Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    32:339 33:338
	Energy of Broken Structure: 36.6
	Energy of Pseudo-Helices:   -2.4
	Pseudoknot Energy Penalty:  7.2
	Total Free Energy:          41.4
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -5.6
		Stack = -1.3  for stack of 668-691
		Stack = -2.1  for stack of 669-690
		Stack = -2.4  for stack of 670-689
		Stack = -1.1  for stack of 671-688
		Stack = -0.9  for stack of 672-687
		Stack = -1.3  for stack of 673-686
		Stack = -1.0  for stack of 674-685
		Stack = -2.1  for stack of 675-684
		Stack = -3.3  for stack of 676-683
	Helix total = -15.5
	Hairpin = 3.1  for closure of 677-682
	Helix total = 0.0
	Internal/bulge = 3.7  for closure of 627-666	Size = 3
		Stack = -1.4  for stack of 629-663
	Helix total = -1.4
	Internal/bulge = 3.0  for closure of 630-662	Size = 3
		Stack = -2.1  for stack of 632-659
	Helix total = -2.1
	Internal/bulge = 0.8  for closure of 633-658	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.0  for closure of 635-656	Size = 3
		Stack = -1.4  for stack of 637-653
		Stack = -0.6  for stack of 638-652
	Helix total = -2.0
	Internal/bulge = -1.4  for closure of 639-651	Size = 2
		Stack = -3.3  for stack of 641-649
		Stack = -3.3  for stack of 642-648
	Helix total = -6.6
	Hairpin = 5.4  for closure of 643-647
		Stack = -2.1  for stack of 343-624
	Helix total = -2.1
	Internal/bulge = 2.3  for closure of 344-623	Size = 1 BP stack across bulge = -1.5
		Stack = -2.5  for stack of 345-621
	Helix total = -2.5
	Internal/bulge = 1.9  for closure of 346-620	Size = 3
		Stack = -2.2  for stack of 349-618
	Helix total = -2.2
	Internal/bulge = 1.7  for closure of 350-617	Size = 1 BP stack across bulge = -2.1
		Stack = -0.9  for stack of 352-616
		Stack = -2.4  for stack of 353-615
		Stack = -2.1  for stack of 354-614
		Stack = -1.3  for stack of 355-613
	Helix total = -6.7
	Multiloop = 9.1  for closure of 356-612
		Stack = -0.9  for stack of 581-601
		Stack = -0.9  for stack of 582-600
		Stack = -0.9  for stack of 583-599
		Stack = -0.9  for stack of 584-598
		Stack = -1.1  for stack of 585-597
	Helix total = -4.7
	Internal/bulge = 1.2  for closure of 586-596	Size = 2
	Helix total = 0.0
	Hairpin = 3.6  for closure of 588-594
		Stack = -2.4  for stack of 362-575
		Stack = -2.1  for stack of 363-574
		Stack = -0.9  for stack of 364-573
		Stack = -0.9  for stack of 365-572
	Helix total = -6.3
	Multiloop = 7.9  for closure of 366-571
	Helix total = 0.0
	Internal/bulge = 2.1  for closure of 536-565	Size = 8
		Stack = -0.9  for stack of 541-560
		Stack = -0.9  for stack of 542-559
		Stack = -1.3  for stack of 543-558
		Stack = -2.1  for stack of 544-557
		Stack = -2.2  for stack of 545-556
		Stack = -0.9  for stack of 546-555
	Helix total = -8.3
	Hairpin = 4.5  for closure of 547-554
		Stack = -1.1  for stack of 525-531
	Helix total = -1.1
	Hairpin = 5.9  for closure of 526-530
		Stack = -2.1  for stack of 369-519
		Stack = -3.3  for stack of 370-518
		Stack = -3.4  for stack of 371-517
		Stack = -2.1  for stack of 372-516
		Stack = 0.3  for stack of 373-515
		Stack = -1.3  for stack of 374-514
		Stack = -0.6  for stack of 375-513
	Helix total = -12.5
	Multiloop = 6.5  for closure of 376-512
		Stack = -2.1  for stack of 403-506
		Stack = -0.9  for stack of 404-505
		Stack = -1.3  for stack of 405-504
		Stack = -0.9  for stack of 406-503
	Helix total = -5.2
	Internal/bulge = 2.1  for closure of 407-502	Size = 1 BP stack across bulge = -1.1
		Stack = -1.3  for stack of 408-500
	Helix total = -1.3
	Internal/bulge = 2.9  for closure of 409-499	Size = 7
		Stack = -1.3  for stack of 414-495
		Stack = -2.2  for stack of 415-494
	Helix total = -3.5
	Internal/bulge = 0.5  for closure of 416-493	Size = 1 BP stack across bulge = -3.3
		Stack = -2.4  for stack of 418-492
	Helix total = -2.4
