Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    55:82 56:81 57:80 58:79 59:78 183:215 184:214 185:213
	    187:212 188:211 240:269 241:268 242:267 243:266 287:324 289:322
	    290:321 291:320 292:319 293:318
	Energy of Broken Structure: -64.0
	Energy of Pseudo-Helices:   -32.3
	Pseudoknot Energy Penalty:  30.5
	Total Free Energy:          -65.8
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-385
		Stack = -1.5  for stack of 2-384
		Stack = -2.1  for stack of 3-383
		Stack = -3.3  for stack of 4-382
		Stack = -3.4  for stack of 5-381
		Stack = -2.4  for stack of 6-380
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-379
		Stack = -3.3  for stack of 362-378
		Stack = -3.3  for stack of 363-377
		Stack = -3.3  for stack of 364-376
		Stack = -3.3  for stack of 365-375
	Helix total = -13.2
	Hairpin = 4.4  for closure of 366-374
		Stack = -2.4  for stack of 20-358
	Helix total = -2.4
	Internal/bulge = 0.5  for closure of 21-357	Size = 2
		Stack = -1.4  for stack of 23-355
		Stack = -2.1  for stack of 24-354
		Stack = -2.2  for stack of 25-353
		Stack = -1.3  for stack of 26-352
	Helix total = -7.0
	Internal/bulge = 3.1  for closure of 27-351	Size = 11
		Stack = -3.3  for stack of 34-345
	Helix total = -3.3
	Internal/bulge = 1.7  for closure of 35-344	Size = 6
		Stack = -2.1  for stack of 39-340
		Stack = -2.5  for stack of 40-339
	Helix total = -4.6
	Internal/bulge = 4.5  for closure of 41-338	Size = 5
		Stack = -2.1  for stack of 43-333
		Stack = -1.1  for stack of 44-332
		Stack = -2.1  for stack of 45-331
		Stack = -2.5  for stack of 46-330
	Helix total = -7.8
	Multiloop = 5.7  for closure of 47-329
		Stack = -2.5  for stack of 273-307
		Stack = -2.4  for stack of 274-306
		Stack = -3.4  for stack of 275-305
		Stack = -2.1  for stack of 276-304
	Helix total = -10.4
	Internal/bulge = 2.1  for closure of 277-303	Size = 1 BP stack across bulge = -0.9
		Stack = -0.9  for stack of 279-302
	Helix total = -0.9
	Internal/bulge = 4.6  for closure of 280-301	Size = 6
		Stack = -1.5  for stack of 283-296
		Stack = -3.3  for stack of 284-295
	Helix total = -4.8
	Hairpin = 4.7  for closure of 285-294
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 225-257	Size = 2
		Stack = -3.4  for stack of 227-255
	Helix total = -3.4
	Internal/bulge = 0.9  for closure of 228-254	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.4  for closure of 230-252	Size = 8
		Stack = -2.5  for stack of 235-247
		Stack = -3.3  for stack of 236-246
		Stack = -2.1  for stack of 237-245
	Helix total = -7.9
	Hairpin = 4.6  for closure of 238-244
		Stack = -3.4  for stack of 171-198
		Stack = -2.4  for stack of 172-197
		Stack = -3.3  for stack of 173-196
		Stack = -2.2  for stack of 174-195
	Helix total = -11.3
	Hairpin = 6.2  for closure of 175-194
		Stack = -1.3  for stack of 155-170
		Stack = -2.1  for stack of 156-169
		Stack = -3.4  for stack of 157-168
		Stack = -2.4  for stack of 158-167
		Stack = -3.3  for stack of 159-166
	Helix total = -12.5
	Hairpin = 4.5  for closure of 160-165
	Helix total = 0.0
	Internal/bulge = 0.9  for closure of 113-150	Size = 10
		Stack = -2.1  for stack of 119-144
		Stack = -0.9  for stack of 120-143
	Helix total = -3.0
	Internal/bulge = 1.7  for closure of 121-142	Size = 4
		Stack = -2.1  for stack of 124-139
		Stack = -3.4  for stack of 125-138
		Stack = -2.1  for stack of 126-137
		Stack = -1.0  for stack of 127-136
		Stack = -2.5  for stack of 128-135
	Helix total = -11.1
	Hairpin = 3.3  for closure of 129-134
		Stack = -2.4  for stack of 48-67
		Stack = -2.2  for stack of 49-66
		Stack = -2.1  for stack of 50-65
		Stack = -2.4  for stack of 51-64
	Helix total = -9.1
	Hairpin = 5.3  for closure of 52-63


	Total energy = -64.0



