Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    107:184 108:183 109:182 110:181 111:180 112:179 113:177 114:176
	    115:175
	Energy of Broken Structure: -122.1
	Energy of Pseudo-Helices:   -14.0
	Pseudoknot Energy Penalty:  8.7
	Total Free Energy:          -127.4
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -4.1
		Stack = -2.4  for stack of 380-441
		Stack = -2.1  for stack of 381-440
		Stack = -3.4  for stack of 382-439
	Helix total = -7.9
	Internal/bulge = 3.3  for closure of 383-438	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 384-435	Size = 2
		Stack = -1.3  for stack of 386-433
		Stack = -1.5  for stack of 387-432
		Stack = -3.3  for stack of 388-431
	Helix total = -6.1
	Internal/bulge = 6.2  for closure of 389-430	Size = 10
		Stack = 1.3  for stack of 398-427
		Stack = -1.4  for stack of 399-426
		Stack = -2.5  for stack of 400-425
		Stack = 0.3  for stack of 401-424
		Stack = -2.5  for stack of 402-423
	Helix total = -4.8
	Internal/bulge = 0.8  for closure of 403-422	Size = 2
		Stack = -2.4  for stack of 405-420
		Stack = -3.3  for stack of 406-419
		Stack = -3.3  for stack of 407-418
	Helix total = -9.0
	Hairpin = 3.4  for closure of 408-417
		Stack = -3.3  for stack of 211-369
		Stack = -2.1  for stack of 212-368
		Stack = -2.1  for stack of 213-367
		Stack = -2.5  for stack of 214-366
		Stack = -1.4  for stack of 215-365
	Helix total = -11.4
	Internal/bulge = 5.3  for closure of 216-364	Size = 21
		Stack = -3.4  for stack of 224-349
		Stack = -3.3  for stack of 225-348
	Helix total = -6.7
	Internal/bulge = 0.5  for closure of 226-347	Size = 1 BP stack across bulge = -3.3
		Stack = -2.4  for stack of 227-345
		Stack = -3.4  for stack of 228-344
		Stack = -3.3  for stack of 229-343
		Stack = -3.3  for stack of 230-342
	Helix total = -12.4
	Internal/bulge = 4.2  for closure of 231-341	Size = 9
		Stack = -3.3  for stack of 235-334
		Stack = -3.3  for stack of 236-333
		Stack = -2.4  for stack of 237-332
		Stack = -3.4  for stack of 238-331
		Stack = -1.4  for stack of 239-330
	Helix total = -13.8
	Internal/bulge = 3.0  for closure of 240-329	Size = 4
		Stack = -3.3  for stack of 242-325
		Stack = -3.3  for stack of 243-324
		Stack = -2.4  for stack of 244-323
		Stack = -3.4  for stack of 245-322
	Helix total = -12.4
	Multiloop = 5.8  for closure of 246-321
		Stack = -2.1  for stack of 301-313
		Stack = -2.4  for stack of 302-312
		Stack = -2.1  for stack of 303-311
		Stack = -2.5  for stack of 304-310
	Helix total = -9.1
	Hairpin = 5.9  for closure of 305-309
		Stack = -2.4  for stack of 255-299
		Stack = -3.4  for stack of 256-298
		Stack = -2.4  for stack of 257-297
		Stack = -3.3  for stack of 258-296
	Helix total = -11.5
	Internal/bulge = 0.4  for closure of 259-295	Size = 1 BP stack across bulge = -3.4
		Stack = -2.4  for stack of 261-294
		Stack = -3.3  for stack of 262-293
		Stack = -3.4  for stack of 263-292
	Helix total = -9.1
	Internal/bulge = 2.6  for closure of 264-291	Size = 5
		Stack = -3.3  for stack of 267-287
		Stack = -3.3  for stack of 268-286
	Helix total = -6.6
	Hairpin = 5.4  for closure of 269-285
		Stack = -3.3  for stack of 18-208
		Stack = -3.3  for stack of 19-207
		Stack = -2.4  for stack of 20-206
		Stack = -3.3  for stack of 21-205
		Stack = -3.3  for stack of 22-204
	Helix total = -15.6
	Internal/bulge = -0.1  for closure of 23-203	Size = 4
		Stack = -3.3  for stack of 26-200
		Stack = -3.3  for stack of 27-199
	Helix total = -6.6
	Internal/bulge = 1.9  for closure of 28-198	Size = 4
	Helix total = 0.0
	Internal/bulge = 3.0  for closure of 31-195	Size = 3
		Stack = -3.3  for stack of 33-192
		Stack = -2.5  for stack of 34-191
		Stack = -1.5  for stack of 35-190
	Helix total = -7.3
	Internal/bulge = 5.9  for closure of 36-189	Size = 69
		Stack = -3.3  for stack of 64-146
		Stack = -3.4  for stack of 65-145
		Stack = -2.4  for stack of 66-144
	Helix total = -9.1
	Internal/bulge = 0.3  for closure of 67-143	Size = 1 BP stack across bulge = -2.2
		Stack = -1.3  for stack of 68-141
		Stack = -2.1  for stack of 69-140
		Stack = -3.3  for stack of 70-139
		Stack = -2.5  for stack of 71-138
	Helix total = -9.2
	Internal/bulge = 2.7  for closure of 72-137	Size = 9
		Stack = -3.4  for stack of 78-132
		Stack = -2.1  for stack of 79-131
		Stack = -0.9  for stack of 80-130
		Stack = -0.9  for stack of 81-129
	Helix total = -7.3
	Internal/bulge = 5.6  for closure of 82-128	Size = 10
		Stack = -2.4  for stack of 90-124
		Stack = -3.4  for stack of 91-123
	Helix total = -5.8
	Internal/bulge = -2.2  for closure of 92-122	Size = 2
		Stack = -2.4  for stack of 94-120
		Stack = -2.5  for stack of 95-119
		Stack = -0.6  for stack of 96-118
		Stack = -2.1  for stack of 97-117
	Helix total = -7.6
	Hairpin = 5.5  for closure of 98-116


	Total energy = -122.1



