RNAstructure efn2 Results
(Calculate the folding free energy of structures in a CT file.)

Thermodynamic details for structure # 1
	Exterior loop = -3.5
		Stack = -1.3  for stack of 967-1000
		Stack = -2.1  for stack of 968-999
		Stack = -2.4  for stack of 969-998
	Helix total = -5.8
	Internal/bulge = 2.4  for closure of 970-997	Size = 6
		Stack = -1.4  for stack of 974-993
		Stack = -1.0  for stack of 975-992
	Helix total = -2.4
	Hairpin = 5.7  for closure of 976-991
		Stack = -2.4  for stack of 67-965
		Stack = -2.1  for stack of 68-964
		Stack = -1.4  for stack of 69-963
	Helix total = -5.9
	Internal/bulge = 1.6  for closure of 70-962	Size = 1 BP stack across bulge = -2.2
		Stack = -1.0  for stack of 71-960
		Stack = -2.1  for stack of 72-959
		Stack = -3.4  for stack of 73-958
		Stack = -2.1  for stack of 74-957
	Helix total = -8.6
	Multiloop = 2.8  for closure of 75-956
		Stack = -2.1  for stack of 912-943
		Stack = -1.1  for stack of 913-942
		Stack = -1.3  for stack of 914-941
	Helix total = -4.5
	Internal/bulge = 3.4  for closure of 915-940	Size = 8
		Stack = -2.1  for stack of 921-936
		Stack = -0.9  for stack of 922-935
		Stack = -2.4  for stack of 923-934
		Stack = -2.1  for stack of 924-933
		Stack = -2.4  for stack of 925-932
	Helix total = -9.9
	Hairpin = 4.6  for closure of 926-931
		Stack = -2.2  for stack of 898-911
		Stack = -2.4  for stack of 899-910
		Stack = -2.1  for stack of 900-909
		Stack = -0.9  for stack of 901-908
	Helix total = -7.6
	Hairpin = 5.3  for closure of 902-907
		Stack = -0.9  for stack of 329-897
		Stack = -1.1  for stack of 330-896
		Stack = -2.4  for stack of 331-895
	Helix total = -4.4
	Internal/bulge = 0.5  for closure of 332-894	Size = 1 BP stack across bulge = -3.3
		Stack = -2.1  for stack of 333-892
		Stack = -1.1  for stack of 334-891
		Stack = -1.0  for stack of 335-890
		Stack = -2.1  for stack of 336-889
		Stack = -3.3  for stack of 337-888
	Helix total = -9.6
	Internal/bulge = 5.1  for closure of 338-887	Size = 11
		Stack = -1.1  for stack of 346-882
		Stack = -2.4  for stack of 347-881
	Helix total = -3.5
	Internal/bulge = 5.2  for closure of 348-880	Size = 10
		Stack = -1.3  for stack of 351-871
		Stack = -2.2  for stack of 352-870
	Helix total = -3.5
	Internal/bulge = 3.3  for closure of 353-869	Size = 2
		Stack = -2.2  for stack of 354-866
		Stack = -2.1  for stack of 355-865
		Stack = -2.1  for stack of 356-864
		Stack = -3.3  for stack of 357-863
	Helix total = -9.7
	Internal/bulge = 5.8  for closure of 358-862	Size = 14
		Stack = -0.9  for stack of 373-861
		Stack = -0.6  for stack of 374-860
		Stack = -2.1  for stack of 375-859
		Stack = -2.5  for stack of 376-858
	Helix total = -6.1
	Internal/bulge = 2.2  for closure of 377-857	Size = 2
		Stack = -2.2  for stack of 379-855
		Stack = -1.3  for stack of 380-854
		Stack = -2.1  for stack of 381-853
	Helix total = -5.6
	Internal/bulge = 3.3  for closure of 382-852	Size = 2
		Stack = -1.4  for stack of 385-851
		Stack = -0.9  for stack of 386-850
		Stack = -1.0  for stack of 387-849
		Stack = -2.1  for stack of 388-848
		Stack = -2.4  for stack of 389-847
	Helix total = -7.8
	Multiloop = 1.0  for closure of 390-846
		Stack = -1.5  for stack of 812-845
		Stack = -3.3  for stack of 813-844
	Helix total = -4.8
