Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    15:608 16:607 17:606 293:314 294:313 295:312
	Energy of Broken Structure: -134.4
	Energy of Pseudo-Helices:   -11.6
	Pseudoknot Energy Penalty:  14.6
	Total Free Energy:          -131.4
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -7.4
		Stack = -0.6  for stack of 1101-1124
		Stack = -2.1  for stack of 1102-1123
		Stack = -3.3  for stack of 1103-1122
		Stack = -1.5  for stack of 1104-1121
		Stack = -2.1  for stack of 1105-1120
		Stack = -2.5  for stack of 1106-1119
		Stack = -1.0  for stack of 1107-1118
		Stack = -2.1  for stack of 1108-1117
		Stack = -3.3  for stack of 1109-1116
	Helix total = -18.5
	Hairpin = 3.1  for closure of 1110-1115
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 992-1099	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.6  for closure of 994-1097	Size = 5
		Stack = -2.4  for stack of 997-1093
	Helix total = -2.4
	Internal/bulge = -0.6  for closure of 998-1092	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.6  for closure of 1000-1090	Size = 5
		Stack = -2.1  for stack of 1003-1086
		Stack = -2.4  for stack of 1004-1085
		Stack = -3.3  for stack of 1005-1084
		Stack = -1.4  for stack of 1006-1083
		Stack = -1.3  for stack of 1007-1082
		Stack = -1.4  for stack of 1008-1081
	Helix total = -11.9
	Internal/bulge = 1.2  for closure of 1009-1080	Size = 4
		Stack = -1.3  for stack of 1012-1077
		Stack = -0.6  for stack of 1013-1076
		Stack = -1.4  for stack of 1014-1075
		Stack = -1.3  for stack of 1015-1074
		Stack = -1.1  for stack of 1016-1073
		Stack = -1.3  for stack of 1017-1072
		Stack = 0.3  for stack of 1018-1071
		Stack = 1.3  for stack of 1019-1070
	Helix total = -5.4
	Internal/bulge = 1.2  for closure of 1020-1069	Size = 2
		Stack = -2.1  for stack of 1022-1067
	Helix total = -2.1
	Internal/bulge = 1.6  for closure of 1023-1066	Size = 14
		Stack = -2.1  for stack of 1031-1058
		Stack = -1.3  for stack of 1032-1057
	Helix total = -3.4
	Internal/bulge = 1.7  for closure of 1033-1056	Size = 1 BP stack across bulge = -2.1
		Stack = -3.3  for stack of 1035-1055
		Stack = -3.4  for stack of 1036-1054
		Stack = -2.1  for stack of 1037-1053
	Helix total = -8.8
	Hairpin = 6.5  for closure of 1038-1052
		Stack = -2.1  for stack of 611-989
	Helix total = -2.1
	Internal/bulge = 0.5  for closure of 612-988	Size = 1 BP stack across bulge = -3.3
		Stack = -3.4  for stack of 613-986
		Stack = -2.1  for stack of 614-985
	Helix total = -5.5
	Internal/bulge = 1.6  for closure of 615-984	Size = 1 BP stack across bulge = -2.2
		Stack = -1.4  for stack of 617-983
		Stack = -1.3  for stack of 618-982
		Stack = -1.1  for stack of 619-981
		Stack = -1.3  for stack of 620-980
		Stack = -2.1  for stack of 621-979
		Stack = -2.4  for stack of 622-978
	Helix total = -9.6
	Multiloop = 7.8  for closure of 623-977
		Stack = -1.4  for stack of 943-966
		Stack = -1.5  for stack of 944-965
		Stack = -2.4  for stack of 945-964
		Stack = -2.2  for stack of 946-963
		Stack = -1.3  for stack of 947-962
		Stack = -2.1  for stack of 948-961
