Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    58:88 59:87 60:86 61:85 175:209 176:208 177:207 178:206
	    179:205 180:204 225:258 226:257 227:256 228:255 230:253 231:252
	    232:251 279:321 280:320 281:319 282:318 283:317 284:316 286:314
	Energy of Broken Structure: -86.1
	Energy of Pseudo-Helices:   -40.8
	Pseudoknot Energy Penalty:  36.0
	Total Free Energy:          -90.9
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-381
		Stack = -1.5  for stack of 2-380
		Stack = -2.1  for stack of 3-379
		Stack = -3.4  for stack of 4-378
		Stack = -2.1  for stack of 5-377
		Stack = -2.1  for stack of 6-376
	Helix total = -14.5
	Multiloop = 5.1  for closure of 7-375
		Stack = -3.3  for stack of 358-374
		Stack = -2.4  for stack of 359-373
		Stack = -3.3  for stack of 360-372
		Stack = -3.3  for stack of 361-371
	Helix total = -12.3
	Hairpin = 4.4  for closure of 362-370
		Stack = -2.1  for stack of 21-354
		Stack = -1.0  for stack of 22-353
		Stack = -2.5  for stack of 23-352
		Stack = -2.4  for stack of 24-351
		Stack = -2.2  for stack of 25-350
	Helix total = -10.2
	Internal/bulge = 1.4  for closure of 26-349	Size = 6
	Helix total = 0.0
	Internal/bulge = 2.2  for closure of 30-345	Size = 5
		Stack = -3.4  for stack of 34-342
		Stack = -2.1  for stack of 35-341
		Stack = -1.3  for stack of 36-340
		Stack = -2.1  for stack of 37-339
		Stack = -3.3  for stack of 38-338
		Stack = -3.3  for stack of 39-337
	Helix total = -15.5
	Internal/bulge = 1.7  for closure of 40-336	Size = 10
		Stack = -2.4  for stack of 45-329
		Stack = -2.2  for stack of 46-328
		Stack = -2.1  for stack of 47-327
		Stack = -3.4  for stack of 48-326
	Helix total = -10.1
	Multiloop = 2.3  for closure of 49-325
		Stack = -3.3  for stack of 261-299
		Stack = -3.4  for stack of 262-298
		Stack = -2.1  for stack of 263-297
		Stack = -2.4  for stack of 264-296
	Helix total = -11.2
	Internal/bulge = 4.1  for closure of 265-295	Size = 4
		Stack = -2.4  for stack of 270-294
		Stack = -3.3  for stack of 271-293
		Stack = -2.4  for stack of 272-292
		Stack = -3.3  for stack of 273-291
	Helix total = -11.4
	Internal/bulge = -1.4  for closure of 274-290	Size = 2
	Helix total = 0.0
	Hairpin = 5.1  for closure of 276-288
		Stack = -2.1  for stack of 213-242
		Stack = 0.3  for stack of 214-241
		Stack = -2.1  for stack of 215-240
		Stack = -2.2  for stack of 216-239
		Stack = -0.9  for stack of 217-238
		Stack = -0.9  for stack of 218-237
		Stack = -2.1  for stack of 219-236
		Stack = -2.5  for stack of 220-235
		Stack = -0.5  for stack of 221-234
	Helix total = -13.0
	Hairpin = 5.4  for closure of 222-233
		Stack = -2.1  for stack of 160-196
		Stack = -2.5  for stack of 161-195
		Stack = -1.5  for stack of 162-194
		Stack = -2.1  for stack of 163-193
		Stack = -2.1  for stack of 164-192
	Helix total = -10.3
	Internal/bulge = 2.3  for closure of 165-191	Size = 4
		Stack = -2.1  for stack of 167-187
		Stack = -1.3  for stack of 168-186
		Stack = -0.6  for stack of 169-185
		Stack = -1.3  for stack of 170-184
		Stack = -1.4  for stack of 171-183
	Helix total = -6.7
	Hairpin = 6.2  for closure of 172-182
		Stack = -2.4  for stack of 119-159
		Stack = -2.2  for stack of 120-158
	Helix total = -4.6
	Internal/bulge = 3.0  for closure of 121-157	Size = 14
		Stack = -2.4  for stack of 129-149
		Stack = -2.4  for stack of 130-148
		Stack = -3.4  for stack of 131-147
	Helix total = -8.2
	Hairpin = 5.8  for closure of 132-146
		Stack = -2.4  for stack of 50-71
		Stack = -3.3  for stack of 51-70
		Stack = -2.2  for stack of 52-69
		Stack = -2.1  for stack of 53-68
	Helix total = -10.0
	Hairpin = 6.0  for closure of 54-67


	Total energy = -86.1



