Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:64 50:63 52:61 250:284 251:283 252:282 254:280 258:277
	    260:272
	Energy of Broken Structure: -62.4
	Energy of Pseudo-Helices:   -7.9
	Pseudoknot Energy Penalty:  15.2
	Total Free Energy:          -55.1
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-362
		Stack = -1.5  for stack of 2-361
		Stack = -2.1  for stack of 3-360
		Stack = -3.3  for stack of 4-359
		Stack = -2.2  for stack of 5-358
		Stack = -2.1  for stack of 6-357
	Helix total = -14.5
	Multiloop = 5.0  for closure of 7-356
		Stack = -2.4  for stack of 339-355
		Stack = -3.3  for stack of 340-354
		Stack = -3.3  for stack of 341-353
		Stack = -3.3  for stack of 342-352
	Helix total = -12.3
	Hairpin = 4.4  for closure of 343-351
		Stack = -2.4  for stack of 20-335
		Stack = -1.5  for stack of 21-334
		Stack = -0.5  for stack of 22-333
		Stack = -0.5  for stack of 23-332
		Stack = -1.4  for stack of 24-331
		Stack = -1.0  for stack of 25-330
		Stack = -1.4  for stack of 26-329
		Stack = -2.1  for stack of 27-328
	Helix total = -10.8
	Internal/bulge = 2.7  for closure of 28-327	Size = 9
		Stack = -2.1  for stack of 33-321
		Stack = -2.5  for stack of 34-320
		Stack = -0.6  for stack of 35-319
	Helix total = -5.2
	Internal/bulge = 2.8  for closure of 36-318	Size = 1 BP stack across bulge = -1.0
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 38-317	Size = 2
		Stack = -0.9  for stack of 40-315
		Stack = -2.1  for stack of 41-314
		Stack = -3.3  for stack of 42-313
	Helix total = -6.3
	Internal/bulge = 4.0  for closure of 43-312	Size = 5
		Stack = -2.4  for stack of 44-306
		Stack = -2.4  for stack of 45-305
		Stack = -2.2  for stack of 46-304
		Stack = -2.1  for stack of 47-303
	Helix total = -9.1
	Multiloop = 4.4  for closure of 48-302
		Stack = -3.4  for stack of 262-296
		Stack = -3.3  for stack of 263-295
		Stack = -2.1  for stack of 264-294
		Stack = -0.6  for stack of 265-293
		Stack = -2.5  for stack of 266-292
		Stack = -3.3  for stack of 267-291
		Stack = -2.1  for stack of 268-290
	Helix total = -17.3
	Hairpin = 6.3  for closure of 269-289
		Stack = -2.1  for stack of 234-249
		Stack = -1.5  for stack of 235-248
		Stack = -3.3  for stack of 236-247
	Helix total = -6.9
	Hairpin = 4.0  for closure of 237-246
		Stack = -0.9  for stack of 172-179
	Helix total = -0.9
	Hairpin = 5.1  for closure of 173-178
	Helix total = 0.0
	Internal/bulge = 0.5  for closure of 162-171	Size = 2
	Helix total = 0.0
	Hairpin = 3.1  for closure of 164-169
		Stack = -2.5  for stack of 105-149
		Stack = -2.1  for stack of 106-148
		Stack = -1.5  for stack of 107-147
		Stack = -3.3  for stack of 108-146
		Stack = -2.4  for stack of 109-145
	Helix total = -11.8
	Internal/bulge = 0.3  for closure of 110-144	Size = 4
		Stack = -0.9  for stack of 113-141
	Helix total = -0.9
	Internal/bulge = 1.9  for closure of 114-140	Size = 2
		Stack = -1.0  for stack of 116-138
		Stack = -2.5  for stack of 117-137
		Stack = -2.1  for stack of 118-136
		Stack = -0.6  for stack of 119-135
		Stack = -2.5  for stack of 120-134
		Stack = -2.1  for stack of 121-133
		Stack = -1.0  for stack of 122-132
		Stack = -2.5  for stack of 123-131
	Helix total = -14.3
	Hairpin = 4.2  for closure of 124-130
		Stack = -2.1  for stack of 54-74
		Stack = -3.3  for stack of 55-73
		Stack = -2.2  for stack of 56-72
	Helix total = -7.6
	Internal/bulge = 1.2  for closure of 57-71	Size = 2
	Helix total = 0.0
	Hairpin = 5.4  for closure of 59-69


	Total energy = -62.4



