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 13-1002
		Stack = 0.3  for stack of 14-1001
		Stack = -1.3  for stack of 15-1000
		Stack = -2.1  for stack of 16-999
	Helix total = -4.4
	Multiloop = 5.9  for closure of 17-998
		Stack = -3.4  for stack of 37-987
		Stack = -2.1  for stack of 38-986
	Helix total = -5.5
	Internal/bulge = 3.7  for closure of 39-985	Size = 3
		Stack = -3.3  for stack of 40-981
		Stack = -2.5  for stack of 41-980
		Stack = -1.5  for stack of 42-979
		Stack = -2.1  for stack of 43-978
	Helix total = -9.4
	Multiloop = 10.1  for closure of 44-977
		Stack = -0.6  for stack of 528-951
		Stack = -2.4  for stack of 529-950
		Stack = -2.1  for stack of 530-949
		Stack = -2.1  for stack of 531-948
		Stack = -2.2  for stack of 532-947
		Stack = -1.3  for stack of 533-946
	Helix total = -10.7
	Internal/bulge = 4.6  for closure of 534-945	Size = 27
		Stack = -1.3  for stack of 548-930
		Stack = -0.6  for stack of 549-929
		Stack = -2.1  for stack of 550-928
		Stack = -3.3  for stack of 551-927
		Stack = -1.5  for stack of 552-926
		Stack = -2.1  for stack of 553-925
		Stack = -2.4  for stack of 554-924
		Stack = -0.9  for stack of 555-923
	Helix total = -14.2
	Internal/bulge = 1.9  for closure of 556-922	Size = 2
		Stack = -2.4  for stack of 558-920
		Stack = -2.1  for stack of 559-919
	Helix total = -4.5
	Multiloop = 8.8  for closure of 560-918
		Stack = -1.3  for stack of 894-915
		Stack = -1.1  for stack of 895-914
	Helix total = -2.4
	Internal/bulge = 1.2  for closure of 896-913	Size = 2
		Stack = -2.2  for stack of 898-911
		Stack = -2.4  for stack of 899-910
	Helix total = -4.6
	Hairpin = 4.0  for closure of 900-909
		Stack = -2.4  for stack of 596-893
		Stack = -1.4  for stack of 597-892
		Stack = -1.4  for stack of 598-891
		Stack = -1.3  for stack of 599-890
		Stack = -2.1  for stack of 600-889
	Helix total = -8.6
	Multiloop = 3.8  for closure of 601-888
		Stack = -0.9  for stack of 749-874
		Stack = -2.1  for stack of 750-873
		Stack = -2.2  for stack of 751-872
		Stack = -1.3  for stack of 752-871
	Helix total = -6.5
	Internal/bulge = 1.7  for closure of 753-870	Size = 1 BP stack across bulge = -2.1
		Stack = -2.4  for stack of 754-868
	Helix total = -2.4
	Internal/bulge = 3.8  for closure of 755-867	Size = 2
		Stack = -2.2  for stack of 758-866
		Stack = -1.4  for stack of 759-865
	Helix total = -3.6
	Internal/bulge = 2.8  for closure of 760-864	Size = 4
		Stack = -0.6  for stack of 763-861
		Stack = -1.3  for stack of 764-860
		Stack = -2.1  for stack of 765-859
	Helix total = -4.0
	Internal/bulge = 0.4  for closure of 766-858	Size = 1 BP stack across bulge = -3.4
		Stack = -2.1  for stack of 768-857
		Stack = -2.1  for stack of 769-856
	Helix total = -4.2
	Internal/bulge = 1.2  for closure of 770-855	Size = 1 BP stack across bulge = -2.2
		Stack = -1.0  for stack of 772-854
		Stack = -2.1  for stack of 773-853
		Stack = -2.4  for stack of 774-852
	Helix total = -5.5
	Internal/bulge = 4.8  for closure of 775-851	Size = 25
		Stack = -1.4  for stack of 789-838
		Stack = -0.5  for stack of 790-837
		Stack = -1.4  for stack of 791-836
		Stack = -1.3  for stack of 792-835
	Helix total = -4.6
	Internal/bulge = 3.7  for closure of 793-834	Size = 3
		Stack = -1.1  for stack of 795-831
		Stack = -1.3  for stack of 796-830
		Stack = -1.1  for stack of 797-829
		Stack = -2.1  for stack of 798-828
	Helix total = -5.6
	Internal/bulge = 0.8  for closure of 799-827	Size = 2
		Stack = -1.3  for stack of 801-825
		Stack = -1.5  for stack of 802-824
		Stack = -2.1  for stack of 803-823
	Helix total = -4.9
	Internal/bulge = 2.6  for closure of 804-822	Size = 3
		Stack = -2.1  for stack of 806-819