	Internal/bulge = 0.5  for closure of 814-843	Size = 1 BP stack across bulge = -3.3
		Stack = -2.1  for stack of 815-841
		Stack = -0.9  for stack of 816-840
		Stack = -2.4  for stack of 817-839
		Stack = -2.1  for stack of 818-838
		Stack = -0.6  for stack of 819-837
	Helix total = -8.1
	Internal/bulge = 4.6  for closure of 820-836	Size = 4
		Stack = -1.1  for stack of 821-831
		Stack = -1.0  for stack of 822-830
	Helix total = -2.1
	Hairpin = 4.7  for closure of 823-829
		Stack = -2.1  for stack of 798-810
		Stack = -2.5  for stack of 799-809
		Stack = -0.5  for stack of 800-808
	Helix total = -5.1
	Hairpin = 4.8  for closure of 801-807
		Stack = -2.2  for stack of 781-794
		Stack = -1.3  for stack of 782-793
		Stack = -2.2  for stack of 783-792
		Stack = -3.3  for stack of 784-791
	Helix total = -9.0
	Hairpin = 4.1  for closure of 785-790
		Stack = -3.3  for stack of 433-779
		Stack = -2.1  for stack of 434-778
		Stack = -1.1  for stack of 435-777
	Helix total = -6.5
	Internal/bulge = 1.0  for closure of 436-776	Size = 1 BP stack across bulge = -2.4
		Stack = -3.3  for stack of 437-774
		Stack = -2.1  for stack of 438-773
		Stack = -1.4  for stack of 439-772
		Stack = -0.5  for stack of 440-771
		Stack = -1.0  for stack of 441-770
	Helix total = -8.3
	Multiloop = 6.0  for closure of 442-769
		Stack = -2.1  for stack of 746-764
		Stack = -1.3  for stack of 747-763
	Helix total = -3.4
	Internal/bulge = 1.2  for closure of 748-762	Size = 2
		Stack = -1.4  for stack of 750-760
		Stack = -2.2  for stack of 751-759
	Helix total = -3.6
	Hairpin = 5.4  for closure of 752-758
		Stack = -2.1  for stack of 453-745
		Stack = -0.9  for stack of 454-744
		Stack = -0.9  for stack of 455-743
	Helix total = -3.9
	Internal/bulge = 3.0  for closure of 456-742	Size = 3
		Stack = -2.1  for stack of 458-739
		Stack = -2.1  for stack of 459-738
		Stack = -3.4  for stack of 460-737
	Helix total = -7.6
	Internal/bulge = 3.3  for closure of 461-736	Size = 2
		Stack = -2.1  for stack of 464-735
		Stack = -2.4  for stack of 465-734
		Stack = -2.2  for stack of 466-733
		Stack = -2.1  for stack of 467-732
	Helix total = -8.8
	Internal/bulge = 1.2  for closure of 468-731	Size = 2
		Stack = -3.3  for stack of 470-729
		Stack = -3.4  for stack of 471-728
	Helix total = -6.7
	Multiloop = 4.3  for closure of 472-727
		Stack = -2.5  for stack of 709-726
		Stack = -2.1  for stack of 710-725
		Stack = -1.3  for stack of 711-724
		Stack = -2.1  for stack of 712-723
		Stack = -2.4  for stack of 713-722
	Helix total = -10.4
	Hairpin = 5.1  for closure of 714-721
		Stack = -1.3  for stack of 675-702
		Stack = -2.2  for stack of 676-701
		Stack = -2.1  for stack of 677-700
		Stack = -2.1  for stack of 678-699
		Stack = -2.5  for stack of 679-698
	Helix total = -10.2
	Internal/bulge = 3.0  for closure of 680-697	Size = 4
		Stack = -3.4  for stack of 684-695
		Stack = -2.1  for stack of 685-694
	Helix total = -5.5
	Hairpin = 5.1  for closure of 686-693
		Stack = -2.1  for stack of 550-673
		Stack = -1.5  for stack of 551-672
	Helix total = -3.6
	Internal/bulge = 1.2  for closure of 552-671	Size = 2
		Stack = -2.4  for stack of 554-669
		Stack = -0.9  for stack of 555-668
		Stack = -0.9  for stack of 556-667
		Stack = -1.1  for stack of 557-666
		Stack = -2.4  for stack of 558-665
		Stack = -2.1  for stack of 559-664
