Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    553:574 554:573 555:572
	Energy of Broken Structure: -77.4
	Energy of Pseudo-Helices:   -6.7
	Pseudoknot Energy Penalty:  7.2
	Total Free Energy:          -76.9
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -2.7
		Stack = -0.6  for stack of 22-604
		Stack = -1.4  for stack of 23-603
	Helix total = -2.0
	Internal/bulge = 2.5  for closure of 24-602	Size = 1 BP stack across bulge = -1.3
		Stack = -1.1  for stack of 26-601
		Stack = -1.3  for stack of 27-600
		Stack = -1.4  for stack of 28-599
		Stack = -1.4  for stack of 29-598
		Stack = -3.4  for stack of 30-597
		Stack = -2.1  for stack of 31-596
	Helix total = -10.7
	Multiloop = 3.6  for closure of 32-595
		Stack = -0.9  for stack of 547-593
		Stack = -2.1  for stack of 548-592
		Stack = -3.3  for stack of 549-591
		Stack = -2.4  for stack of 550-590
		Stack = -2.1  for stack of 551-589
	Helix total = -10.8
	Internal/bulge = 4.6  for closure of 552-588	Size = 7
		Stack = -2.1  for stack of 560-587
		Stack = -2.1  for stack of 561-586
		Stack = -3.3  for stack of 562-585
	Helix total = -7.5
	Hairpin = 5.6  for closure of 563-584
		Stack = -2.2  for stack of 517-537
	Helix total = -2.2
	Hairpin = 6.6  for closure of 518-536
		Stack = -2.1  for stack of 481-510
		Stack = -0.9  for stack of 482-509
	Helix total = -3.0
	Internal/bulge = 2.3  for closure of 483-508	Size = 1 BP stack across bulge = -1.1
		Stack = -1.3  for stack of 484-506
		Stack = -2.2  for stack of 485-505
		Stack = -3.3  for stack of 486-504
		Stack = -1.4  for stack of 487-503
		Stack = -2.1  for stack of 488-502
		Stack = -1.5  for stack of 489-501
		Stack = -2.5  for stack of 490-500
		Stack = -2.1  for stack of 491-499
		Stack = -2.4  for stack of 492-498
	Helix total = -18.8
	Hairpin = 5.4  for closure of 493-497
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 35-475	Size = 2
	Helix total = 0.0
	Multiloop = 7.2  for closure of 37-473
	Helix total = 0.0
	Internal/bulge = 2.1  for closure of 441-466	Size = 1 BP stack across bulge = -1.3
		Stack = -2.2  for stack of 443-465
		Stack = -3.3  for stack of 444-464
	Helix total = -5.5
	Internal/bulge = 3.0  for closure of 445-463	Size = 4
		Stack = -1.5  for stack of 449-461
		Stack = -3.3  for stack of 450-460
		Stack = -2.1  for stack of 451-459
		Stack = -1.4  for stack of 452-458
	Helix total = -8.3
	Hairpin = 5.4  for closure of 453-457
	Helix total = 0.0
	Internal/bulge = 4.4  for closure of 42-435	Size = 6
		Stack = -3.4  for stack of 48-433
		Stack = -3.3  for stack of 49-432
	Helix total = -6.7
	Internal/bulge = 1.7  for closure of 50-431	Size = 1 BP stack across bulge = -2.1
		Stack = -2.1  for stack of 52-430
		Stack = -3.4  for stack of 53-429
	Helix total = -5.5
	Multiloop = 0.1  for closure of 54-428
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 413-424	Size = 2
		Stack = -2.4  for stack of 415-422
	Helix total = -2.4
	Hairpin = 3.3  for closure of 416-421
		Stack = -3.3  for stack of 390-411
	Helix total = -3.3
	Internal/bulge = 1.2  for closure of 391-410	Size = 2
		Stack = -2.1  for stack of 393-408
		Stack = -3.4  for stack of 394-407
	Helix total = -5.5
	Hairpin = 5.5  for closure of 395-406
		Stack = -2.1  for stack of 98-388
		Stack = -2.4  for stack of 99-387
	Helix total = -4.5
	Multiloop = 2.6  for closure of 100-386
		Stack = -2.4  for stack of 363-385
		Stack = -3.3  for stack of 364-384
		Stack = -2.4  for stack of 365-383
	Helix total = -8.1
	Internal/bulge = 3.7  for closure of 366-382	Size = 3
		Stack = -2.4  for stack of 367-378
		Stack = -0.9  for stack of 368-377
