Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    56:85 57:84 58:83 59:82 60:81 178:212 179:211 180:210
	    181:209 182:208 183:207 228:262 229:261 230:260 231:259 232:258
	    233:257 280:318 281:317 282:316 283:315 284:314 285:313
	Energy of Broken Structure: -98.0
	Energy of Pseudo-Helices:   -48.7
	Pseudoknot Energy Penalty:  35.5
	Total Free Energy:          -111.2
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-378
		Stack = -1.5  for stack of 2-377
		Stack = -2.1  for stack of 3-376
		Stack = -2.4  for stack of 4-375
		Stack = -1.1  for stack of 5-374
		Stack = -2.1  for stack of 6-373
	Helix total = -12.5
	Multiloop = 4.8  for closure of 7-372
		Stack = -2.4  for stack of 356-370
		Stack = -3.3  for stack of 357-369
		Stack = -3.3  for stack of 358-368
	Helix total = -9.0
	Hairpin = 4.4  for closure of 359-367
		Stack = -2.1  for stack of 19-351
		Stack = -2.1  for stack of 20-350
	Helix total = -4.2
	Internal/bulge = 0.5  for closure of 21-349	Size = 2
		Stack = -3.3  for stack of 23-347
		Stack = -2.4  for stack of 24-346
	Helix total = -5.7
	Internal/bulge = 2.6  for closure of 25-345	Size = 4
	Helix total = 0.0
	Internal/bulge = 2.4  for closure of 28-342	Size = 1 BP stack across bulge = -1.0
		Stack = -1.3  for stack of 30-341
	Helix total = -1.3
	Internal/bulge = 2.1  for closure of 31-340	Size = 4
		Stack = -2.1  for stack of 34-337
		Stack = -2.1  for stack of 35-336
		Stack = -3.3  for stack of 36-335
		Stack = -3.3  for stack of 37-334
	Helix total = -10.8
	Internal/bulge = 1.7  for closure of 38-333	Size = 10
		Stack = -2.4  for stack of 43-326
		Stack = -2.4  for stack of 44-325
		Stack = -2.1  for stack of 45-324
		Stack = -3.4  for stack of 46-323
	Helix total = -10.3
	Multiloop = 0.7  for closure of 47-322
		Stack = -3.3  for stack of 264-300
		Stack = -3.4  for stack of 265-299
		Stack = -3.3  for stack of 266-298
		Stack = -2.1  for stack of 267-297
	Helix total = -12.1
	Internal/bulge = 3.8  for closure of 268-296	Size = 2
		Stack = -2.1  for stack of 271-295
		Stack = -3.3  for stack of 272-294
		Stack = -3.4  for stack of 273-293
		Stack = -2.4  for stack of 274-292
		Stack = -3.3  for stack of 275-291
	Helix total = -14.5
	Hairpin = 5.7  for closure of 276-290
		Stack = -3.3  for stack of 217-245
		Stack = -1.4  for stack of 218-244
		Stack = -1.4  for stack of 219-243
		Stack = -2.4  for stack of 220-242
		Stack = -3.3  for stack of 221-241
		Stack = -2.4  for stack of 222-240
		Stack = -3.4  for stack of 223-239
		Stack = -3.3  for stack of 224-238
		Stack = -3.3  for stack of 225-237
	Helix total = -24.2
	Hairpin = 4.0  for closure of 226-236
		Stack = -2.1  for stack of 164-199
		Stack = -2.5  for stack of 165-198
		Stack = -1.5  for stack of 166-197
		Stack = -2.1  for stack of 167-196
		Stack = -2.1  for stack of 168-195
	Helix total = -10.3
	Internal/bulge = 2.3  for closure of 169-194	Size = 4
		Stack = -3.3  for stack of 171-190
		Stack = -2.4  for stack of 172-189
		Stack = -3.3  for stack of 173-188
		Stack = -3.3  for stack of 174-187
	Helix total = -12.3
	Hairpin = 4.0  for closure of 175-186
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 122-162	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.2  for closure of 124-160	Size = 4
		Stack = -2.4  for stack of 127-157
		Stack = -3.4  for stack of 128-156
		Stack = -2.1  for stack of 129-155
	Helix total = -7.9
	Internal/bulge = 1.9  for closure of 130-154	Size = 2
		Stack = -2.4  for stack of 132-152
		Stack = -2.4  for stack of 133-151
	Helix total = -4.8
	Internal/bulge = 1.2  for closure of 134-150	Size = 2
		Stack = -2.1  for stack of 136-148
		Stack = -3.4  for stack of 137-147
	Helix total = -5.5
	Hairpin = 5.0  for closure of 138-146
		Stack = -2.4  for stack of 48-70
		Stack = -2.4  for stack of 49-69
		Stack = -2.1  for stack of 50-68
		Stack = -1.5  for stack of 51-67
	Helix total = -8.4
	Hairpin = 7.0  for closure of 52-66


	Total energy = -98.0



