Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    55:74 56:73 57:72 58:71 152:189 153:188 154:187 155:186
	    156:185 157:184 207:237 208:236 209:235 210:234 211:233 255:295
	    256:294 257:293 258:292 259:291 260:290 261:289
	Energy of Broken Structure: -74.2
	Energy of Pseudo-Helices:   -44.1
	Pseudoknot Energy Penalty:  32.3
	Total Free Energy:          -86.0
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 = -2.4  for stack of 4-354
		Stack = -2.2  for stack of 5-353
		Stack = -2.4  for stack of 6-352
	Helix total = -13.9
	Multiloop = 5.1  for closure of 7-351
		Stack = -2.2  for stack of 334-350
		Stack = -2.1  for stack of 335-349
		Stack = -3.3  for stack of 336-348
		Stack = -3.3  for stack of 337-347
	Helix total = -10.9
	Hairpin = 4.4  for closure of 338-346
		Stack = -2.1  for stack of 20-330
		Stack = -2.1  for stack of 21-329
		Stack = -1.5  for stack of 22-328
		Stack = -1.3  for stack of 23-327
		Stack = -0.9  for stack of 24-326
		Stack = -1.1  for stack of 25-325
		Stack = -1.3  for stack of 26-324
		Stack = -0.6  for stack of 27-323
	Helix total = -10.9
	Internal/bulge = 1.7  for closure of 28-322	Size = 6
	Helix total = 0.0
	Internal/bulge = 1.6  for closure of 32-318	Size = 2
		Stack = -2.5  for stack of 34-316
		Stack = -2.1  for stack of 35-315
		Stack = -0.9  for stack of 36-314
		Stack = -1.3  for stack of 37-313
		Stack = -0.9  for stack of 38-312
		Stack = -2.1  for stack of 39-311
		Stack = -2.5  for stack of 40-310
	Helix total = -12.3
	Internal/bulge = 3.6  for closure of 41-309	Size = 7
		Stack = -2.4  for stack of 44-303
		Stack = -2.4  for stack of 45-302
		Stack = -2.1  for stack of 46-301
		Stack = -3.4  for stack of 47-300
	Helix total = -10.3
	Multiloop = 2.5  for closure of 48-299
		Stack = -3.4  for stack of 240-276
		Stack = -3.3  for stack of 241-275
	Helix total = -6.7
	Internal/bulge = 1.2  for closure of 242-274	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.6  for closure of 244-272	Size = 11
		Stack = -2.1  for stack of 250-265
		Stack = -3.4  for stack of 251-264
		Stack = -3.3  for stack of 252-263
	Helix total = -8.8
	Hairpin = 4.5  for closure of 253-262
		Stack = -2.1  for stack of 195-221
	Helix total = -2.1
	Internal/bulge = 1.9  for closure of 196-220	Size = 2
		Stack = -2.4  for stack of 198-218
		Stack = -2.1  for stack of 199-217
		Stack = -2.2  for stack of 200-216
		Stack = -3.3  for stack of 201-215
		Stack = -3.3  for stack of 202-214
	Helix total = -13.3
	Hairpin = 4.3  for closure of 203-213
		Stack = -2.2  for stack of 137-174
		Stack = -1.3  for stack of 138-173
		Stack = -1.5  for stack of 139-172
		Stack = -3.3  for stack of 140-171
		Stack = -2.4  for stack of 141-170
	Helix total = -10.7
	Internal/bulge = 2.3  for closure of 142-169	Size = 4
		Stack = -3.3  for stack of 144-165
		Stack = -2.1  for stack of 145-164
	Helix total = -5.4
	Internal/bulge = 1.4  for closure of 146-163	Size = 1 BP stack across bulge = -2.4
		Stack = -3.3  for stack of 147-161
		Stack = -2.1  for stack of 148-160
		Stack = -1.4  for stack of 149-159
	Helix total = -6.8
	Hairpin = 6.0  for closure of 150-158
		Stack = -1.0  for stack of 113-134
	Helix total = -1.0
	Internal/bulge = 1.4  for closure of 114-133	Size = 4
		Stack = -2.1  for stack of 117-130
		Stack = -3.4  for stack of 118-129
	Helix total = -5.5
	Hairpin = 4.5  for closure of 119-128
		Stack = -2.4  for stack of 49-64
		Stack = -2.4  for stack of 50-63
		Stack = -2.1  for stack of 51-62
	Helix total = -6.9
	Hairpin = 3.0  for closure of 52-61


	Total energy = -74.2



