Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    399:471 400:470 401:469 402:468 403:467
	Energy of Broken Structure: -128.6
	Energy of Pseudo-Helices:   5600.0
	Pseudoknot Energy Penalty:  8.0
	Total Free Energy:          5479.4
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 2-482
		Stack = -2.4  for stack of 3-481
		Stack = -2.2  for stack of 4-480
	Helix total = -7.9
	Internal/bulge = 1.7  for closure of 5-479	Size = 1 BP stack across bulge = -2.1
		Stack = -0.9  for stack of 7-478
		Stack = -2.2  for stack of 8-477
		Stack = -2.4  for stack of 9-476
		Stack = -3.4  for stack of 10-475
		Stack = -2.1  for stack of 11-474
	Helix total = -11.0
	Multiloop = 1.5  for closure of 12-473
		Stack = -2.1  for stack of 437-466
		Stack = -2.4  for stack of 438-465
		Stack = -2.1  for stack of 439-464
		Stack = -2.1  for stack of 440-463
		Stack = -2.2  for stack of 441-462
		Stack = -1.0  for stack of 442-461
	Helix total = -11.9
	Hairpin = 6.9  for closure of 443-460
		Stack = -0.9  for stack of 387-422
		Stack = -1.3  for stack of 388-421
		Stack = -1.5  for stack of 389-420
		Stack = -2.1  for stack of 390-419
		Stack = -2.4  for stack of 391-418
		Stack = -2.1  for stack of 392-417
		Stack = -2.1  for stack of 393-416
		Stack = -2.4  for stack of 394-415
	Helix total = -14.8
	Hairpin = 5.9  for closure of 395-414
		Stack = -3.4  for stack of 355-385
		Stack = -2.1  for stack of 356-384
		Stack = -2.1  for stack of 357-383
	Helix total = -7.6
	Internal/bulge = 1.2  for closure of 358-382	Size = 11
		Stack = -1.5  for stack of 365-376
		Stack = -2.5  for stack of 366-375
		Stack = -3.3  for stack of 367-374
	Helix total = -7.3
	Hairpin = 4.6  for closure of 368-373
		Stack = -3.4  for stack of 14-352
		Stack = -2.4  for stack of 15-351
		Stack = -3.3  for stack of 16-350
		Stack = -3.4  for stack of 17-349
		Stack = -2.1  for stack of 18-348
	Helix total = -14.6
	Internal/bulge = 2.3  for closure of 19-347	Size = 1 BP stack across bulge = -1.1
		Stack = -2.1  for stack of 20-345
		Stack = -3.4  for stack of 21-344
	Helix total = -5.5
	Multiloop = 7.0  for closure of 22-343
		Stack = -1.3  for stack of 317-342
		Stack = -1.5  for stack of 318-341
		Stack = -2.4  for stack of 319-340
	Helix total = -5.2
	Internal/bulge = 3.0  for closure of 320-339	Size = 4
		Stack = 0.3  for stack of 324-337
		Stack = -2.1  for stack of 325-336
		Stack = -3.3  for stack of 326-335
		Stack = -3.4  for stack of 327-334
	Helix total = -8.5
	Hairpin = 3.3  for closure of 328-333
		Stack = -2.1  for stack of 27-308
		Stack = -2.2  for stack of 28-307
	Helix total = -4.3
	Internal/bulge = 1.7  for closure of 29-306	Size = 1 BP stack across bulge = -2.1
		Stack = -2.1  for stack of 31-305
		Stack = -3.4  for stack of 32-304
	Helix total = -5.5
	Multiloop = 1.4  for closure of 33-303
		Stack = -2.1  for stack of 288-299
		Stack = -2.4  for stack of 289-298
		Stack = -3.3  for stack of 290-297
	Helix total = -7.8
	Hairpin = 2.8  for closure of 291-296
		Stack = -2.1  for stack of 265-286
		Stack = -2.1  for stack of 266-285
		Stack = -3.3  for stack of 267-284
		Stack = -3.3  for stack of 268-283
	Helix total = -10.8
	Internal/bulge = 0.5  for closure of 269-282	Size = 2
