Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    552:573 553:572 554:571
	Energy of Broken Structure: -63.5
	Energy of Pseudo-Helices:   -6.7
	Pseudoknot Energy Penalty:  7.2
	Total Free Energy:          -63.0
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -2.8
		Stack = -0.6  for stack of 22-603
		Stack = -1.4  for stack of 23-602
	Helix total = -2.0
	Internal/bulge = 2.5  for closure of 24-601	Size = 1 BP stack across bulge = -1.3
		Stack = -1.1  for stack of 26-600
		Stack = -1.3  for stack of 27-599
		Stack = -1.4  for stack of 28-598
		Stack = -1.4  for stack of 29-597
		Stack = -3.4  for stack of 30-596
		Stack = -2.1  for stack of 31-595
	Helix total = -10.7
	Multiloop = 3.6  for closure of 32-594
		Stack = -0.9  for stack of 546-592
		Stack = -2.1  for stack of 547-591
		Stack = -3.3  for stack of 548-590
		Stack = -2.4  for stack of 549-589
		Stack = -2.1  for stack of 550-588
	Helix total = -10.8
	Internal/bulge = 4.6  for closure of 551-587	Size = 7
		Stack = -2.1  for stack of 559-586
		Stack = -2.1  for stack of 560-585
		Stack = -3.3  for stack of 561-584
	Helix total = -7.5
	Hairpin = 5.6  for closure of 562-583
		Stack = -2.2  for stack of 516-536
	Helix total = -2.2
	Hairpin = 6.6  for closure of 517-535
		Stack = -1.4  for stack of 479-509
		Stack = -1.3  for stack of 480-508
	Helix total = -2.7
	Internal/bulge = 2.3  for closure of 481-507	Size = 1 BP stack across bulge = -1.1
		Stack = -1.3  for stack of 482-505
		Stack = -2.2  for stack of 483-504
		Stack = -2.1  for stack of 484-503
		Stack = -0.6  for stack of 485-502
		Stack = -2.1  for stack of 486-501
		Stack = -1.5  for stack of 487-500
		Stack = -2.5  for stack of 488-499
		Stack = -3.3  for stack of 489-498
		Stack = -3.3  for stack of 490-497
	Helix total = -18.9
	Hairpin = 4.1  for closure of 491-496
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 35-473	Size = 2
	Helix total = 0.0
	Multiloop = 7.2  for closure of 37-471
	Helix total = 0.0
	Internal/bulge = 2.1  for closure of 439-464	Size = 1 BP stack across bulge = -1.3
		Stack = -2.2  for stack of 441-463
		Stack = -3.3  for stack of 442-462
	Helix total = -5.5
	Internal/bulge = 3.0  for closure of 443-461	Size = 4
		Stack = -1.5  for stack of 447-459
		Stack = -3.3  for stack of 448-458
		Stack = -2.1  for stack of 449-457
	Helix total = -6.9
	Hairpin = 5.4  for closure of 450-456
	Helix total = 0.0
	Internal/bulge = 4.4  for closure of 42-433	Size = 6
		Stack = -3.4  for stack of 48-431
		Stack = -3.3  for stack of 49-430
	Helix total = -6.7
	Internal/bulge = 1.7  for closure of 50-429	Size = 1 BP stack across bulge = -2.1
		Stack = -2.1  for stack of 52-428
		Stack = -3.4  for stack of 53-427
	Helix total = -5.5
	Multiloop = 0.1  for closure of 54-426
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 411-422	Size = 2
		Stack = -2.4  for stack of 413-420
	Helix total = -2.4
	Hairpin = 3.3  for closure of 414-419
		Stack = -3.3  for stack of 388-409
	Helix total = -3.3
	Internal/bulge = 1.2  for closure of 389-408	Size = 2
		Stack = -2.1  for stack of 391-406
		Stack = -3.4  for stack of 392-405
	Helix total = -5.5
	Hairpin = 5.5  for closure of 393-404
		Stack = -2.1  for stack of 97-386
		Stack = -2.4  for stack of 98-385
	Helix total = -4.5
	Multiloop = 2.6  for closure of 99-384
		Stack = -2.4  for stack of 361-383
		Stack = -3.3  for stack of 362-382
		Stack = -1.5  for stack of 363-381