	Helix total = -10.9
	Hairpin = 5.2  for closure of 949-960
		Stack = -2.4  for stack of 628-938
		Stack = -3.4  for stack of 629-937
		Stack = -2.4  for stack of 630-936
		Stack = -1.5  for stack of 631-935
		Stack = -1.4  for stack of 632-934
	Helix total = -11.1
	Multiloop = 6.4  for closure of 633-933
	Helix total = 0.0
	Internal/bulge = 1.4  for closure of 850-927	Size = 8
		Stack = -2.1  for stack of 855-922
		Stack = -3.3  for stack of 856-921
		Stack = -2.4  for stack of 857-920
		Stack = -2.1  for stack of 858-919
	Helix total = -9.9
	Internal/bulge = 6.7  for closure of 859-918	Size = 33
		Stack = -0.9  for stack of 874-898
		Stack = -2.2  for stack of 875-897
	Helix total = -3.1
	Internal/bulge = 1.2  for closure of 876-896	Size = 2
		Stack = -1.1  for stack of 878-894
	Helix total = -1.1
	Internal/bulge = 1.2  for closure of 879-893	Size = 2
		Stack = -2.1  for stack of 881-891
		Stack = -0.6  for stack of 882-890
	Helix total = -2.7
	Hairpin = 4.7  for closure of 883-889
		Stack = -1.3  for stack of 809-844
		Stack = -1.4  for stack of 810-843
		Stack = -3.3  for stack of 811-842
		Stack = -2.4  for stack of 812-841
		Stack = -2.2  for stack of 813-840
		Stack = -2.1  for stack of 814-839
	Helix total = -12.7
	Hairpin = 7.1  for closure of 815-838
		Stack = -0.9  for stack of 636-805
		Stack = -1.1  for stack of 637-804
		Stack = -1.3  for stack of 638-803
		Stack = -1.4  for stack of 639-802
		Stack = -1.4  for stack of 640-801
		Stack = -3.4  for stack of 641-800
		Stack = -2.1  for stack of 642-799
	Helix total = -11.6
	Internal/bulge = 2.4  for closure of 643-798	Size = 1 BP stack across bulge = -1.4
		Stack = -2.2  for stack of 644-796
	Helix total = -2.2
	Multiloop = 8.2  for closure of 645-795
		Stack = -3.3  for stack of 674-791
		Stack = -2.1  for stack of 675-790
		Stack = -2.2  for stack of 676-789
		Stack = -2.1  for stack of 677-788
		Stack = -1.3  for stack of 678-787
		Stack = -0.6  for stack of 679-786
	Helix total = -11.6
	Internal/bulge = 4.5  for closure of 680-785	Size = 11
		Stack = -3.4  for stack of 688-780
	Helix total = -3.4
	Internal/bulge = 0.5  for closure of 689-779	Size = 1 BP stack across bulge = -3.3
		Stack = -2.1  for stack of 691-778
		Stack = -0.5  for stack of 692-777
		Stack = 0.3  for stack of 693-776
	Helix total = -2.3
	Internal/bulge = 3.8  for closure of 694-775	Size = 2
	Helix total = 0.0
	Internal/bulge = 5.2  for closure of 697-774	Size = 5
		Stack = -2.5  for stack of 699-769
		Stack = -2.1  for stack of 700-768
	Helix total = -4.6
	Hairpin = 7.0  for closure of 701-767
		Stack = -2.4  for stack of 652-663
	Helix total = -2.4
	Hairpin = 4.2  for closure of 653-662
		Stack = -2.1  for stack of 584-595
		Stack = -2.2  for stack of 585-594
		Stack = -2.1  for stack of 586-593
	Helix total = -6.4
	Hairpin = 3.1  for closure of 587-592
		Stack = -3.3  for stack of 355-574
		Stack = -3.4  for stack of 356-573
	Helix total = -6.7
	Internal/bulge = 4.0  for closure of 357-572	Size = 5
	Helix total = 0.0
	Multiloop = 4.6  for closure of 363-571
