Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    93:169 94:168 95:167 96:166 97:165 98:164 99:162 100:161
	    101:160
	Energy of Broken Structure: -139.1
	Energy of Pseudo-Helices:   -14.0
	Pseudoknot Energy Penalty:  9.0
	Total Free Energy:          -144.1
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -4.1
		Stack = -2.4  for stack of 360-418
		Stack = -2.1  for stack of 361-417
		Stack = -3.4  for stack of 362-416
	Helix total = -7.9
	Internal/bulge = 0.0  for closure of 363-415	Size = 4
		Stack = -2.2  for stack of 366-412
		Stack = -2.4  for stack of 367-411
		Stack = -3.3  for stack of 368-410
		Stack = -2.1  for stack of 369-409
	Helix total = -10.0
	Internal/bulge = 5.8  for closure of 370-408	Size = 7
		Stack = -2.2  for stack of 377-406
		Stack = -2.1  for stack of 378-405
		Stack = -3.4  for stack of 379-404
		Stack = -2.1  for stack of 380-403
		Stack = -2.2  for stack of 381-402
	Helix total = -12.0
	Internal/bulge = 1.0  for closure of 382-401	Size = 4
		Stack = -3.3  for stack of 385-398
		Stack = -3.3  for stack of 386-397
	Helix total = -6.6
	Hairpin = 3.4  for closure of 387-396
		Stack = -3.3  for stack of 195-349
		Stack = -2.1  for stack of 196-348
		Stack = -2.1  for stack of 197-347
		Stack = -3.4  for stack of 198-346
		Stack = -2.4  for stack of 199-345
		Stack = -3.3  for stack of 200-344
	Helix total = -16.6
	Internal/bulge = 6.1  for closure of 201-343	Size = 17
	Helix total = 0.0
	Internal/bulge = -0.6  for closure of 208-331	Size = 2
	Helix total = 0.0
	Internal/bulge = 0.5  for closure of 210-329	Size = 1 BP stack across bulge = -3.3
	Helix total = 0.0
	Internal/bulge = 0.8  for closure of 211-327	Size = 3
		Stack = -3.3  for stack of 213-324
		Stack = -2.4  for stack of 214-323
	Helix total = -5.7
	Internal/bulge = 2.8  for closure of 215-322	Size = 2
		Stack = -3.4  for stack of 216-319
		Stack = -3.3  for stack of 217-318
		Stack = -3.3  for stack of 218-317
		Stack = -3.3  for stack of 219-316
		Stack = -3.3  for stack of 220-315
		Stack = -2.4  for stack of 221-314
	Helix total = -19.0
	Internal/bulge = 3.5  for closure of 222-313	Size = 8
		Stack = -3.3  for stack of 226-307
		Stack = -3.3  for stack of 227-306
		Stack = -2.4  for stack of 228-305
		Stack = -3.4  for stack of 229-304
	Helix total = -12.4
	Multiloop = 5.9  for closure of 230-303
		Stack = -2.1  for stack of 283-295
		Stack = -2.4  for stack of 284-294
		Stack = -2.1  for stack of 285-293
	Helix total = -6.6
	Hairpin = 4.1  for closure of 286-292
		Stack = -2.4  for stack of 237-281
		Stack = -3.4  for stack of 238-280
		Stack = -2.4  for stack of 239-279
		Stack = -3.3  for stack of 240-278
	Helix total = -11.5
	Internal/bulge = -0.9  for closure of 241-277	Size = 1 BP stack across bulge = -3.4
		Stack = -2.4  for stack of 243-276
		Stack = -3.3  for stack of 244-275
		Stack = -3.4  for stack of 245-274
	Helix total = -9.1
	Internal/bulge = 1.9  for closure of 246-273	Size = 5
		Stack = -3.3  for stack of 249-269
		Stack = -3.3  for stack of 250-268
	Helix total = -6.6
	Hairpin = 4.7  for closure of 251-267
	Helix total = 0.0
	Internal/bulge = 1.0  for closure of 6-191	Size = 1 BP stack across bulge = -2.4
		Stack = -3.3  for stack of 7-189
		Stack = -3.3  for stack of 8-188
		Stack = -2.4  for stack of 9-187
		Stack = -2.1  for stack of 10-186
		Stack = -3.3  for stack of 11-185
		Stack = -3.3  for stack of 12-184
		Stack = -3.3  for stack of 13-183
		Stack = -2.5  for stack of 14-182
		Stack = -1.4  for stack of 15-181
		Stack = -3.3  for stack of 16-180
	Helix total = -28.2
	Internal/bulge = 2.3  for closure of 17-179	Size = 4
		Stack = -3.3  for stack of 19-175
		Stack = -2.5  for stack of 20-174
		Stack = -1.5  for stack of 21-173
	Helix total = -7.3
	Internal/bulge = 5.9  for closure of 22-172	Size = 67
		Stack = -2.4  for stack of 50-131
		Stack = -2.2  for stack of 51-130
		Stack = -2.4  for stack of 52-129
	Helix total = -7.0
	Internal/bulge = 0.3  for closure of 53-128	Size = 1 BP stack across bulge = -2.2
		Stack = -1.0  for stack of 54-126
		Stack = -2.1  for stack of 55-125
		Stack = -3.3  for stack of 56-124
		Stack = -2.5  for stack of 57-123
	Helix total = -8.9
	Internal/bulge = 2.7  for closure of 58-122	Size = 9
		Stack = -2.5  for stack of 64-117
		Stack = -0.6  for stack of 65-116
		Stack = -0.9  for stack of 66-115
		Stack = -0.9  for stack of 67-114
	Helix total = -4.9
	Internal/bulge = 6.3  for closure of 68-113	Size = 11
		Stack = -3.4  for stack of 77-109
		Stack = -2.1  for stack of 78-108
		Stack = -2.2  for stack of 79-107
		Stack = -2.4  for stack of 80-106
		Stack = -3.4  for stack of 81-105
		Stack = -2.1  for stack of 82-104
		Stack = -2.1  for stack of 83-103
	Helix total = -17.7
	Hairpin = 5.5  for closure of 84-102


	Total energy = -139.1



