Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    55:78 56:77 57:76 58:75 59:74 148:219 149:218 150:217
	    151:216 152:215 153:214 235:266 237:264 238:263 239:262 240:261
	    283:323 284:322 285:321 286:320 287:319 288:318 289:317
	Energy of Broken Structure: -120.2
	Energy of Pseudo-Helices:   -39.6
	Pseudoknot Energy Penalty:  31.1
	Total Free Energy:          -128.7
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-383
		Stack = -1.5  for stack of 2-382
		Stack = -2.1  for stack of 3-381
		Stack = -3.4  for stack of 4-380
		Stack = -3.3  for stack of 5-379
		Stack = -2.4  for stack of 6-378
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-377
		Stack = -3.3  for stack of 360-376
		Stack = -3.3  for stack of 361-375
		Stack = -3.3  for stack of 362-374
		Stack = -3.3  for stack of 363-373
	Helix total = -13.2
	Hairpin = 4.4  for closure of 364-372
		Stack = -2.4  for stack of 20-356
		Stack = -2.5  for stack of 21-355
		Stack = 0.3  for stack of 22-354
		Stack = -0.5  for stack of 23-353
		Stack = -2.1  for stack of 24-352
		Stack = -2.5  for stack of 25-351
		Stack = -1.5  for stack of 26-350
	Helix total = -11.2
	Internal/bulge = 1.2  for closure of 27-349	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.4  for closure of 29-347	Size = 7
		Stack = -2.1  for stack of 34-343
		Stack = -0.6  for stack of 35-342
	Helix total = -2.7
	Internal/bulge = 5.1  for closure of 36-341	Size = 1 BP stack across bulge = 1.3
		Stack = -1.5  for stack of 38-340
		Stack = -2.1  for stack of 39-339
		Stack = -2.1  for stack of 40-338
	Helix total = -5.7
	Internal/bulge = 2.9  for closure of 41-337	Size = 7
		Stack = -2.1  for stack of 44-331
		Stack = -1.1  for stack of 45-330
		Stack = -2.1  for stack of 46-329
		Stack = -3.4  for stack of 47-328
	Helix total = -8.7
	Multiloop = 2.0  for closure of 48-327
		Stack = -3.3  for stack of 269-303
		Stack = -3.3  for stack of 270-302
		Stack = -2.1  for stack of 271-301
		Stack = -2.1  for stack of 272-300
		Stack = -3.3  for stack of 273-299
	Helix total = -14.1
	Internal/bulge = -0.6  for closure of 274-298	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.0  for closure of 276-296	Size = 3
		Stack = -2.1  for stack of 278-293
		Stack = -3.4  for stack of 279-292
		Stack = -3.3  for stack of 280-291
	Helix total = -8.8
	Hairpin = 4.4  for closure of 281-290
		Stack = -2.5  for stack of 224-251
		Stack = -3.3  for stack of 225-250
		Stack = -2.1  for stack of 226-249
	Helix total = -7.9
	Internal/bulge = 1.2  for closure of 227-248	Size = 2
		Stack = -2.4  for stack of 229-246
		Stack = -3.4  for stack of 230-245
		Stack = -2.1  for stack of 231-244
		Stack = -1.4  for stack of 232-243
	Helix total = -9.3
	Hairpin = 3.0  for closure of 233-242
		Stack = -2.4  for stack of 133-206
		Stack = -3.4  for stack of 134-205
		Stack = -2.1  for stack of 135-204
		Stack = -2.1  for stack of 136-203
		Stack = -3.4  for stack of 137-202
	Helix total = -13.4
	Multiloop = 3.1  for closure of 138-201
		Stack = -3.4  for stack of 160-199
		Stack = -2.4  for stack of 161-198
		Stack = -3.3  for stack of 162-197
	Helix total = -9.1
	Multiloop = 4.3  for closure of 163-196
		Stack = -3.3  for stack of 181-192
		Stack = -3.3  for stack of 182-191
		Stack = -3.3  for stack of 183-190
	Helix total = -9.9
	Hairpin = 3.1  for closure of 184-189
		Stack = -3.3  for stack of 164-179
		Stack = -3.3  for stack of 165-178
		Stack = -2.4  for stack of 166-177
		Stack = -0.9  for stack of 167-176
		Stack = -2.1  for stack of 168-175
	Helix total = -12.0
	Hairpin = 3.1  for closure of 169-174
		Stack = -2.1  for stack of 140-159
		Stack = -2.1  for stack of 141-158
		Stack = -2.4  for stack of 142-157
		Stack = -1.4  for stack of 143-156
		Stack = -1.5  for stack of 144-155
	Helix total = -9.5
	Hairpin = 4.5  for closure of 145-154
		Stack = -2.1  for stack of 112-131
		Stack = -2.4  for stack of 113-130
		Stack = -1.4  for stack of 114-129
		Stack = -2.5  for stack of 115-128
		Stack = -3.3  for stack of 116-127
		Stack = -2.4  for stack of 117-126
		Stack = -3.4  for stack of 118-125
	Helix total = -17.5
	Hairpin = 4.6  for closure of 119-124
		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 = -3.4  for stack of 52-63
	Helix total = -10.3
	Hairpin = 4.0  for closure of 53-62


	Total energy = -120.2