		Stack = -1.4  for stack of 369-376
	Helix total = -4.7
	Hairpin = 5.4  for closure of 370-375
		Stack = -3.3  for stack of 311-359
		Stack = -2.1  for stack of 312-358
	Helix total = -5.4
	Internal/bulge = 4.1  for closure of 313-357	Size = 10
		Stack = -2.2  for stack of 318-350
		Stack = -2.1  for stack of 319-349
	Helix total = -4.3
	Internal/bulge = 4.6  for closure of 320-348	Size = 4
		Stack = -1.1  for stack of 325-347
		Stack = -2.1  for stack of 326-346
		Stack = -3.3  for stack of 327-345
		Stack = -2.2  for stack of 328-344
		Stack = -1.3  for stack of 329-343
		Stack = -2.1  for stack of 330-342
		Stack = -3.3  for stack of 331-341
	Helix total = -15.4
	Hairpin = 4.7  for closure of 332-340
		Stack = -2.1  for stack of 108-309
		Stack = -2.1  for stack of 109-308
	Helix total = -4.2
	Internal/bulge = 0.8  for closure of 110-307	Size = 2
		Stack = -1.3  for stack of 112-305
	Helix total = -1.3
	Internal/bulge = 3.7  for closure of 113-304	Size = 4
		Stack = -0.9  for stack of 117-302
	Helix total = -0.9
	Internal/bulge = 3.5  for closure of 118-301	Size = 7
		Stack = -2.1  for stack of 123-297
		Stack = -2.4  for stack of 124-296
		Stack = -1.1  for stack of 125-295
		Stack = -2.1  for stack of 126-294
	Helix total = -7.7
	Multiloop = 6.2  for closure of 127-293
		Stack = -2.4  for stack of 268-290
		Stack = -2.4  for stack of 269-289
		Stack = -3.4  for stack of 270-288
	Helix total = -8.2
	Internal/bulge = 0.5  for closure of 271-287	Size = 1 BP stack across bulge = -3.3
		Stack = -2.1  for stack of 273-286
		Stack = -2.1  for stack of 274-285
		Stack = -3.4  for stack of 275-284
	Helix total = -7.6
	Hairpin = 4.6  for closure of 276-283
		Stack = -0.9  for stack of 206-258
		Stack = -1.3  for stack of 207-257
		Stack = -1.1  for stack of 208-256
		Stack = -1.3  for stack of 209-255
		Stack = -1.0  for stack of 210-254
	Helix total = -5.6
	Internal/bulge = 3.5  for closure of 211-253	Size = 14
		Stack = -1.4  for stack of 220-246
		Stack = -2.4  for stack of 221-245
		Stack = -2.1  for stack of 222-244
		Stack = -0.9  for stack of 223-243
	Helix total = -6.8
	Internal/bulge = 1.2  for closure of 224-242	Size = 2
		Stack = -3.4  for stack of 226-240
		Stack = -2.4  for stack of 227-239
		Stack = -1.5  for stack of 228-238
		Stack = -2.1  for stack of 229-237
		Stack = -3.4  for stack of 230-236
	Helix total = -12.8
	Hairpin = 5.4  for closure of 231-235
		Stack = -1.1  for stack of 180-201
		Stack = -2.4  for stack of 181-200
		Stack = -3.3  for stack of 182-199
		Stack = -3.3  for stack of 183-198
	Helix total = -10.1
	Internal/bulge = -0.2  for closure of 184-197	Size = 4
		Stack = -2.1  for stack of 187-194
	Helix total = -2.1
	Hairpin = 5.4  for closure of 188-193
	Helix total = 0.0
	Internal/bulge = -0.1  for closure of 138-173	Size = 2
		Stack = -2.4  for stack of 140-171
	Helix total = -2.4
	Internal/bulge = 2.2  for closure of 141-170	Size = 11
	Helix total = 0.0
	Internal/bulge = 0.2  for closure of 147-163	Size = 4
		Stack = -1.3  for stack of 150-160
		Stack = -2.1  for stack of 151-159
	Helix total = -3.4
	Hairpin = 4.1  for closure of 152-158
		Stack = -2.5  for stack of 57-91
	Helix total = -2.5
	Internal/bulge = 4.2  for closure of 58-90	Size = 3
		Stack = -2.1  for stack of 62-89
		Stack = -2.2  for stack of 63-88
	Helix total = -4.3
	Hairpin = 6.8  for closure of 64-87
		Stack = -2.1  for stack of 4-20
		Stack = -2.1  for stack of 5-19
		Stack = -3.3  for stack of 6-18
		Stack = -2.5  for stack of 7-17
	Helix total = -10.0
	Hairpin = 5.1  for closure of 8-16


	Total energy = -77.4



