Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:67 49:66 50:65 51:64 52:63 188:222 189:221 190:220
	    191:219 192:218 238:269 239:268 240:267 241:266 242:265 243:264
	    286:324 287:323 288:322 290:319 291:318 292:317
	Energy of Broken Structure: -69.2
	Energy of Pseudo-Helices:   -41.1
	Pseudoknot Energy Penalty:  32.8
	Total Free Energy:          -77.5
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-384
		Stack = -1.5  for stack of 2-383
		Stack = -2.1  for stack of 3-382
		Stack = -3.4  for stack of 4-381
		Stack = -3.3  for stack of 5-380
		Stack = -2.4  for stack of 6-379
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-378
		Stack = -3.3  for stack of 361-377
		Stack = -3.3  for stack of 362-376
		Stack = -3.3  for stack of 363-375
		Stack = -3.3  for stack of 364-374
	Helix total = -13.2
	Hairpin = 4.4  for closure of 365-373
		Stack = -2.4  for stack of 20-357
		Stack = -3.4  for stack of 21-356
		Stack = -3.3  for stack of 22-355
		Stack = -1.4  for stack of 23-354
		Stack = -2.1  for stack of 24-353
		Stack = -2.2  for stack of 25-352
		Stack = -1.0  for stack of 26-351
	Helix total = -15.8
	Internal/bulge = 1.9  for closure of 27-350	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.9  for closure of 29-348	Size = 8
		Stack = -0.6  for stack of 35-344
	Helix total = -0.6
	Internal/bulge = 2.2  for closure of 36-343	Size = 5
		Stack = -3.3  for stack of 39-339
		Stack = -2.2  for stack of 40-338
		Stack = -1.0  for stack of 41-337
	Helix total = -6.5
	Internal/bulge = 3.7  for closure of 42-336	Size = 3
		Stack = -2.1  for stack of 43-332
		Stack = -1.1  for stack of 44-331
		Stack = -2.1  for stack of 45-330
		Stack = -3.4  for stack of 46-329
	Helix total = -8.7
	Multiloop = 2.1  for closure of 47-328
		Stack = -2.5  for stack of 272-306
		Stack = -3.3  for stack of 273-305
		Stack = -3.3  for stack of 274-304
	Helix total = -9.1
	Internal/bulge = 2.2  for closure of 275-303	Size = 5
	Helix total = 0.0
	Internal/bulge = 3.4  for closure of 279-300	Size = 7
		Stack = -3.3  for stack of 283-295
		Stack = -2.1  for stack of 284-294
	Helix total = -5.4
	Hairpin = 5.7  for closure of 285-293
		Stack = -3.4  for stack of 226-254
		Stack = -3.3  for stack of 227-253
		Stack = -2.4  for stack of 228-252
	Helix total = -9.1
	Internal/bulge = 0.7  for closure of 229-251	Size = 8
		Stack = -2.2  for stack of 234-246
	Helix total = -2.2
	Hairpin = 5.9  for closure of 235-245
		Stack = -2.1  for stack of 172-208
		Stack = -0.9  for stack of 173-207
		Stack = -1.1  for stack of 174-206
		Stack = -2.4  for stack of 175-205
		Stack = -2.1  for stack of 176-204
		Stack = -1.1  for stack of 177-203
	Helix total = -9.7
	Internal/bulge = 3.3  for closure of 178-202	Size = 5
		Stack = -3.3  for stack of 181-198
		Stack = -3.3  for stack of 182-197
	Helix total = -6.6
	Internal/bulge = 0.1  for closure of 183-196	Size = 4
	Helix total = 0.0
	Hairpin = 5.1  for closure of 186-193
		Stack = -2.1  for stack of 153-171
		Stack = -2.1  for stack of 154-170
		Stack = -3.3  for stack of 155-169
	Helix total = -7.5
	Internal/bulge = 1.4  for closure of 156-168	Size = 1 BP stack across bulge = -2.4
		Stack = -2.1  for stack of 158-167
		Stack = -3.4  for stack of 159-166
	Helix total = -5.5
	Hairpin = 3.7  for closure of 160-165
		Stack = -0.5  for stack of 115-152
	Helix total = -0.5
	Internal/bulge = 3.4  for closure of 116-151	Size = 6
	Helix total = 0.0
	Internal/bulge = 3.4  for closure of 120-147	Size = 12
		Stack = -3.4  for stack of 127-140
		Stack = -2.1  for stack of 128-139
		Stack = -2.1  for stack of 129-138
		Stack = -3.4  for stack of 130-137
	Helix total = -11.0
	Hairpin = 3.3  for closure of 131-136
		Stack = -2.5  for stack of 55-82
		Stack = -1.0  for stack of 56-81
		Stack = -0.9  for stack of 57-80
		Stack = -2.2  for stack of 58-79
		Stack = -2.1  for stack of 59-78
		Stack = -2.1  for stack of 60-77
	Helix total = -10.8
	Hairpin = 5.8  for closure of 61-76


	Total energy = -69.2



