Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    42:52 161:196 162:195 163:194 164:193 165:192 214:243 215:242
	    216:241 217:240 218:239 246:282 247:281 258:271 259:270 260:269
	Energy of Broken Structure: 16.8
	Energy of Pseudo-Helices:   -29.0
	Pseudoknot Energy Penalty:  31.1
	Total Free Energy:          18.9
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
	Helix total = 0.0
	Multiloop = 7.4  for closure of 3-356
		Stack = -2.1  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 = -12.0
	Hairpin = 4.4  for closure of 343-351
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 14-337	Size = 2
		Stack = -2.1  for stack of 16-335
	Helix total = -2.1
	Internal/bulge = 2.5  for closure of 17-334	Size = 8
	Helix total = 0.0
	Internal/bulge = 3.1  for closure of 22-329	Size = 9
	Helix total = 0.0
	Internal/bulge = 1.0  for closure of 28-324	Size = 2
		Stack = -2.5  for stack of 30-322
	Helix total = -2.5
	Internal/bulge = 1.6  for closure of 31-321	Size = 4
	Helix total = 0.0
	Internal/bulge = 1.4  for closure of 34-318	Size = 4
		Stack = -1.4  for stack of 37-315
	Helix total = -1.4
	Internal/bulge = 5.2  for closure of 38-314	Size = 5
	Helix total = 0.0
	Multiloop = 5.3  for closure of 40-309
		Stack = -2.2  for stack of 262-301
		Stack = -1.3  for stack of 263-300
		Stack = -1.0  for stack of 264-299
	Helix total = -4.5
	Internal/bulge = 1.2  for closure of 265-298	Size = 2
		Stack = -3.4  for stack of 267-296
	Helix total = -3.4
	Hairpin = 5.2  for closure of 268-295
		Stack = -2.1  for stack of 202-228
		Stack = -1.3  for stack of 203-227
		Stack = -0.9  for stack of 204-226
		Stack = -0.9  for stack of 205-225
		Stack = -1.4  for stack of 206-224
		Stack = -0.6  for stack of 207-223
		Stack = -0.9  for stack of 208-222
		Stack = -0.9  for stack of 209-221
	Helix total = -9.0
	Hairpin = 5.5  for closure of 210-220
		Stack = -1.4  for stack of 146-181
		Stack = -0.5  for stack of 147-180
		Stack = -0.5  for stack of 148-179
		Stack = -0.6  for stack of 149-178
	Helix total = -3.0
	Internal/bulge = 3.8  for closure of 150-177	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 151-174	Size = 2
		Stack = -2.4  for stack of 153-172
	Helix total = -2.4
	Internal/bulge = 0.5  for closure of 154-171	Size = 1 BP stack across bulge = -3.3
		Stack = -3.4  for stack of 155-169
		Stack = -2.1  for stack of 156-168
		Stack = -1.4  for stack of 157-167
	Helix total = -6.9
	Hairpin = 6.0  for closure of 158-166
		Stack = -2.1  for stack of 117-142
		Stack = -0.9  for stack of 118-141
		Stack = -0.9  for stack of 119-140
	Helix total = -3.9
	Internal/bulge = 3.4  for closure of 120-139	Size = 6
	Helix total = 0.0
	Hairpin = 5.6  for closure of 124-135
	Helix total = 0.0
	Internal/bulge = 0.4  for closure of 44-66	Size = 4
		Stack = -2.4  for stack of 47-63
		Stack = -1.4  for stack of 48-62
		Stack = 1.3  for stack of 49-61
	Helix total = -2.5
	Hairpin = 6.2  for closure of 50-60


	Total energy = 16.8