		Stack = -1.5  for stack of 807-818
	Helix total = -3.6
	Hairpin = 5.3  for closure of 808-817
		Stack = -2.1  for stack of 738-747
		Stack = -3.4  for stack of 739-746
	Helix total = -5.5
	Hairpin = 4.6  for closure of 740-745
		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 = -0.9  for stack of 604-707
		Stack = -1.3  for stack of 605-706
		Stack = -0.9  for stack of 606-705
	Helix total = -3.1
	Multiloop = 4.8  for closure of 607-704
		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 = -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 = -1.4  for stack of 563-583
		Stack = -1.4  for stack of 564-582
		Stack = -2.4  for stack of 565-581
		Stack = -2.1  for stack of 566-580
	Helix total = -7.3
	Hairpin = 6.3  for closure of 567-579
		Stack = -0.9  for stack of 47-524
		Stack = -1.0  for stack of 48-523
		Stack = -2.5  for stack of 49-522
		Stack = -2.1  for stack of 50-521
		Stack = -0.9  for stack of 51-520
		Stack = -1.3  for stack of 52-519
		Stack = -1.4  for stack of 53-518
	Helix total = -10.1
	Internal/bulge = 5.8  for closure of 54-517	Size = 7
		Stack = -2.1  for stack of 56-510
		Stack = -0.9  for stack of 57-509
	Helix total = -3.0
	Internal/bulge = 3.1  for closure of 58-508	Size = 4
		Stack = -0.6  for stack of 61-505
		Stack = -2.1  for stack of 62-504
		Stack = -2.5  for stack of 63-503
		Stack = -1.0  for stack of 64-502
	Helix total = -6.2
	Internal/bulge = 1.9  for closure of 65-501	Size = 2
		Stack = -2.4  for stack of 67-499
		Stack = -2.1  for stack of 68-498
		Stack = -2.1  for stack of 69-497
		Stack = -2.2  for stack of 70-496
		Stack = -2.1  for stack of 71-495
	Helix total = -10.9
	Internal/bulge = 5.9  for closure of 72-494	Size = 15
		Stack = -0.6  for stack of 88-493
		Stack = -0.9  for stack of 89-492
		Stack = -2.1  for stack of 90-491
	Helix total = -3.6
	Internal/bulge = -0.8  for closure of 91-490	Size = 4
		Stack = -3.3  for stack of 94-487
		Stack = -2.1  for stack of 95-486
	Helix total = -5.4
	Internal/bulge = 5.6  for closure of 96-485	Size = 16
		Stack = -1.1  for stack of 106-477
		Stack = -2.4  for stack of 107-476
		Stack = -2.1  for stack of 108-475
	Helix total = -5.6
	Internal/bulge = 2.2  for closure of 109-474	Size = 3
		Stack = -3.3  for stack of 111-471
		Stack = -2.1  for stack of 112-470
		Stack = -0.9  for stack of 113-469
		Stack = -2.1  for stack of 114-468
	Helix total = -8.4
	Multiloop = 4.1  for closure of 115-467
		Stack = -2.4  for stack of 371-466
		Stack = -2.1  for stack of 372-465
		Stack = -0.9  for stack of 373-464
	Helix total = -5.4
	Internal/bulge = 1.2  for closure of 374-463	Size = 2
		Stack = -2.5  for stack of 376-461
		Stack = -1.0  for stack of 377-460
		Stack = -2.1  for stack of 378-459
		Stack = -2.2  for stack of 379-458
		Stack = -1.3  for stack of 380-457
		Stack = -0.6  for stack of 381-456
	Helix total = -9.7
	Internal/bulge = 4.2  for closure of 382-455	Size = 3
		Stack = -0.9  for stack of 383-451
		Stack = -2.1  for stack of 384-450
		Stack = -2.5  for stack of 385-449
		Stack = -0.6  for stack of 386-448
		Stack = -2.1  for stack of 387-447
		Stack = -3.3  for stack of 388-446
	Helix total = -11.5
	Internal/bulge = 6.5  for closure of 389-445	Size = 13
		Stack = -0.9  for stack of 400-441
		Stack = -1.1  for stack of 401-440
	Helix total = -2.0
	Internal/bulge = 4.1  for closure of 402-439	Size = 13
		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 = -2.2  for stack of 157-369
		Stack = -0.9  for stack of 158-368
	Helix total = -3.1
	Internal/bulge = 2.6  for closure of 159-367	Size = 3
		Stack = -2.4  for stack of 161-364
	Helix total = -2.4
	Internal/bulge = 1.2  for closure of 162-363	Size = 2
		Stack = -2.1  for stack of 164-361
