Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    55:76 57:74 58:73 59:72 60:71 155:187 156:186 157:185
	    158:184 159:183 205:234 206:233 207:232 208:231 209:230 256:297
	    257:296 258:295 259:294 260:293 261:292 262:291
	Energy of Broken Structure: -68.5
	Energy of Pseudo-Helices:   -36.9
	Pseudoknot Energy Penalty:  31.7
	Total Free Energy:          -73.7
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 = -1.1  for stack of 5-354
		Stack = -2.1  for stack of 6-353
	Helix total = -12.5
	Multiloop = 6.6  for closure of 7-352
		Stack = -2.1  for stack of 335-351
		Stack = -3.3  for stack of 336-350
		Stack = -3.3  for stack of 337-349
		Stack = -3.3  for stack of 338-348
	Helix total = -12.0
	Hairpin = 4.4  for closure of 339-347
		Stack = -2.1  for stack of 21-331
		Stack = -0.6  for stack of 22-330
		Stack = -0.5  for stack of 23-329
		Stack = -2.5  for stack of 24-328
		Stack = -2.4  for stack of 25-327
		Stack = -3.4  for stack of 26-326
		Stack = -2.1  for stack of 27-325
	Helix total = -13.6
	Internal/bulge = 1.7  for closure of 28-324	Size = 6
	Helix total = 0.0
	Internal/bulge = 0.7  for closure of 32-320	Size = 4
		Stack = -1.4  for stack of 35-317
		Stack = -2.5  for stack of 36-316
		Stack = -2.1  for stack of 37-315
		Stack = -1.0  for stack of 38-314
		Stack = -0.5  for stack of 39-313
		Stack = -1.4  for stack of 40-312
		Stack = -1.3  for stack of 41-311
	Helix total = -10.2
	Internal/bulge = 4.5  for closure of 42-310	Size = 5
		Stack = -2.4  for stack of 44-305
		Stack = -2.4  for stack of 45-304
		Stack = -1.1  for stack of 46-303
		Stack = -1.3  for stack of 47-302
	Helix total = -7.2
	Multiloop = 5.8  for closure of 48-301
		Stack = -2.5  for stack of 237-278
		Stack = -3.3  for stack of 238-277
		Stack = -2.4  for stack of 239-276
	Helix total = -8.2
	Internal/bulge = 0.6  for closure of 240-275	Size = 2
		Stack = -3.3  for stack of 242-273
		Stack = -3.4  for stack of 243-272
	Helix total = -6.7
	Internal/bulge = 1.1  for closure of 244-271	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.8  for closure of 246-269	Size = 7
		Stack = -3.4  for stack of 251-265
		Stack = -3.3  for stack of 252-264
	Helix total = -6.7
	Hairpin = 5.6  for closure of 253-263
		Stack = -2.1  for stack of 193-219
		Stack = -1.3  for stack of 194-218
		Stack = -1.4  for stack of 195-217
		Stack = -3.4  for stack of 196-216
	Helix total = -8.2
	Internal/bulge = 1.2  for closure of 197-215	Size = 2
		Stack = -1.3  for stack of 199-213
		Stack = -1.1  for stack of 200-212
	Helix total = -2.4
	Hairpin = 6.2  for closure of 201-211
		Stack = -1.0  for stack of 138-174
		Stack = -2.5  for stack of 139-173
		Stack = -3.3  for stack of 140-172
	Helix total = -6.8
	Internal/bulge = 2.3  for closure of 141-171	Size = 8
		Stack = -2.4  for stack of 146-166
		Stack = -2.2  for stack of 147-165
		Stack = -2.1  for stack of 148-164
		Stack = -1.4  for stack of 149-163
		Stack = -3.4  for stack of 150-162
		Stack = -3.3  for stack of 151-161
	Helix total = -14.8
	Hairpin = 3.9  for closure of 152-160
	Helix total = 0.0
	Internal/bulge = 1.7  for closure of 114-136	Size = 6
		Stack = -3.4  for stack of 118-132
		Stack = -2.1  for stack of 119-131
		Stack = -2.1  for stack of 120-130
	Helix total = -7.6
	Hairpin = 5.5  for closure of 121-129
		Stack = -2.4  for stack of 49-65
		Stack = -2.2  for stack of 50-64
		Stack = -1.3  for stack of 51-63
		Stack = -2.1  for stack of 52-62
	Helix total = -8.0
	Hairpin = 4.5  for closure of 53-61


	Total energy = -68.5



