Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    12:524 13:523 14:522 238:263 239:262 240:261
	Energy of Broken Structure: -68.9
	Energy of Pseudo-Helices:   -9.5
	Pseudoknot Energy Penalty:  14.5
	Total Free Energy:          -63.9
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -9.7
		Stack = -1.0  for stack of 924-947
		Stack = -0.9  for stack of 925-946
		Stack = -2.1  for stack of 926-945
		Stack = -2.2  for stack of 927-944
		Stack = -2.1  for stack of 928-943
		Stack = -2.5  for stack of 929-942
		Stack = -1.0  for stack of 930-941
		Stack = -2.2  for stack of 931-940
		Stack = -2.1  for stack of 932-939
	Helix total = -16.1
	Hairpin = 4.1  for closure of 933-938
	Helix total = 0.0
	Internal/bulge = 2.3  for closure of 836-922	Size = 3
	Helix total = 0.0
	Internal/bulge = 2.6  for closure of 838-919	Size = 5
		Stack = -2.4  for stack of 841-915
	Helix total = -2.4
	Internal/bulge = -0.6  for closure of 842-914	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.7  for closure of 844-912	Size = 7
		Stack = -2.1  for stack of 848-907
		Stack = -2.4  for stack of 849-906
		Stack = -3.3  for stack of 850-905
		Stack = -2.1  for stack of 851-904
		Stack = -2.4  for stack of 852-903
	Helix total = -12.3
	Internal/bulge = 3.0  for closure of 853-902	Size = 3
		Stack = -1.4  for stack of 856-900
		Stack = -1.3  for stack of 857-899
		Stack = -1.1  for stack of 858-898
		Stack = -1.3  for stack of 859-897
	Helix total = -5.1
	Hairpin = 7.6  for closure of 860-896
		Stack = -2.1  for stack of 527-833
	Helix total = -2.1
	Internal/bulge = 2.3  for closure of 528-832	Size = 1 BP stack across bulge = -1.5
		Stack = -2.5  for stack of 529-830
		Stack = -2.4  for stack of 530-829
	Helix total = -4.9
	Internal/bulge = 0.9  for closure of 531-828	Size = 1 BP stack across bulge = -2.5
		Stack = -1.4  for stack of 533-827
		Stack = -3.4  for stack of 534-826
		Stack = -2.1  for stack of 535-825
		Stack = -0.9  for stack of 536-824
		Stack = -2.4  for stack of 537-823
		Stack = -2.1  for stack of 538-822
	Helix total = -12.3
	Multiloop = 9.1  for closure of 539-821
		Stack = -0.9  for stack of 787-809
		Stack = -2.2  for stack of 788-808
		Stack = -2.1  for stack of 789-807
		Stack = -1.3  for stack of 790-806
		Stack = -0.9  for stack of 791-805
		Stack = -2.1  for stack of 792-804
	Helix total = -9.5
	Hairpin = 5.1  for closure of 793-803
		Stack = -2.1  for stack of 547-781
		Stack = -1.3  for stack of 548-780
		Stack = -0.6  for stack of 549-779
		Stack = -1.3  for stack of 550-778
	Helix total = -5.3
	Multiloop = 6.1  for closure of 551-777
	Helix total = 0.0
	Internal/bulge = 1.7  for closure of 741-771	Size = 4
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 744-768	Size = 2
		Stack = -2.5  for stack of 746-766
		Stack = -3.3  for stack of 747-765
		Stack = -3.3  for stack of 748-764
		Stack = -2.1  for stack of 749-763
		Stack = -0.9  for stack of 750-762
	Helix total = -12.1
	Hairpin = 6.1  for closure of 751-761
		Stack = -0.9  for stack of 723-735
		Stack = -2.4  for stack of 724-734
		Stack = -2.1  for stack of 725-733
	Helix total = -5.4
	Hairpin = 5.4  for closure of 726-732
		Stack = -2.1  for stack of 554-717
		Stack = -3.4  for stack of 555-716
		Stack = -3.3  for stack of 556-715
		Stack = -2.1  for stack of 557-714
		Stack = 0.3  for stack of 558-713
		Stack = -1.4  for stack of 559-712
		Stack = -0.9  for stack of 560-711
	Helix total = -12.9
	Internal/bulge = 0.8  for closure of 561-710	Size = 1 BP stack across bulge = -2.4
		Stack = -2.1  for stack of 562-708
	Helix total = -2.1
