Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    55:78 56:77 57:76 58:75 59:74 151:194 152:193 153:192
	    154:191 155:190 156:189 208:243 209:242 210:241 211:240 212:239
	    213:238 214:237 215:236 216:235 259:297 260:296 261:295 263:292
	    264:291 265:290
	Energy of Broken Structure: -88.5
	Energy of Pseudo-Helices:   -41.5
	Pseudoknot Energy Penalty:  35.3
	Total Free Energy:          -94.7
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-357
		Stack = -1.5  for stack of 2-356
		Stack = -2.1  for stack of 3-355
		Stack = -3.4  for stack of 4-354
		Stack = -3.3  for stack of 5-353
		Stack = -2.4  for stack of 6-352
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-351
		Stack = -3.3  for stack of 334-350
		Stack = -3.3  for stack of 335-349
		Stack = -3.3  for stack of 336-348
		Stack = -3.3  for stack of 337-347
	Helix total = -13.2
	Hairpin = 4.4  for closure of 338-346
		Stack = -2.4  for stack of 20-330
		Stack = -2.5  for stack of 21-329
		Stack = 0.3  for stack of 22-328
		Stack = -0.5  for stack of 23-327
		Stack = -2.1  for stack of 24-326
		Stack = -2.5  for stack of 25-325
		Stack = -0.5  for stack of 26-324
	Helix total = -10.2
	Internal/bulge = 2.4  for closure of 27-323	Size = 9
		Stack = -2.5  for stack of 33-318
		Stack = -2.1  for stack of 34-317
		Stack = -2.1  for stack of 35-316
	Helix total = -6.7
	Internal/bulge = 2.3  for closure of 36-315	Size = 3
		Stack = -2.1  for stack of 39-313
		Stack = -2.1  for stack of 40-312
	Helix total = -4.2
	Internal/bulge = 2.9  for closure of 41-311	Size = 7
		Stack = -2.1  for stack of 44-305
		Stack = -1.1  for stack of 45-304
		Stack = -1.3  for stack of 46-303
		Stack = -2.2  for stack of 47-302
	Helix total = -6.7
	Multiloop = 5.1  for closure of 48-301
		Stack = -2.5  for stack of 244-279
		Stack = -3.3  for stack of 245-278
		Stack = -2.1  for stack of 246-277
		Stack = -2.1  for stack of 247-276
	Helix total = -10.0
	Internal/bulge = 3.4  for closure of 248-275	Size = 7
	Helix total = 0.0
	Internal/bulge = 1.7  for closure of 253-271	Size = 1 BP stack across bulge = -1.5
		Stack = -1.4  for stack of 254-269
		Stack = -2.5  for stack of 255-268
		Stack = -2.1  for stack of 256-267
	Helix total = -6.0
	Hairpin = 4.6  for closure of 257-266
		Stack = -1.4  for stack of 198-226
		Stack = -2.1  for stack of 199-225
		Stack = -2.2  for stack of 200-224
		Stack = -0.9  for stack of 201-223
		Stack = -2.1  for stack of 202-222
		Stack = -2.2  for stack of 203-221
		Stack = -1.3  for stack of 204-220
		Stack = -1.1  for stack of 205-219
		Stack = -0.9  for stack of 206-218
	Helix total = -14.2
	Hairpin = 6.1  for closure of 207-217
		Stack = -2.4  for stack of 136-181
		Stack = -3.4  for stack of 137-180
		Stack = -2.1  for stack of 138-179
		Stack = -2.1  for stack of 139-178
		Stack = -3.4  for stack of 140-177
	Helix total = -13.4
	Multiloop = 3.1  for closure of 141-176
		Stack = -3.4  for stack of 163-174
		Stack = -2.4  for stack of 164-173
		Stack = -3.3  for stack of 165-172
	Helix total = -9.1
	Hairpin = 3.1  for closure of 166-171
		Stack = -3.3  for stack of 143-162
		Stack = -2.4  for stack of 144-161
		Stack = -3.3  for stack of 145-160
	Helix total = -9.0
	Hairpin = 5.4  for closure of 146-159
		Stack = -2.4  for stack of 112-135
		Stack = -2.1  for stack of 113-134
		Stack = -1.0  for stack of 114-133
		Stack = -2.1  for stack of 115-132
		Stack = -3.4  for stack of 116-131
		Stack = -3.3  for stack of 117-130
		Stack = -2.4  for stack of 118-129
	Helix total = -16.7
	Hairpin = 4.8  for closure of 119-128
		Stack = -2.4  for stack of 49-66
		Stack = -2.4  for stack of 50-65
		Stack = -2.1  for stack of 51-64
		Stack = -3.3  for stack of 52-63
	Helix total = -10.2
	Hairpin = 4.4  for closure of 53-62


	Total energy = -88.5