	Helix total = -7.2
	Internal/bulge = 3.7  for closure of 364-380	Size = 3
		Stack = -2.4  for stack of 365-376
		Stack = -0.9  for stack of 366-375
		Stack = -1.4  for stack of 367-374
	Helix total = -4.7
	Hairpin = 5.0  for closure of 368-373
		Stack = -3.3  for stack of 309-357
		Stack = -2.1  for stack of 310-356
	Helix total = -5.4
	Internal/bulge = 5.1  for closure of 311-355	Size = 10
		Stack = -2.2  for stack of 316-348
		Stack = -2.1  for stack of 317-347
	Helix total = -4.3
	Internal/bulge = 4.6  for closure of 318-346	Size = 4
		Stack = -1.1  for stack of 323-345
		Stack = -2.1  for stack of 324-344
		Stack = -3.3  for stack of 325-343
		Stack = -2.2  for stack of 326-342
		Stack = -1.3  for stack of 327-341
		Stack = -2.1  for stack of 328-340
		Stack = -3.3  for stack of 329-339
	Helix total = -15.4
	Hairpin = 4.7  for closure of 330-338
		Stack = -2.1  for stack of 107-307
		Stack = -2.1  for stack of 108-306
	Helix total = -4.2
	Internal/bulge = 0.3  for closure of 109-305	Size = 4
	Helix total = 0.0
	Internal/bulge = 3.7  for closure of 112-302	Size = 4
		Stack = -0.9  for stack of 116-300
	Helix total = -0.9
	Internal/bulge = 3.5  for closure of 117-299	Size = 7
		Stack = -2.1  for stack of 122-295
		Stack = -2.4  for stack of 123-294
	Helix total = -4.5
	Multiloop = 7.5  for closure of 124-293
		Stack = -2.4  for stack of 267-288
		Stack = -2.4  for stack of 268-287
		Stack = -3.4  for stack of 269-286
	Helix total = -8.2
	Internal/bulge = 1.7  for closure of 270-285	Size = 1 BP stack across bulge = -2.1
		Stack = 0.3  for stack of 272-284
		Stack = -2.1  for stack of 273-283
		Stack = -3.4  for stack of 274-282
	Helix total = -5.2
	Hairpin = 4.9  for closure of 275-281
		Stack = -0.9  for stack of 208-257
		Stack = -1.3  for stack of 209-256
		Stack = -1.1  for stack of 210-255
		Stack = -0.9  for stack of 211-254
		Stack = -1.3  for stack of 212-253
	Helix total = -5.5
	Internal/bulge = 3.5  for closure of 213-252	Size = 14
		Stack = -1.1  for stack of 222-245
		Stack = -2.4  for stack of 223-244
		Stack = -2.1  for stack of 224-243
		Stack = -0.9  for stack of 225-242
	Helix total = -6.5
	Internal/bulge = 3.0  for closure of 226-241	Size = 4
		Stack = -2.2  for stack of 228-237
		Stack = -2.4  for stack of 229-236
	Helix total = -4.6
	Hairpin = 3.7  for closure of 230-235
		Stack = -1.1  for stack of 182-203
		Stack = -2.4  for stack of 183-202
		Stack = -2.1  for stack of 184-201
		Stack = -2.4  for stack of 185-200
	Helix total = -8.0
	Internal/bulge = -0.2  for closure of 186-199	Size = 4
		Stack = -3.3  for stack of 189-196
	Helix total = -3.3
	Hairpin = 4.8  for closure of 190-195
		Stack = -2.1  for stack of 139-175
		Stack = -1.1  for stack of 140-174
		Stack = -2.1  for stack of 141-173
	Helix total = -5.3
	Internal/bulge = 1.7  for closure of 142-172	Size = 12
		Stack = -2.1  for stack of 149-165
	Helix total = -2.1
	Internal/bulge = -0.7  for closure of 150-164	Size = 2
		Stack = -1.0  for stack of 152-162
		Stack = -2.1  for stack of 153-161
	Helix total = -3.1
	Hairpin = 4.1  for closure of 154-160
		Stack = -2.5  for stack of 57-90
	Helix total = -2.5
	Internal/bulge = 4.2  for closure of 58-89	Size = 3
		Stack = -2.1  for stack of 62-88
		Stack = -2.2  for stack of 63-87
	Helix total = -4.3
	Hairpin = 6.8  for closure of 64-86
		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 = -63.5