	Helix total = -9.8
	Multiloop = 6.2  for closure of 560-663
		Stack = -3.4  for stack of 621-655
		Stack = -3.3  for stack of 622-654
		Stack = -2.1  for stack of 623-653
		Stack = -2.1  for stack of 624-652
		Stack = -2.2  for stack of 625-651
	Helix total = -13.1
	Internal/bulge = 5.8  for closure of 626-650	Size = 9
		Stack = -2.1  for stack of 636-649
		Stack = -2.2  for stack of 637-648
		Stack = -1.3  for stack of 638-647
		Stack = -1.0  for stack of 639-646
	Helix total = -6.6
	Hairpin = 5.3  for closure of 640-645
		Stack = -3.3  for stack of 610-618
		Stack = -2.4  for stack of 611-617
	Helix total = -5.7
	Hairpin = 5.9  for closure of 612-616
		Stack = -2.2  for stack of 564-588
	Helix total = -2.2
	Internal/bulge = 1.9  for closure of 565-587	Size = 2
		Stack = -1.3  for stack of 567-585
		Stack = -2.2  for stack of 568-584
	Helix total = -3.5
	Internal/bulge = 1.7  for closure of 569-583	Size = 1 BP stack across bulge = -2.1
		Stack = -2.4  for stack of 570-581
	Helix total = -2.4
	Hairpin = 4.0  for closure of 571-580
		Stack = -2.2  for stack of 524-543
		Stack = -2.1  for stack of 525-542
		Stack = -0.6  for stack of 526-541
		Stack = -1.4  for stack of 527-540
		Stack = -0.9  for stack of 528-539
		Stack = -2.4  for stack of 529-538
		Stack = -2.1  for stack of 530-537
	Helix total = -11.7
	Hairpin = 4.1  for closure of 531-536
		Stack = -2.5  for stack of 487-518
		Stack = -2.1  for stack of 488-517
		Stack = -2.2  for stack of 489-516
	Helix total = -6.8
	Internal/bulge = 1.9  for closure of 490-515	Size = 3
		Stack = -2.1  for stack of 492-512
		Stack = -3.4  for stack of 493-511
	Helix total = -5.5
	Internal/bulge = 4.5  for closure of 494-510	Size = 5
		Stack = -0.9  for stack of 500-509
		Stack = -2.1  for stack of 501-508
	Helix total = -3.0
	Hairpin = 4.9  for closure of 502-507
		Stack = -3.4  for stack of 409-431
		Stack = -2.1  for stack of 410-430
		Stack = -1.1  for stack of 411-429
		Stack = -1.3  for stack of 412-428
		Stack = -1.1  for stack of 413-427
	Helix total = -9.0
	Internal/bulge = 2.9  for closure of 414-426	Size = 1 BP stack across bulge = -0.9
		Stack = -0.9  for stack of 416-425
		Stack = -1.3  for stack of 417-424
	Helix total = -2.2
	Hairpin = 4.7  for closure of 418-423
		Stack = -0.6  for stack of 81-327
		Stack = -1.3  for stack of 82-326
		Stack = -1.1  for stack of 83-325
		Stack = -1.0  for stack of 84-324
		Stack = -1.4  for stack of 85-323
		Stack = -2.4  for stack of 86-322
	Helix total = -7.8
	Multiloop = 1.8  for closure of 87-321
		Stack = -0.9  for stack of 304-320
		Stack = -1.3  for stack of 305-319
		Stack = -0.6  for stack of 306-318
		Stack = -2.5  for stack of 307-317
	Helix total = -5.3
	Hairpin = 3.9  for closure of 308-316
		Stack = -1.3  for stack of 293-302
		Stack = -0.9  for stack of 294-301
	Helix total = -2.2
	Hairpin = 5.3  for closure of 295-300
		Stack = -1.5  for stack of 107-289
		Stack = -2.1  for stack of 108-288
		Stack = -1.1  for stack of 109-287
	Helix total = -4.7
	Internal/bulge = 1.0  for closure of 110-286	Size = 1 BP stack across bulge = -2.4
		Stack = -3.3  for stack of 111-284
		Stack = -2.1  for stack of 112-283
		Stack = -0.9  for stack of 113-282
	Helix total = -6.3
	Internal/bulge = -0.7  for closure of 114-281	Size = 2
		Stack = -2.4  for stack of 116-279
