Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    482:503 483:502 484:501
	Energy of Broken Structure: -146.0
	Energy of Pseudo-Helices:   -6.7
	Pseudoknot Energy Penalty:  6.9
	Total Free Energy:          -145.8
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -3.7
		Stack = -2.4  for stack of 27-533
		Stack = -0.9  for stack of 28-532
		Stack = -1.1  for stack of 29-531
	Helix total = -4.4
	Internal/bulge = 2.5  for closure of 30-530	Size = 1 BP stack across bulge = -1.3
		Stack = -0.9  for stack of 32-529
		Stack = -2.2  for stack of 33-528
		Stack = -2.4  for stack of 34-527
		Stack = -2.2  for stack of 35-526
		Stack = -0.9  for stack of 36-525
	Helix total = -8.6
	Multiloop = 2.4  for closure of 37-524
		Stack = -3.3  for stack of 477-522
		Stack = -3.3  for stack of 478-521
		Stack = -3.4  for stack of 479-520
		Stack = -3.3  for stack of 480-519
	Helix total = -13.3
	Internal/bulge = 4.9  for closure of 481-518	Size = 6
		Stack = -2.4  for stack of 488-517
		Stack = -2.1  for stack of 489-516
		Stack = -2.4  for stack of 490-515
		Stack = -2.4  for stack of 491-514
	Helix total = -9.3
	Hairpin = 6.1  for closure of 492-513
		Stack = -1.3  for stack of 421-469
		Stack = -2.1  for stack of 422-468
		Stack = -3.3  for stack of 423-467
	Helix total = -6.7
	Internal/bulge = 0.7  for closure of 424-466	Size = 8
	Helix total = 0.0
	Internal/bulge = 2.3  for closure of 429-461	Size = 9
		Stack = -2.5  for stack of 434-455
		Stack = -2.1  for stack of 435-454
		Stack = -1.3  for stack of 436-453
		Stack = -2.1  for stack of 437-452
		Stack = -1.5  for stack of 438-451
		Stack = -2.1  for stack of 439-450
		Stack = -3.3  for stack of 440-449
	Helix total = -14.9
	Hairpin = 3.9  for closure of 441-448
		Stack = -3.4  for stack of 385-415
		Stack = -2.4  for stack of 386-414
		Stack = -3.3  for stack of 387-413
	Helix total = -9.1
	Internal/bulge = 1.9  for closure of 388-412	Size = 11
		Stack = -0.5  for stack of 395-406
		Stack = -2.5  for stack of 396-405
		Stack = -3.3  for stack of 397-404
	Helix total = -6.3
	Hairpin = 3.7  for closure of 398-403
		Stack = -3.4  for stack of 39-382
		Stack = -2.4  for stack of 40-381
		Stack = -3.3  for stack of 41-380
		Stack = -3.4  for stack of 42-379
		Stack = -2.1  for stack of 43-378
	Helix total = -14.6
	Internal/bulge = 2.4  for closure of 44-377	Size = 1 BP stack across bulge = -1.4
		Stack = -1.4  for stack of 45-375
	Helix total = -1.4
	Multiloop = 5.0  for closure of 46-374
	Helix total = 0.0
	Internal/bulge = 1.0  for closure of 346-372	Size = 1 BP stack across bulge = -2.4
		Stack = -2.4  for stack of 348-371
		Stack = -3.3  for stack of 349-370
	Helix total = -5.7
	Internal/bulge = 3.0  for closure of 350-369	Size = 4
		Stack = 0.3  for stack of 354-367
		Stack = -2.1  for stack of 355-366
		Stack = -3.3  for stack of 356-365
		Stack = -3.4  for stack of 357-364
	Helix total = -8.5
	Hairpin = 3.3  for closure of 358-363
		Stack = -1.5  for stack of 52-338
		Stack = -2.5  for stack of 53-337
	Helix total = -4.0
	Internal/bulge = 1.7  for closure of 54-336	Size = 1 BP stack across bulge = -2.1
		Stack = -2.1  for stack of 56-335
		Stack = -3.4  for stack of 57-334
	Helix total = -5.5