	Internal/bulge = 0.6  for closure of 419-491	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.3  for closure of 421-489	Size = 2
		Stack = -1.0  for stack of 424-488
	Helix total = -1.0
	Internal/bulge = 4.2  for closure of 425-487	Size = 3
		Stack = -1.1  for stack of 426-483
		Stack = -2.4  for stack of 427-482
	Helix total = -3.5
	Internal/bulge = 2.4  for closure of 428-481	Size = 1 BP stack across bulge = -1.4
		Stack = -1.4  for stack of 429-479
		Stack = -0.9  for stack of 430-478
		Stack = -0.9  for stack of 431-477
	Helix total = -3.2
	Internal/bulge = 7.5  for closure of 432-476	Size = 17
		Stack = -0.9  for stack of 434-459
		Stack = -0.9  for stack of 435-458
		Stack = -0.9  for stack of 436-457
		Stack = -1.3  for stack of 437-456
	Helix total = -4.0
	Internal/bulge = 6.5  for closure of 438-455	Size = 7
		Stack = -2.4  for stack of 440-448
		Stack = -2.1  for stack of 441-447
	Helix total = -4.5
	Hairpin = 5.9  for closure of 442-446
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 382-397	Size = 2
		Stack = -2.1  for stack of 384-395
	Helix total = -2.1
	Hairpin = 4.0  for closure of 385-394
		Stack = -0.9  for stack of 317-327
		Stack = -0.6  for stack of 318-326
		Stack = -1.4  for stack of 319-325
	Helix total = -2.9
	Hairpin = 5.9  for closure of 320-324
		Stack = -0.6  for stack of 179-306
	Helix total = -0.6
	Internal/bulge = 5.0  for closure of 180-305	Size = 5
	Helix total = 0.0
	Multiloop = 7.1  for closure of 186-304
		Stack = -0.9  for stack of 260-297
		Stack = -0.9  for stack of 261-296
		Stack = -2.1  for stack of 262-295
		Stack = -2.2  for stack of 263-294
	Helix total = -6.1
	Internal/bulge = 4.1  for closure of 264-293	Size = 4
	Helix total = 0.0
	Internal/bulge = 1.3  for closure of 269-292	Size = 8
		Stack = -2.1  for stack of 274-287
		Stack = -2.1  for stack of 275-286
	Helix total = -4.2
	Hairpin = 4.0  for closure of 276-285
		Stack = -0.9  for stack of 188-255
		Stack = -0.9  for stack of 189-254
	Helix total = -1.8
	Internal/bulge = 6.1  for closure of 190-253	Size = 24
		Stack = -0.6  for stack of 201-238
	Helix total = -0.6
	Internal/bulge = 1.4  for closure of 202-237	Size = 4
	Helix total = 0.0
	Internal/bulge = 1.5  for closure of 205-234	Size = 2
		Stack = -1.3  for stack of 207-232
		Stack = -0.6  for stack of 208-231
		Stack = -1.3  for stack of 209-230
		Stack = -1.1  for stack of 210-229
	Helix total = -4.3
	Internal/bulge = 2.3  for closure of 211-228	Size = 4
	Helix total = 0.0
	Internal/bulge = 1.6  for closure of 214-225	Size = 2
	Helix total = 0.0
	Hairpin = 4.4  for closure of 216-223
		Stack = -0.6  for stack of 42-174
	Helix total = -0.6
	Internal/bulge = 1.9  for closure of 43-173	Size = 2
		Stack = -1.0  for stack of 45-171
		Stack = -1.3  for stack of 46-170
	Helix total = -2.3
	Internal/bulge = 1.5  for closure of 47-169	Size = 4
		Stack = -1.3  for stack of 50-166
	Helix total = -1.3
	Multiloop = 8.0  for closure of 51-165
		Stack = -3.4  for stack of 115-161
	Helix total = -3.4
	Internal/bulge = 1.1  for closure of 116-160	Size = 1 BP stack across bulge = -2.1
		Stack = -0.9  for stack of 117-158
		Stack = -1.0  for stack of 118-157
	Helix total = -1.9
	Internal/bulge = 5.4  for closure of 119-156	Size = 6
		Stack = -2.2  for stack of 126-155
	Helix total = -2.2
	Internal/bulge = -0.4  for closure of 127-154	Size = 4
	Helix total = 0.0
	Hairpin = 6.1  for closure of 130-151
		Stack = -0.9  for stack of 52-111
		Stack = -0.9  for stack of 53-110
		Stack = -1.1  for stack of 54-109
	Helix total = -2.9
	Internal/bulge = 1.2  for closure of 55-108	Size = 2
		Stack = -2.5  for stack of 57-106
	Helix total = -2.5
	Hairpin = 7.5  for closure of 58-105
		Stack = -0.9  for stack of 24-40
		Stack = -0.9  for stack of 25-39
		Stack = -1.4  for stack of 26-38
		Stack = -0.5  for stack of 27-37
	Helix total = -3.7
	Hairpin = 5.1  for closure of 28-36


	Total energy = 36.6



