Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    55:83 56:82 57:81 58:80 59:79 157:193 158:192 159:191
	    160:190 161:189 162:188 210:243 211:242 212:241 213:240 214:239
	    215:238 260:297 261:296 262:295 263:294 264:293 265:292 266:291
	Energy of Broken Structure: -72.0
	Energy of Pseudo-Helices:   -28.4
	Pseudoknot Energy Penalty:  32.0
	Total Free Energy:          -68.4
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-358
		Stack = -1.5  for stack of 2-357
		Stack = -2.1  for stack of 3-356
		Stack = -2.4  for stack of 4-355
		Stack = -2.2  for stack of 5-354
		Stack = -2.4  for stack of 6-353
	Helix total = -13.9
	Multiloop = 5.2  for closure of 7-352
		Stack = -3.4  for stack of 335-351
		Stack = -2.4  for stack of 336-350
		Stack = -3.3  for stack of 337-349
		Stack = -3.3  for stack of 338-348
	Helix total = -12.4
	Hairpin = 4.4  for closure of 339-347
		Stack = -2.1  for stack of 21-331
		Stack = -2.1  for stack of 22-330
		Stack = -1.5  for stack of 23-329
		Stack = -2.1  for stack of 24-328
		Stack = -3.3  for stack of 25-327
		Stack = -2.2  for stack of 26-326
		Stack = -2.4  for stack of 27-325
		Stack = -3.3  for stack of 28-324
	Helix total = -19.0
	Internal/bulge = 3.3  for closure of 29-323	Size = 5
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 33-320	Size = 2
		Stack = -2.5  for stack of 35-318
	Helix total = -2.5
	Internal/bulge = -0.1  for closure of 36-317	Size = 2
		Stack = -2.1  for stack of 38-315
		Stack = -1.1  for stack of 39-314
		Stack = -1.3  for stack of 40-313
	Helix total = -4.5
	Internal/bulge = 4.9  for closure of 41-312	Size = 9
		Stack = -2.4  for stack of 45-305
		Stack = -2.2  for stack of 46-304
		Stack = -2.1  for stack of 47-303
		Stack = -2.2  for stack of 48-302
	Helix total = -8.9
	Multiloop = 5.2  for closure of 49-301
		Stack = -3.4  for stack of 246-280
		Stack = -2.1  for stack of 247-279
		Stack = -1.1  for stack of 248-278
		Stack = -2.4  for stack of 249-277
		Stack = -2.1  for stack of 250-276
		Stack = -1.1  for stack of 251-275
		Stack = -2.1  for stack of 252-274
	Helix total = -14.3
	Internal/bulge = 2.7  for closure of 253-273	Size = 5
		Stack = -2.1  for stack of 256-269
		Stack = -2.2  for stack of 257-268
	Helix total = -4.3
	Hairpin = 5.4  for closure of 258-267
		Stack = -2.1  for stack of 198-226
		Stack = -1.3  for stack of 199-225
		Stack = -0.9  for stack of 200-224
		Stack = -0.9  for stack of 201-223
		Stack = -2.2  for stack of 202-222
		Stack = -2.1  for stack of 203-221
	Helix total = -9.5
	Hairpin = 6.7  for closure of 204-220
		Stack = -1.1  for stack of 141-178
		Stack = -2.4  for stack of 142-177
		Stack = -2.4  for stack of 143-176
		Stack = -3.4  for stack of 144-175
	Helix total = -9.3
	Internal/bulge = 3.0  for closure of 145-174	Size = 3
		Stack = -1.3  for stack of 147-171
		Stack = -0.9  for stack of 148-170
		Stack = -2.2  for stack of 149-169
		Stack = -2.1  for stack of 150-168
		Stack = -2.1  for stack of 151-167
		Stack = -3.4  for stack of 152-166
		Stack = -2.1  for stack of 153-165
		Stack = -1.4  for stack of 154-164
	Helix total = -15.5
	Hairpin = 5.1  for closure of 155-163
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 118-138	Size = 2
		Stack = -2.1  for stack of 120-136
	Helix total = -2.1
	Internal/bulge = 1.6  for closure of 121-135	Size = 1 BP stack across bulge = -2.2
		Stack = -2.1  for stack of 123-134
		Stack = -3.4  for stack of 124-133
	Helix total = -5.5
	Hairpin = 4.3  for closure of 125-132
		Stack = -2.4  for stack of 50-65
		Stack = -1.5  for stack of 51-64
		Stack = -1.3  for stack of 52-63
		Stack = -2.1  for stack of 53-62
	Helix total = -7.3
	Hairpin = 3.2  for closure of 54-61


	Total energy = -72.0