		Stack = -0.9  for stack of 550-570
		Stack = -1.3  for stack of 551-569
		Stack = -1.1  for stack of 552-568
		Stack = -1.3  for stack of 553-567
		Stack = -2.1  for stack of 554-566
	Helix total = -6.7
	Hairpin = 4.8  for closure of 555-565
		Stack = -2.2  for stack of 497-539
		Stack = -0.9  for stack of 498-538
		Stack = -0.9  for stack of 499-537
		Stack = -2.1  for stack of 500-536
		Stack = -3.3  for stack of 501-535
		Stack = -1.5  for stack of 502-534
	Helix total = -10.9
	Internal/bulge = 3.7  for closure of 503-533	Size = 3
	Helix total = 0.0
	Internal/bulge = 2.0  for closure of 507-532	Size = 9
		Stack = -2.4  for stack of 512-526
		Stack = -3.3  for stack of 513-525
	Helix total = -5.7
	Hairpin = 4.9  for closure of 514-524
		Stack = -3.4  for stack of 365-492
		Stack = -2.4  for stack of 366-491
		Stack = -2.2  for stack of 367-490
	Helix total = -8.0
	Internal/bulge = 2.3  for closure of 368-489	Size = 4
		Stack = -1.3  for stack of 371-486
		Stack = -2.1  for stack of 372-485
		Stack = -3.4  for stack of 373-484
	Helix total = -6.8
	Internal/bulge = 6.0  for closure of 374-483	Size = 20
		Stack = -2.2  for stack of 388-475
		Stack = -2.1  for stack of 389-474
		Stack = -1.3  for stack of 390-473
		Stack = -0.6  for stack of 391-472
	Helix total = -6.2
	Internal/bulge = 3.7  for closure of 392-471	Size = 3
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 395-469	Size = 2
		Stack = -2.2  for stack of 397-467
		Stack = -0.9  for stack of 398-466
		Stack = -2.1  for stack of 399-465
		Stack = -3.3  for stack of 400-464
	Helix total = -8.5
	Multiloop = 5.3  for closure of 401-463
		Stack = -3.4  for stack of 454-461
	Helix total = -3.4
	Hairpin = 3.3  for closure of 455-460
	Helix total = 0.0
	Internal/bulge = 2.3  for closure of 403-445	Size = 4
		Stack = -1.0  for stack of 406-442
		Stack = -1.1  for stack of 407-441
		Stack = -1.3  for stack of 408-440
		Stack = -1.5  for stack of 409-439
		Stack = -2.4  for stack of 410-438
		Stack = -3.3  for stack of 411-437
		Stack = -2.4  for stack of 412-436
	Helix total = -13.0
	Internal/bulge = 4.6  for closure of 413-435	Size = 9
		Stack = -2.4  for stack of 417-428
		Stack = -1.4  for stack of 418-427
	Helix total = -3.8
	Hairpin = 4.4  for closure of 419-426
		Stack = -3.4  for stack of 25-344
		Stack = -2.1  for stack of 26-343
		Stack = -0.9  for stack of 27-342
	Helix total = -6.4
	Internal/bulge = 3.7  for closure of 28-341	Size = 3
		Stack = -1.1  for stack of 31-339
		Stack = -1.0  for stack of 32-338
		Stack = -2.5  for stack of 33-337
	Helix total = -4.6
	Multiloop = 7.5  for closure of 34-336
		Stack = -2.2  for stack of 288-333
		Stack = -2.1  for stack of 289-332
		Stack = -2.2  for stack of 290-331
		Stack = -3.3  for stack of 291-330
	Helix total = -9.8
	Internal/bulge = 4.4  for closure of 292-329	Size = 6
		Stack = -3.4  for stack of 299-328
		Stack = -2.1  for stack of 300-327
		Stack = -2.2  for stack of 301-326
		Stack = -2.4  for stack of 302-325
	Helix total = -10.1
	Hairpin = 6.1  for closure of 303-324
