Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    460:481 461:480 462:479
	Energy of Broken Structure: -116.8
	Energy of Pseudo-Helices:   -6.7
	Pseudoknot Energy Penalty:  6.9
	Total Free Energy:          -116.6
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -3.7
		Stack = -3.3  for stack of 28-511
		Stack = -2.4  for stack of 29-510
		Stack = -1.1  for stack of 30-509
	Helix total = -6.8
	Internal/bulge = 2.5  for closure of 31-508	Size = 1 BP stack across bulge = -1.3
		Stack = -0.9  for stack of 33-507
		Stack = -2.2  for stack of 34-506
		Stack = -2.4  for stack of 35-505
		Stack = -3.4  for stack of 36-504
		Stack = -2.1  for stack of 37-503
	Helix total = -11.0
	Multiloop = 2.2  for closure of 38-502
		Stack = -3.4  for stack of 455-500
		Stack = -2.1  for stack of 456-499
		Stack = -1.1  for stack of 457-498
		Stack = -2.4  for stack of 458-497
	Helix total = -9.0
	Internal/bulge = 4.4  for closure of 459-496	Size = 6
		Stack = -2.1  for stack of 466-495
		Stack = -2.4  for stack of 467-494
		Stack = -2.1  for stack of 468-493
		Stack = -2.1  for stack of 469-492
	Helix total = -8.7
	Hairpin = 6.1  for closure of 470-491
		Stack = -2.4  for stack of 420-447
		Stack = -2.1  for stack of 421-446
		Stack = -2.1  for stack of 422-445
		Stack = -2.4  for stack of 423-444
	Helix total = -9.0
	Internal/bulge = 1.4  for closure of 424-443	Size = 7
	Helix total = 0.0
	Hairpin = 5.3  for closure of 428-438
		Stack = -3.3  for stack of 384-414
		Stack = -2.4  for stack of 385-413
		Stack = -2.1  for stack of 386-412
	Helix total = -7.8
	Internal/bulge = 1.2  for closure of 387-411	Size = 11
		Stack = -1.5  for stack of 394-405
		Stack = -2.5  for stack of 395-404
		Stack = -2.1  for stack of 396-403
	Helix total = -6.1
	Hairpin = 5.4  for closure of 397-402
		Stack = -3.4  for stack of 40-381
		Stack = -2.4  for stack of 41-380
		Stack = -3.3  for stack of 42-379
		Stack = -3.4  for stack of 43-378
		Stack = -2.1  for stack of 44-377
	Helix total = -14.6
	Internal/bulge = 2.3  for closure of 45-376	Size = 1 BP stack across bulge = -1.1
		Stack = -2.1  for stack of 46-374
	Helix total = -2.1
	Multiloop = 5.2  for closure of 47-373
	Helix total = 0.0
	Internal/bulge = 0.6  for closure of 346-371	Size = 1 BP stack across bulge = -2.4
		Stack = -3.3  for stack of 348-370
		Stack = -2.4  for stack of 349-369
	Helix total = -5.7
	Internal/bulge = 3.0  for closure of 350-368	Size = 4
		Stack = 0.3  for stack of 354-366
	Helix total = 0.3
	Hairpin = 5.3  for closure of 355-365
	Helix total = 0.0
	Internal/bulge = 3.8  for closure of 48-340	Size = 5
		Stack = -2.1  for stack of 53-338
		Stack = -2.2  for stack of 54-337
	Helix total = -4.3
	Internal/bulge = 1.7  for closure of 55-336	Size = 1 BP stack across bulge = -2.1
		Stack = -2.1  for stack of 57-335
		Stack = -3.4  for stack of 58-334
	Helix total = -5.5
	Multiloop = -0.3  for closure of 59-333
		Stack = -2.1  for stack of 318-329
		Stack = -2.4  for stack of 319-328
		Stack = -2.1  for stack of 320-327
	Helix total = -6.6
	Hairpin = 5.4  for closure of 321-326
		Stack = -2.1  for stack of 295-316
		Stack = -2.1  for stack of 296-315
		Stack = -3.3  for stack of 297-314
		Stack = -3.3  for stack of 298-313
	Helix total = -10.8
	Hairpin = 5.4  for closure of 299-312