	Multiloop = 7.9  for closure of 563-707
		Stack = -3.3  for stack of 591-704
		Stack = -2.1  for stack of 592-703
		Stack = -2.2  for stack of 593-702
		Stack = -3.3  for stack of 594-701
		Stack = -2.1  for stack of 595-700
		Stack = -2.4  for stack of 596-699
	Helix total = -15.4
	Internal/bulge = 3.8  for closure of 597-698	Size = 11
		Stack = -3.4  for stack of 605-693
	Helix total = -3.4
	Internal/bulge = 0.4  for closure of 606-692	Size = 1 BP stack across bulge = -2.1
		Stack = -1.3  for stack of 608-691
		Stack = -1.4  for stack of 609-690
		Stack = -1.0  for stack of 610-689
	Helix total = -3.7
	Internal/bulge = 3.3  for closure of 611-688	Size = 2
		Stack = -3.3  for stack of 614-687
	Helix total = -3.3
	Internal/bulge = 3.7  for closure of 615-686	Size = 3
		Stack = -2.5  for stack of 616-682
		Stack = -3.3  for stack of 617-681
	Helix total = -5.8
	Internal/bulge = 1.7  for closure of 618-680	Size = 1 BP stack across bulge = -2.1
	Helix total = 0.0
	Internal/bulge = 0.8  for closure of 619-678	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 621-676	Size = 2
	Helix total = 0.0
	Multiloop = 7.3  for closure of 623-674
		Stack = -1.3  for stack of 661-670
		Stack = -2.2  for stack of 662-669
	Helix total = -3.5
	Hairpin = 4.5  for closure of 663-668
		Stack = -3.4  for stack of 626-655
	Helix total = -3.4
	Internal/bulge = 2.0  for closure of 627-654	Size = 4
		Stack = -2.2  for stack of 630-651
	Helix total = -2.2
	Internal/bulge = 4.6  for closure of 631-650	Size = 7
		Stack = -3.3  for stack of 632-642
		Stack = -2.1  for stack of 633-641
	Helix total = -5.4
	Hairpin = 4.2  for closure of 634-640
		Stack = -1.1  for stack of 567-582
		Stack = -2.4  for stack of 568-581
		Stack = -2.4  for stack of 569-580
	Helix total = -5.9
	Hairpin = 4.0  for closure of 570-579
		Stack = -2.4  for stack of 491-518
	Helix total = -2.4
	Internal/bulge = 5.3  for closure of 492-517	Size = 12
		Stack = -1.3  for stack of 500-511
		Stack = -2.1  for stack of 501-510
		Stack = -3.4  for stack of 502-509
	Helix total = -6.8
	Hairpin = 4.6  for closure of 503-508
		Stack = -3.3  for stack of 286-489
		Stack = -3.4  for stack of 287-488
	Helix total = -6.7
	Multiloop = 5.1  for closure of 288-487
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 462-485	Size = 2
		Stack = -2.1  for stack of 464-483
		Stack = -2.1  for stack of 465-482
		Stack = -2.2  for stack of 466-481
		Stack = -0.9  for stack of 467-480
	Helix total = -7.3
	Hairpin = 6.0  for closure of 468-479
		Stack = -3.4  for stack of 410-451
		Stack = -2.1  for stack of 411-450
		Stack = -1.3  for stack of 412-449
		Stack = -0.9  for stack of 413-448
		Stack = -2.1  for stack of 414-447
	Helix total = -9.8
	Internal/bulge = 4.5  for closure of 415-446	Size = 5
	Helix total = 0.0
	Internal/bulge = 3.4  for closure of 420-444	Size = 6
		Stack = -2.1  for stack of 424-440
		Stack = -3.3  for stack of 425-439
		Stack = -3.3  for stack of 426-438
	Helix total = -8.7
	Hairpin = 4.9  for closure of 427-437
		Stack = -2.1  for stack of 297-404
		Stack = -2.2  for stack of 298-403
	Helix total = -4.3
	Internal/bulge = 3.7  for closure of 299-402	Size = 9
		Stack = -2.4  for stack of 304-396
	Helix total = -2.4
	Internal/bulge = 7.7  for closure of 305-395	Size = 20
		Stack = -1.3  for stack of 321-389
		Stack = -0.9  for stack of 322-388
		Stack = -0.9  for stack of 323-387
		Stack = -2.1  for stack of 324-386
		Stack = -3.4  for stack of 325-385
	Helix total = -8.6
	Multiloop = 6.5  for closure of 326-384
		Stack = -2.2  for stack of 375-382
	Helix total = -2.2
