Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    53:77 56:74 58:72 192:221 193:220 194:219 195:218 196:217
	    236:264 237:263 238:262 239:261 240:260 284:321 285:320 286:319
	    287:318 288:317 289:316 290:315 291:314 292:313
	Energy of Broken Structure: -39.0
	Energy of Pseudo-Helices:   -26.1
	Pseudoknot Energy Penalty:  43.5
	Total Free Energy:          -21.6
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 = -0.5  for stack of 3-381
		Stack = -1.3  for stack of 4-380
		Stack = -1.1  for stack of 5-379
		Stack = -2.1  for stack of 6-378
	Helix total = -9.8
	Multiloop = 5.0  for closure of 7-377
		Stack = -3.3  for stack of 360-376
		Stack = -2.4  for stack of 361-375
		Stack = -3.3  for stack of 362-374
		Stack = -3.3  for stack of 363-373
	Helix total = -12.3
	Hairpin = 4.4  for closure of 364-372
		Stack = -2.1  for stack of 20-356
	Helix total = -2.1
	Internal/bulge = -0.7  for closure of 21-355	Size = 2
		Stack = -2.5  for stack of 23-353
		Stack = -2.1  for stack of 24-352
		Stack = -1.1  for stack of 25-351
		Stack = -0.9  for stack of 26-350
		Stack = -1.3  for stack of 27-349
	Helix total = -7.9
	Internal/bulge = 3.7  for closure of 28-348	Size = 5
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 31-344	Size = 4
		Stack = -2.1  for stack of 34-341
		Stack = -0.9  for stack of 35-340
		Stack = -1.3  for stack of 36-339
		Stack = -1.1  for stack of 37-338
		Stack = -1.3  for stack of 38-337
		Stack = -0.9  for stack of 39-336
	Helix total = -7.6
	Internal/bulge = 5.2  for closure of 40-335	Size = 5
		Stack = -2.5  for stack of 42-330
		Stack = -2.1  for stack of 43-329
		Stack = -2.1  for stack of 44-328
		Stack = -2.2  for stack of 45-327
	Helix total = -8.9
	Multiloop = 5.6  for closure of 46-326
		Stack = -2.1  for stack of 266-305
		Stack = -2.4  for stack of 267-304
		Stack = -1.1  for stack of 268-303
		Stack = -0.9  for stack of 269-302
	Helix total = -6.5
	Internal/bulge = 3.7  for closure of 270-301	Size = 3
	Helix total = 0.0
	Internal/bulge = 3.0  for closure of 273-299	Size = 3
		Stack = -2.1  for stack of 275-296
		Stack = -2.4  for stack of 276-295
		Stack = -0.9  for stack of 277-294
	Helix total = -5.4
	Hairpin = 5.7  for closure of 278-293
		Stack = -2.4  for stack of 227-249
		Stack = -0.9  for stack of 228-248
		Stack = -0.6  for stack of 229-247
		Stack = -1.4  for stack of 230-246
		Stack = -0.9  for stack of 231-245
		Stack = -2.1  for stack of 232-244
	Helix total = -8.3
	Hairpin = 5.9  for closure of 233-243
		Stack = -2.1  for stack of 179-210
		Stack = -3.4  for stack of 180-209
	Helix total = -5.5
	Internal/bulge = 1.3  for closure of 181-208	Size = 1 BP stack across bulge = -2.1
		Stack = -2.4  for stack of 182-206
		Stack = -3.3  for stack of 183-205
		Stack = -2.1  for stack of 184-204
		Stack = -1.1  for stack of 185-203
		Stack = -0.9  for stack of 186-202
		Stack = -1.3  for stack of 187-201
		Stack = -1.1  for stack of 188-200
	Helix total = -12.2
	Hairpin = 5.9  for closure of 189-199
		Stack = -2.1  for stack of 150-177
		Stack = -1.3  for stack of 151-176
		Stack = -2.1  for stack of 152-175
		Stack = -3.4  for stack of 153-174
		Stack = -2.1  for stack of 154-173
	Helix total = -11.0
	Internal/bulge = 1.9  for closure of 155-172	Size = 2
		Stack = -0.6  for stack of 157-170
	Helix total = -0.6
	Hairpin = 6.2  for closure of 158-169
		Stack = -2.1  for stack of 47-67
		Stack = -2.5  for stack of 48-66
	Helix total = -4.6
	Internal/bulge = 1.6  for closure of 49-65	Size = 2
	Helix total = 0.0
	Hairpin = 5.1  for closure of 51-63


	Total energy = -39.0