	Helix total = -2.4
	Internal/bulge = 0.4  for closure of 117-278	Size = 1 BP stack across bulge = -2.1
		Stack = -0.9  for stack of 119-277
		Stack = -2.4  for stack of 120-276
		Stack = -2.1  for stack of 121-275
		Stack = -2.1  for stack of 122-274
		Stack = -3.3  for stack of 123-273
	Helix total = -10.8
	Multiloop = 1.4  for closure of 124-272
		Stack = -3.3  for stack of 228-267
		Stack = -3.4  for stack of 229-266
	Helix total = -6.7
	Internal/bulge = 1.1  for closure of 230-265	Size = 2
		Stack = -0.5  for stack of 232-263
		Stack = -0.6  for stack of 233-262
		Stack = -1.3  for stack of 234-261
	Helix total = -2.4
	Internal/bulge = 5.4  for closure of 235-260	Size = 6
		Stack = -0.6  for stack of 242-259
		Stack = -1.0  for stack of 243-258
		Stack = -1.3  for stack of 244-257
		Stack = -1.4  for stack of 245-256
		Stack = 0.3  for stack of 246-255
		Stack = -1.4  for stack of 247-254
	Helix total = -5.4
	Hairpin = 5.1  for closure of 248-253
		Stack = -3.3  for stack of 208-226
		Stack = -2.1  for stack of 209-225
		Stack = -1.1  for stack of 210-224
	Helix total = -6.5
	Hairpin = 6.4  for closure of 211-223
		Stack = -0.6  for stack of 139-197
	Helix total = -0.6
	Internal/bulge = -0.7  for closure of 140-196	Size = 2
		Stack = -2.1  for stack of 142-194
		Stack = -2.2  for stack of 143-193
		Stack = -1.0  for stack of 144-192
	Helix total = -5.3
	Internal/bulge = 3.7  for closure of 145-191	Size = 4
		Stack = -2.1  for stack of 149-189
		Stack = -3.3  for stack of 150-188
		Stack = -2.4  for stack of 151-187
	Helix total = -7.8
	Internal/bulge = 2.8  for closure of 152-186	Size = 1 BP stack across bulge = -0.6
		Stack = -2.1  for stack of 154-185
		Stack = -2.4  for stack of 155-184
		Stack = -2.1  for stack of 156-183
		Stack = -2.5  for stack of 157-182
	Helix total = -9.1
	Hairpin = 6.4  for closure of 158-181
		Stack = -1.0  for stack of 126-138
		Stack = -1.1  for stack of 127-137
		Stack = -0.9  for stack of 128-136
	Helix total = -3.0
	Hairpin = 5.6  for closure of 129-135
		Stack = -2.1  for stack of 90-105
		Stack = -3.3  for stack of 91-104
	Helix total = -5.4
	Hairpin = 5.2  for closure of 92-103
		Stack = -2.1  for stack of 5-45
		Stack = -2.1  for stack of 6-44
	Helix total = -4.2
	Internal/bulge = 1.0  for closure of 7-43	Size = 1 BP stack across bulge = -2.4
		Stack = -2.2  for stack of 9-42
		Stack = -3.3  for stack of 10-41
	Helix total = -5.5
	Internal/bulge = 4.1  for closure of 11-40	Size = 4
		Stack = -2.1  for stack of 16-39
	Helix total = -2.1
	Internal/bulge = 1.4  for closure of 17-38	Size = 1 BP stack across bulge = -2.4
		Stack = -2.1  for stack of 18-36
		Stack = -2.5  for stack of 19-35
		Stack = -1.0  for stack of 20-34
		Stack = -2.2  for stack of 21-33
		Stack = -2.1  for stack of 22-32
		Stack = -0.6  for stack of 23-31
		Stack = -2.1  for stack of 24-30
	Helix total = -12.6
	Hairpin = 5.4  for closure of 25-29


	Total energy = -173.1
Download this file: efn2.txt
Command Line:
efn2 Structure1_1_.ct efn2.txt --temperature 310.15 --writedetails
RNAstructure

Web Servers for RNA Secondary Structure Prediction

RNAstructure efn2 Results(Calculate the folding free energy of structures in a CT file.)

RNAstructure efn2 Results
(Calculate the folding free energy of structures in a CT file.)