		Stack = -1.3  for stack of 38-281
		Stack = -2.1  for stack of 39-280
		Stack = -3.4  for stack of 40-279
		Stack = -1.4  for stack of 41-278
		Stack = -2.1  for stack of 42-277
	Helix total = -10.3
	Multiloop = 7.8  for closure of 43-276
	Helix total = 0.0
	Internal/bulge = 0.9  for closure of 244-271	Size = 1 BP stack across bulge = -2.1
		Stack = -3.3  for stack of 246-270
		Stack = -2.4  for stack of 247-269
	Helix total = -5.7
	Internal/bulge = 3.7  for closure of 248-268	Size = 4
		Stack = -1.5  for stack of 252-266
		Stack = -2.4  for stack of 253-265
		Stack = -3.4  for stack of 254-264
		Stack = -2.1  for stack of 255-263
	Helix total = -9.4
	Hairpin = 5.6  for closure of 256-262
	Helix total = 0.0
	Internal/bulge = 5.2  for closure of 46-238	Size = 5
		Stack = -1.0  for stack of 51-236
		Stack = -2.2  for stack of 52-235
	Helix total = -3.2
	Internal/bulge = 1.7  for closure of 53-234	Size = 1 BP stack across bulge = -2.1
		Stack = -2.1  for stack of 55-233
		Stack = -3.4  for stack of 56-232
	Helix total = -5.5
	Multiloop = 1.5  for closure of 57-231
		Stack = -2.2  for stack of 216-227
		Stack = -0.9  for stack of 217-226
		Stack = -2.4  for stack of 218-225
	Helix total = -5.5
	Hairpin = 3.5  for closure of 219-224
		Stack = -2.2  for stack of 194-214
		Stack = -2.1  for stack of 195-213
		Stack = -3.3  for stack of 196-212
		Stack = -3.4  for stack of 197-211
	Helix total = -11.0
	Hairpin = 5.2  for closure of 198-210
		Stack = -2.2  for stack of 80-192
		Stack = -2.1  for stack of 81-191
	Helix total = -4.3
	Multiloop = 5.1  for closure of 82-190
		Stack = -3.4  for stack of 168-189
		Stack = -3.3  for stack of 169-188
		Stack = -2.1  for stack of 170-187
	Helix total = -8.8
	Internal/bulge = 3.3  for closure of 171-186	Size = 6
		Stack = -2.1  for stack of 174-181
	Helix total = -2.1
	Hairpin = 5.5  for closure of 175-180
		Stack = -2.1  for stack of 114-165
		Stack = -3.3  for stack of 115-164
	Helix total = -5.4
	Internal/bulge = 2.3  for closure of 116-163	Size = 8
		Stack = -3.4  for stack of 121-158
	Helix total = -3.4
	Internal/bulge = 2.9  for closure of 122-157	Size = 6
		Stack = -2.1  for stack of 127-154
		Stack = -3.3  for stack of 128-153
		Stack = -3.3  for stack of 129-152
		Stack = -2.5  for stack of 130-151
		Stack = -1.5  for stack of 131-150
		Stack = -2.4  for stack of 132-149
	Helix total = -15.1
	Hairpin = 5.8  for closure of 133-148
		Stack = -1.4  for stack of 88-113
	Helix total = -1.4
	Internal/bulge = 1.2  for closure of 89-112	Size = 2
		Stack = -2.4  for stack of 91-110
		Stack = -1.5  for stack of 92-109
		Stack = -2.1  for stack of 93-108
	Helix total = -6.0
	Hairpin = 5.6  for closure of 94-107
		Stack = -2.5  for stack of 60-73
		Stack = -2.1  for stack of 61-72
		Stack = -0.9  for stack of 62-71
	Helix total = -5.5
	Hairpin = 4.9  for closure of 63-70
		Stack = -2.4  for stack of 7-23
		Stack = -2.1  for stack of 8-22
		Stack = -2.5  for stack of 9-21
		Stack = -0.5  for stack of 10-20
	Helix total = -7.5
	Hairpin = 5.1  for closure of 11-19


	Total energy = -134.4