	Multiloop = -0.3  for closure of 58-333
		Stack = -2.1  for stack of 318-329
		Stack = -2.2  for stack of 319-328
		Stack = -3.3  for stack of 320-327
	Helix total = -7.6
	Hairpin = 2.8  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 = -2.4  for stack of 103-293
		Stack = -2.1  for stack of 104-292
	Helix total = -4.5
	Multiloop = 5.1  for closure of 105-291
		Stack = -2.1  for stack of 268-290
		Stack = -3.3  for stack of 269-289
		Stack = -3.3  for stack of 270-288
	Helix total = -8.7
	Internal/bulge = 3.7  for closure of 271-287	Size = 3
		Stack = -1.4  for stack of 272-283
		Stack = -2.1  for stack of 273-282
		Stack = -2.5  for stack of 274-281
	Helix total = -6.0
	Hairpin = 4.7  for closure of 275-280
		Stack = -2.4  for stack of 219-265
		Stack = -2.5  for stack of 220-264
	Helix total = -4.9
	Internal/bulge = 4.4  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 = -1.3  for stack of 235-249
		Stack = -2.1  for stack of 236-248
		Stack = -3.3  for stack of 237-247
	Helix total = -15.2
	Hairpin = 3.8  for closure of 238-246
		Stack = -2.2  for stack of 112-218
		Stack = -2.4  for stack of 113-217
		Stack = -2.2  for stack of 114-216
		Stack = -1.3  for stack of 115-215
		Stack = -2.1  for stack of 116-214
		Stack = -3.3  for stack of 117-213
	Helix total = -13.5
	Internal/bulge = 1.1  for closure of 118-212	Size = 3
		Stack = -3.3  for stack of 121-210
	Helix total = -3.3
	Internal/bulge = 2.6  for closure of 122-209	Size = 5
		Stack = -2.1  for stack of 126-206
		Stack = -0.9  for stack of 127-205
		Stack = -2.4  for stack of 128-204
		Stack = -1.4  for stack of 129-203
		Stack = -2.1  for stack of 130-202
		Stack = -3.3  for stack of 131-201
	Helix total = -12.2
	Multiloop = 2.6  for closure of 132-200
		Stack = -3.3  for stack of 188-198
	Helix total = -3.3
	Hairpin = 4.4  for closure of 189-197
		Stack = -2.2  for stack of 174-183
		Stack = -0.9  for stack of 175-182
	Helix total = -3.1
	Hairpin = 5.4  for closure of 176-181
		Stack = -2.1  for stack of 134-168
		Stack = -2.1  for stack of 135-167
		Stack = -3.3  for stack of 136-166
	Helix total = -7.5
	Internal/bulge = 1.2  for closure of 137-165	Size = 11
		Stack = -2.4  for stack of 143-158
		Stack = -3.3  for stack of 144-157
		Stack = -3.4  for stack of 145-156
		Stack = -1.4  for stack of 146-155
		Stack = -2.1  for stack of 147-154
	Helix total = -12.6
	Hairpin = 3.1  for closure of 148-153
		Stack = -2.5  for stack of 61-96
		Stack = -1.5  for stack of 62-95
	Helix total = -4.0
	Internal/bulge = 2.8  for closure of 63-94	Size = 2
		Stack = -3.4  for stack of 66-93
	Helix total = -3.4
	Internal/bulge = -0.1  for closure of 67-92	Size = 2
	Helix total = 0.0
	Internal/bulge = 0.5  for closure of 69-90	Size = 4
		Stack = -1.0  for stack of 72-87
		Stack = -1.1  for stack of 73-86
		Stack = -2.1  for stack of 74-85
		Stack = -2.2  for stack of 75-84
		Stack = -1.3  for stack of 76-83
	Helix total = -7.7
	Hairpin = 4.4  for closure of 77-82
		Stack = -2.4  for stack of 9-25
		Stack = -2.1  for stack of 10-24
		Stack = -2.5  for stack of 11-23
		Stack = -0.5  for stack of 12-22
	Helix total = -7.5
	Hairpin = 5.1  for closure of 13-21


	Total energy = -146.0