		Stack = -2.2  for stack of 105-293
		Stack = -2.1  for stack of 106-292
	Helix total = -4.3
	Multiloop = 4.4  for closure of 107-291
		Stack = -3.4  for stack of 268-290
		Stack = -2.1  for stack of 269-289
		Stack = -2.1  for stack of 270-288
	Helix total = -7.6
	Internal/bulge = 3.7  for closure of 271-287	Size = 3
		Stack = -1.4  for stack of 272-283
		Stack = -2.4  for stack of 273-282
		Stack = -2.1  for stack of 274-281
	Helix total = -5.9
	Hairpin = 4.7  for closure of 275-280
		Stack = -2.1  for stack of 219-265
		Stack = -2.1  for stack of 220-264
	Helix total = -4.2
	Internal/bulge = 2.7  for closure of 221-263	Size = 10
		Stack = -3.4  for stack of 226-256
		Stack = -2.1  for stack of 227-255
	Helix total = -5.5
	Internal/bulge = 3.8  for closure of 228-254	Size = 2
		Stack = -0.9  for stack of 231-253
		Stack = -2.1  for stack of 232-252
		Stack = -3.3  for stack of 233-251
		Stack = -2.2  for stack of 234-250
		Stack = -1.0  for stack of 235-249
		Stack = -1.3  for stack of 236-248
		Stack = -2.1  for stack of 237-247
	Helix total = -12.9
	Hairpin = 3.8  for closure of 238-246
		Stack = -2.5  for stack of 114-218
		Stack = -2.4  for stack of 115-217
		Stack = -2.5  for stack of 116-216
		Stack = -1.0  for stack of 117-215
		Stack = -0.9  for stack of 118-214
		Stack = -2.1  for stack of 119-213
	Helix total = -11.4
	Internal/bulge = 1.1  for closure of 120-212	Size = 3
		Stack = -3.3  for stack of 123-210
	Helix total = -3.3
	Internal/bulge = 2.6  for closure of 124-209	Size = 5
		Stack = -3.3  for stack of 128-206
		Stack = -2.1  for stack of 129-205
		Stack = -0.9  for stack of 130-204
		Stack = -1.0  for stack of 131-203
		Stack = -2.1  for stack of 132-202
		Stack = -3.3  for stack of 133-201
	Helix total = -12.7
	Multiloop = 1.4  for closure of 134-200
		Stack = -3.3  for stack of 189-198
		Stack = -2.4  for stack of 190-197
	Helix total = -5.7
	Hairpin = 4.4  for closure of 191-196
		Stack = -3.4  for stack of 175-184
		Stack = -2.1  for stack of 176-183
	Helix total = -5.5
	Hairpin = 4.1  for closure of 177-182
		Stack = -3.3  for stack of 136-170
		Stack = -3.3  for stack of 137-169
		Stack = -3.3  for stack of 138-168
	Helix total = -9.9
	Internal/bulge = 2.2  for closure of 139-167	Size = 11
		Stack = -2.1  for stack of 145-160
		Stack = -0.6  for stack of 146-159
		Stack = -2.5  for stack of 147-158
		Stack = -2.1  for stack of 148-157
		Stack = -1.4  for stack of 149-156
	Helix total = -8.7
	Hairpin = 3.1  for closure of 150-155
		Stack = -2.5  for stack of 62-98
		Stack = -1.5  for stack of 63-97
	Helix total = -4.0
	Internal/bulge = 3.3  for closure of 64-96	Size = 2
		Stack = -2.2  for stack of 67-95
	Helix total = -2.2
	Internal/bulge = 0.5  for closure of 68-94	Size = 2
		Stack = -3.3  for stack of 70-92
		Stack = -2.4  for stack of 71-91
		Stack = -0.9  for stack of 72-90
		Stack = -0.6  for stack of 73-89
	Helix total = -7.2
	Internal/bulge = -0.7  for closure of 74-88	Size = 2
		Stack = -1.4  for stack of 76-86
		Stack = -1.5  for stack of 77-85
	Helix total = -2.9
	Hairpin = 4.9  for closure of 78-84
		Stack = -2.4  for stack of 10-26
		Stack = -2.1  for stack of 11-25
		Stack = -2.5  for stack of 12-24
		Stack = -0.5  for stack of 13-23
	Helix total = -7.5
	Hairpin = 5.1  for closure of 14-22


	Total energy = -116.8



