUAGUCACAAU", "structure": "UAAGUAGUUUAGUCACAAU ..................."}], "reactions": [{"reactants": {"UACGCUUUCUAGCAGUUAUUCAUUCAACUC": 1, "CGUUAAUUACUCCUCCGGAAUUUGUCCUAC": 1}, "products": {"UACGCUUUCUAGCAGUUAUUCAUUCAACUC": 1, "CGUUAAU": 1, "UACUCCUCCGGAAUUUGUCCUAC": 1}, "rate": null, "count": null}, {"reactants": {"UACGCUUUCUAGCAGUUAUUCAUUCAACUC": 1, "GGGGUUAAGUAGUUUAGUCACAAUGUUUCC": 1}, "products": {"UACGCUUUCUAGCAGUUAUUCAUUCAACUC": 1, "GGGGUUAAGUAGUUUAGUCACAAU": 1, "GUUUCC": 1}, "rate": null, "count": null}, {"reactants": {"CCUGUAUUAAACCAUCUUAGUAACACCGGC": 1, "CGCACGCUCGUUCAGGUCCACGUUAGUCCU": 1}, "products": {"CCUGUAUUAAACCAUCUUAGUAACACCGGC": 1, "CGCACGCUCGUUCAGGU": 1, "CCACGUUAGUCCU": 1}, "rate": null, "count": null}, {"reactants": {"CCUGUAUUAAACCAUCUUAGUAACACCGGC": 1, "GGGGUUAAGUAGUUUAGUCACAAUGUUUCC": 1}, "products": {"CCUGUAUUAAACCAUCUUAGUAACACCGGC": 1, "GGGGU": 1, "UAAGUAGUUUAGUCACAAUGUUUCC": 1}, "rate": null, "count": null}, {"reactants": {"CCUGUAUUAAACCAUCUUAGUAACACCGGC": 1, "GCUAUGCGCUUCCAGGUUUUUAACCUUCGG": 1}, "products": {"CCUGUAUUAAACCAUCUUAGUAACACCGGC": 1, "GCUAUGCGCUUCCAGGU": 1, "UUUUAACCUUCGG": 1}, "rate": null, "count": null}, {"reactants": {"UACGCUUUCUAGCAGUUAUUCAUUCAACUC": 1, "UACUCCUCCGGAAUUUGUCCUAC": 1}, "products": {"UACGCUUUCUAGCAGUUAUUCAUUCAACUC": 1, "UACUCCUCCGGAAU": 1, "UUGUCCUAC": 1}, "rate": null, "count": null}, {"reactants": {"UACGCUUUCUAGCAGUUAUUCAUUCAACUC": 1, "UAAGUAGUUUAGUCACAAUGUUUCC": 1}, "products": {"UACGCUUUCUAGCAGUUAUUCAUUCAACUC": 1, "UAAGUAGUUUAGUCACAAU": 1, "GUUUCC": 1}, "rate": null, "count": null}, {"reactants": {"CCUGUAUUAAACCAUCUUAGUAACACCGGC": 1, "GGGGUUAAGUAGUUUAGUCACAAU": 1}, "products": {"CCUGUAUUAAACCAUCUUAGUAACACCGGC": 1, "GGGGU": 1, "UAAGUAGUUUAGUCACAAU": 1}, "rate": null, "count": null}], "status": "complete", "initial_state": {"CGUUAAUUACUCCUCCGGAAUUUGUCCUAC": 1.0, "ACUACCUAGCAUACCCAUGUAGCGUCGACU": 1.0, "CGCACGCUCGUUCAGGUCCACGUUAGUCCU": 1.0, "GGGGUUAAGUAGUUUAGUCACAAUGUUUCC": 1.0, "GCUAUGCGCUUCCAGGUUUUUAACCUUCGG": 1.0, "UACGCUUUCUAGCAGUUAUUCAUUCAACUC": 1.0, "AGGAGCGAGCGCGACGUCAGGGACUUCGAU": 1.0, "CCUGUAUUAAACCAUCUUAGUAACACCGGC": 1.0}, "inflow": null, "outflow": null, "extras": {"energies": {"CGUUAAUUACUCCUCCGGAAUUUGUCCUAC": -1.7, "ACUACCUAGCAUACCCAUGUAGCGUCGACU": -1.8, "CGCACGCUCGUUCAGGUCCACGUUAGUCCU": -1.2, "GGGGUUAAGUAGUUUAGUCACAAUGUUUCC": 0.0, "GCUAUGCGCUUCCAGGUUUUUAACCUUCGG": -3.0, "UACGCUUUCUAGCAGUUAUUCAUUCAACUC": -2.4, "AGGAGCGAGCGCGACGUCAGGGACUUCGAU": -4.1, "CCUGUAUUAAACCAUCUUAGUAACACCGGC": -1.5, "CGUUAAU": 0.0, "UACUCCUCCGGAAUUUGUCCUAC": -1.7, "GGGGUUAAGUAGUUUAGUCACAAU": 0.0, "GUUUCC": 0.0, "CGCACGCUCGUUCAGGU": 0.0, "CCACGUUAGUCCU": 0.0, "GGGGU": 0.0, "UAAGUAGUUUAGUCACAAUGUUUCC": 0.0, "GCUAUGCGCUUCCAGGU": -0.3, "UUUUAACCUUCGG": 0.0, "UACUCCUCCGGAAU": -0.8, "UUGUCCUAC": 0.0, "UAAGUAGUUUAGUCACAAU": 0.0}, "conservation": [{"name": "nucleotides", "vector": [30, 30, 30, 30, 30, 30, 30, 30, 7, 23, 24, 6, 17, 13, 5, 25, 17, 13, 14, 9, 19]}], "functions": {"ACUACCUAGCAUACCCAUGUAGCGUCGACU": {"its_size": 6, "stems": 1, "loop_sequence": "CCAU", "site": "UGG", "reaction": "cleavage"}, "CGCACGCUCGUUCAGGUCCACGUUAGUCCU": {"its_size": 10, "stems": 2, "loop_sequence": "GCUUUA", "site": "AGC", "reaction": "ligation"}, "UACGCUUUCUAGCAGUUAUUCAUUCAACUC": {"its_size": 10, "stems": 1, "loop_sequence": "AUUCAUUC", "site": "AAU", "reaction": "cleavage"}, "CCUGUAUUAAACCAUCUUAGUAACACCGGC": {"its_size": 8, "stems": 1, "loop_sequence": "ACCAUC", "site": "GGU", "reaction": "cleavage"}}, "analysis": {"catalytic_species": 4, "cleavases": 3, "ligases": 1, "sequence_to_function": "MFE fold (Vienna RNA); the longest loop cycle is the ITS; even size in [its_min, its_max] with one stem (hairpin) gives cleavage, two stems (interior/bulge) give ligation; the recognition site is the reverse complement of the loop sequence"}}, "chemistry": "rna-folding-ac", "params": {"seq_length": 30, "pool": 8, "mode": "closure", "max_species": 60, "steps": 500, "dilution": "none", "its_min": 4, "its_max": 12, "min_recognition": 3, "min_fragment": 2}, "seed": 1}