Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    55:78 56:77 57:76 58:75 59:74 150:194 151:193 152:192
	    153:191 154:190 155:189 210:240 211:239 212:238 213:237 214:236
	    258:296 259:295 260:294 261:293 262:291 263:290 264:289
	Energy of Broken Structure: -84.1
	Energy of Pseudo-Helices:   -38.9
	Pseudoknot Energy Penalty:  31.7
	Total Free Energy:          -91.3
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-356
		Stack = -1.5  for stack of 2-355
		Stack = -2.1  for stack of 3-354
		Stack = -3.4  for stack of 4-353
		Stack = -3.3  for stack of 5-352
		Stack = -2.4  for stack of 6-351
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-350
		Stack = -3.4  for stack of 333-349
		Stack = -2.4  for stack of 334-348
		Stack = -3.3  for stack of 335-347
		Stack = -3.3  for stack of 336-346
	Helix total = -12.4
	Hairpin = 4.4  for closure of 337-345
		Stack = -2.4  for stack of 20-329
		Stack = -2.5  for stack of 21-328
		Stack = 0.3  for stack of 22-327
		Stack = -0.5  for stack of 23-326
		Stack = -2.1  for stack of 24-325
		Stack = -2.2  for stack of 25-324
		Stack = -1.3  for stack of 26-323
	Helix total = -10.7
	Internal/bulge = 3.4  for closure of 27-322	Size = 9
		Stack = -2.5  for stack of 33-317
		Stack = -2.1  for stack of 34-316
		Stack = -2.1  for stack of 35-315
	Helix total = -6.7
	Internal/bulge = 1.4  for closure of 36-314	Size = 1 BP stack across bulge = -2.4
		Stack = -2.1  for stack of 38-313
		Stack = -3.4  for stack of 39-312
		Stack = -2.4  for stack of 40-311
	Helix total = -7.9
	Internal/bulge = 2.9  for closure of 41-310	Size = 7
		Stack = -2.1  for stack of 44-304
		Stack = -1.1  for stack of 45-303
		Stack = -1.3  for stack of 46-302
		Stack = -2.2  for stack of 47-301
	Helix total = -6.7
	Multiloop = 4.8  for closure of 48-300
		Stack = 1.3  for stack of 243-278
		Stack = -1.5  for stack of 244-277
		Stack = -2.4  for stack of 245-276
	Helix total = -2.6
	Internal/bulge = 1.9  for closure of 246-275	Size = 14
		Stack = -3.4  for stack of 254-267
		Stack = -2.4  for stack of 255-266
	Helix total = -5.8
	Hairpin = 4.5  for closure of 256-265
		Stack = -2.1  for stack of 199-225
		Stack = -0.5  for stack of 200-224
		Stack = -1.5  for stack of 201-223
		Stack = -2.4  for stack of 202-222
		Stack = -3.3  for stack of 203-221
		Stack = -3.4  for stack of 204-220
		Stack = -3.3  for stack of 205-219
	Helix total = -16.5
	Hairpin = 5.1  for closure of 206-218
		Stack = -3.3  for stack of 135-181
		Stack = -2.1  for stack of 136-180
		Stack = -2.4  for stack of 137-179
		Stack = -2.4  for stack of 138-178
		Stack = -3.4  for stack of 139-177
	Helix total = -13.6
	Multiloop = 3.3  for closure of 140-176
		Stack = -3.3  for stack of 162-173
		Stack = -3.4  for stack of 163-172
		Stack = -3.3  for stack of 164-171
	Helix total = -10.0
	Hairpin = 3.3  for closure of 165-170
		Stack = -2.1  for stack of 142-161
		Stack = -1.3  for stack of 143-160
		Stack = -2.1  for stack of 144-159
		Stack = -3.4  for stack of 145-158
		Stack = -2.1  for stack of 146-157
	Helix total = -11.0
	Hairpin = 5.3  for closure of 147-156
		Stack = -2.5  for stack of 111-134
	Helix total = -2.5
	Internal/bulge = 1.4  for closure of 112-133	Size = 1 BP stack across bulge = -2.4
		Stack = -3.3  for stack of 114-132
		Stack = -3.4  for stack of 115-131
	Helix total = -6.7
	Hairpin = 5.7  for closure of 116-130
		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 = -84.1