		Stack = -3.3  for stack of 165-360
	Helix total = -5.4
	Internal/bulge = 2.6  for closure of 166-359	Size = 7
		Stack = -2.1  for stack of 170-354
	Helix total = -2.1
	Internal/bulge = 1.4  for closure of 171-353	Size = 1 BP stack across bulge = -2.4
		Stack = -1.1  for stack of 172-351
	Helix total = -1.1
	Internal/bulge = -1.4  for closure of 173-350	Size = 2
		Stack = -2.4  for stack of 175-348
		Stack = -1.1  for stack of 176-347
		Stack = -0.9  for stack of 177-346
		Stack = -2.1  for stack of 178-345
		Stack = -2.5  for stack of 179-344
		Stack = -1.4  for stack of 180-343
	Helix total = -10.4
	Multiloop = 5.6  for closure of 181-342
		Stack = -1.3  for stack of 206-339
		Stack = -1.5  for stack of 207-338
		Stack = -3.3  for stack of 208-337
		Stack = -2.1  for stack of 209-336
		Stack = -1.1  for stack of 210-335
	Helix total = -9.3
	Internal/bulge = 4.1  for closure of 211-334	Size = 8
		Stack = -1.3  for stack of 215-328
		Stack = -0.9  for stack of 216-327
		Stack = -0.9  for stack of 217-326
		Stack = -1.1  for stack of 218-325
		Stack = -1.0  for stack of 219-324
	Helix total = -5.2
	Internal/bulge = 6.6  for closure of 220-323	Size = 19
	Helix total = 0.0
	Internal/bulge = -0.7  for closure of 240-322	Size = 2
		Stack = -0.9  for stack of 242-320
		Stack = -1.0  for stack of 243-319
		Stack = -1.3  for stack of 244-318
		Stack = -1.4  for stack of 245-317
		Stack = 0.3  for stack of 246-316
		Stack = -1.4  for stack of 247-315
	Helix total = -5.7
	Internal/bulge = 2.1  for closure of 248-314	Size = 1 BP stack across bulge = -1.3
		Stack = -2.1  for stack of 249-312
		Stack = -3.4  for stack of 250-311
		Stack = -2.1  for stack of 251-310
	Helix total = -7.6
	Internal/bulge = 3.3  for closure of 252-309	Size = 2
		Stack = -2.5  for stack of 255-308
		Stack = -0.6  for stack of 256-307
		Stack = -1.3  for stack of 257-306
		Stack = -0.6  for stack of 258-305
		Stack = -1.4  for stack of 259-304
		Stack = -1.3  for stack of 260-303
		Stack = -0.6  for stack of 261-302
		Stack = -0.5  for stack of 262-301
		Stack = -1.4  for stack of 263-300
	Helix total = -10.2
	Internal/bulge = 6.2  for closure of 264-299	Size = 10
		Stack = -3.3  for stack of 266-289
		Stack = -2.1  for stack of 267-288
		Stack = -1.1  for stack of 268-287
	Helix total = -6.5
	Internal/bulge = 1.2  for closure of 269-286	Size = 2
		Stack = -3.3  for stack of 271-284
	Helix total = -3.3
	Hairpin = 5.5  for closure of 272-283
		Stack = -2.1  for stack of 182-199
		Stack = -2.4  for stack of 183-198
		Stack = -2.1  for stack of 184-197
		Stack = -1.3  for stack of 185-196
	Helix total = -7.9
	Hairpin = 5.5  for closure of 186-195
		Stack = -2.4  for stack of 116-156
		Stack = -3.3  for stack of 117-155
		Stack = -2.1  for stack of 118-154
		Stack = -0.9  for stack of 119-153
		Stack = -2.4  for stack of 120-152
		Stack = -2.1  for stack of 121-151
	Helix total = -13.2
	Internal/bulge = 3.2  for closure of 122-150	Size = 1 BP stack across bulge = 0.3
		Stack = -0.5  for stack of 123-148
		Stack = -1.3  for stack of 124-147
		Stack = -1.4  for stack of 125-146
		Stack = -1.0  for stack of 126-145
		Stack = -1.4  for stack of 127-144
		Stack = -0.5  for stack of 128-143
		Stack = -1.5  for stack of 129-142
		Stack = -2.1  for stack of 130-141
		Stack = -0.9  for stack of 131-140
		Stack = -2.2  for stack of 132-139
	Helix total = -12.8
	Hairpin = 4.8  for closure of 133-138
		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
		Stack = -3.3  for stack of 3-11
	Helix total = -3.3
	Hairpin = 4.6  for closure of 4-10


	Total energy = -163.0
Download this file: efn2.txt
Command Line:
efn2 2_5_2_3.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.)