	Helix total = 0.0
	Hairpin = 4.1  for closure of 271-280
		Stack = -2.2  for stack of 73-263
		Stack = -2.1  for stack of 74-262
	Helix total = -4.3
	Multiloop = 4.4  for closure of 75-261
		Stack = -3.4  for stack of 238-260
		Stack = -2.1  for stack of 239-259
		Stack = -2.1  for stack of 240-258
	Helix total = -7.6
	Internal/bulge = 3.7  for closure of 241-257	Size = 3
		Stack = -1.4  for stack of 242-253
		Stack = -2.4  for stack of 243-252
		Stack = -2.1  for stack of 244-251
	Helix total = -5.9
	Hairpin = 4.7  for closure of 245-250
		Stack = -2.1  for stack of 189-235
		Stack = -2.1  for stack of 190-234
		Stack = -2.4  for stack of 191-233
		Stack = -1.1  for stack of 192-232
		Stack = -1.3  for stack of 193-231
	Helix total = -9.0
	Internal/bulge = 3.0  for closure of 194-230	Size = 4
		Stack = -3.4  for stack of 196-226
		Stack = -2.1  for stack of 197-225
	Helix total = -5.5
	Internal/bulge = 3.8  for closure of 198-224	Size = 2
		Stack = -0.9  for stack of 201-223
		Stack = -2.1  for stack of 202-222
		Stack = -3.3  for stack of 203-221
		Stack = -2.2  for stack of 204-220
		Stack = -1.0  for stack of 205-219
		Stack = -2.1  for stack of 206-218
		Stack = -3.3  for stack of 207-217
	Helix total = -14.9
	Hairpin = 3.8  for closure of 208-216
		Stack = -2.5  for stack of 82-188
		Stack = -2.4  for stack of 83-187
		Stack = -2.5  for stack of 84-186
		Stack = -1.0  for stack of 85-185
		Stack = -0.9  for stack of 86-184
		Stack = -2.1  for stack of 87-183
	Helix total = -11.4
	Internal/bulge = 1.1  for closure of 88-182	Size = 3
		Stack = -3.3  for stack of 91-180
	Helix total = -3.3
	Internal/bulge = 2.6  for closure of 92-179	Size = 5
		Stack = -2.1  for stack of 96-176
		Stack = -1.3  for stack of 97-175
		Stack = -1.1  for stack of 98-174
		Stack = -2.4  for stack of 99-173
		Stack = -2.4  for stack of 100-172
		Stack = -3.3  for stack of 101-171
	Helix total = -12.6
	Multiloop = 3.5  for closure of 102-170
		Stack = -3.3  for stack of 158-168
		Stack = -2.2  for stack of 159-167
	Helix total = -5.5
	Hairpin = 4.2  for closure of 160-166
		Stack = -2.5  for stack of 144-153
		Stack = -2.1  for stack of 145-152
	Helix total = -4.6
	Hairpin = 4.1  for closure of 146-151
		Stack = -3.3  for stack of 104-138
		Stack = -3.3  for stack of 105-137
		Stack = -3.3  for stack of 106-136
	Helix total = -9.9
	Internal/bulge = 1.2  for closure of 107-135	Size = 2
		Stack = -1.1  for stack of 109-133
	Helix total = -1.1
	Internal/bulge = 3.3  for closure of 110-132	Size = 5
		Stack = -2.1  for stack of 113-128
		Stack = -0.6  for stack of 114-127
		Stack = 1.3  for stack of 115-126
		Stack = 0.3  for stack of 116-125
		Stack = -2.1  for stack of 117-124
	Helix total = -3.2
	Hairpin = 3.1  for closure of 118-123
		Stack = -2.2  for stack of 41-63
	Helix total = -2.2
	Internal/bulge = 1.2  for closure of 42-62	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.2  for closure of 44-60	Size = 1 BP stack across bulge = -0.6
		Stack = -2.5  for stack of 45-58
		Stack = -2.1  for stack of 46-57
		Stack = -0.9  for stack of 47-56
		Stack = -0.9  for stack of 48-55
	Helix total = -6.4
	Hairpin = 4.4  for closure of 49-54


	Total energy = -128.6