	Hairpin = 3.3  for closure of 376-381
	Helix total = 0.0
	Internal/bulge = 4.4  for closure of 327-366	Size = 9
		Stack = -2.4  for stack of 333-361
		Stack = -2.1  for stack of 334-360
	Helix total = -4.5
	Internal/bulge = 3.9  for closure of 335-359	Size = 11
		Stack = -2.2  for stack of 341-352
		Stack = -0.9  for stack of 342-351
	Helix total = -3.1
	Hairpin = 3.9  for closure of 343-350
		Stack = -2.4  for stack of 22-281
		Stack = -2.1  for stack of 23-280
		Stack = -1.3  for stack of 24-279
		Stack = -1.1  for stack of 25-278
		Stack = -0.9  for stack of 26-277
	Helix total = -7.8
	Internal/bulge = 1.9  for closure of 27-276	Size = 2
		Stack = -2.5  for stack of 29-274
		Stack = -2.1  for stack of 30-273
	Helix total = -4.6
	Multiloop = 5.7  for closure of 31-272
		Stack = -3.3  for stack of 225-270
		Stack = -3.3  for stack of 226-269
		Stack = -2.2  for stack of 227-268
		Stack = -0.9  for stack of 228-267
	Helix total = -9.7
	Internal/bulge = 5.8  for closure of 229-266	Size = 14
		Stack = -3.3  for stack of 230-251
		Stack = -2.2  for stack of 231-250
	Helix total = -5.5
	Hairpin = 6.9  for closure of 232-249
		Stack = -0.9  for stack of 33-219
		Stack = -1.3  for stack of 34-218
		Stack = -2.1  for stack of 35-217
		Stack = -2.2  for stack of 36-216
		Stack = -1.3  for stack of 37-215
	Helix total = -7.8
	Internal/bulge = 2.9  for closure of 38-214	Size = 1 BP stack across bulge = -0.9
		Stack = -2.1  for stack of 39-212
	Helix total = -2.1
	Multiloop = 5.6  for closure of 40-211
	Helix total = 0.0
	Internal/bulge = 2.3  for closure of 183-209	Size = 1 BP stack across bulge = -0.9
		Stack = -1.3  for stack of 185-208
		Stack = -2.1  for stack of 186-207
	Helix total = -3.4
	Internal/bulge = 3.0  for closure of 187-206	Size = 4
		Stack = -1.3  for stack of 191-204
		Stack = -0.9  for stack of 192-203
		Stack = -0.9  for stack of 193-202
		Stack = -2.2  for stack of 194-201
	Helix total = -5.3
	Hairpin = 3.3  for closure of 195-200
		Stack = -2.1  for stack of 45-175
		Stack = -2.2  for stack of 46-174
	Helix total = -4.3
	Internal/bulge = 1.7  for closure of 47-173	Size = 1 BP stack across bulge = -2.1
		Stack = -2.1  for stack of 49-172
		Stack = -3.4  for stack of 50-171
	Helix total = -5.5
	Multiloop = 2.9  for closure of 51-170
		Stack = -3.3  for stack of 157-164
	Helix total = -3.3
	Hairpin = 3.7  for closure of 158-163
		Stack = -2.2  for stack of 68-153
		Stack = -2.1  for stack of 69-152
	Helix total = -4.3
	Multiloop = 4.2  for closure of 70-151
		Stack = -3.4  for stack of 144-150
	Helix total = -3.4
	Hairpin = 5.4  for closure of 145-149
		Stack = -2.1  for stack of 107-141
		Stack = -3.4  for stack of 108-140
	Helix total = -5.5
	Internal/bulge = 4.4  for closure of 109-139	Size = 10
		Stack = -2.1  for stack of 114-132
		Stack = -3.4  for stack of 115-131
	Helix total = -5.5
	Internal/bulge = 2.3  for closure of 116-130	Size = 3
		Stack = -3.4  for stack of 119-128
		Stack = -2.1  for stack of 120-127
	Helix total = -5.5
	Hairpin = 4.4  for closure of 121-126
		Stack = -3.3  for stack of 78-102
		Stack = -2.1  for stack of 79-101
	Helix total = -5.4
	Internal/bulge = 3.7  for closure of 80-100	Size = 8
		Stack = -1.1  for stack of 85-95
		Stack = -2.4  for stack of 86-94
	Helix total = -3.5
	Hairpin = 4.2  for closure of 87-93
	Helix total = 0.0
	Hairpin = 4.7  for closure of 54-61
		Stack = -2.1  for stack of 4-20
		Stack = -3.3  for stack of 5-19
		Stack = -2.5  for stack of 6-18
		Stack = -0.6  for stack of 7-17
	Helix total = -8.5
	Hairpin = 5.1  for closure of 8-16


	Total energy = -68.9



