Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    47:65 48:64 49:63 50:62 51:61 150:185 151:184 152:183
	    153:182 154:181 155:180 156:179 201:235 202:234 203:233 204:232
	    205:231 206:230 207:229 254:291 255:290 256:289 257:288 258:287
	    259:286 260:285
	Energy of Broken Structure: -117.6
	Energy of Pseudo-Helices:   -58.0
	Pseudoknot Energy Penalty:  33.2
	Total Free Energy:          -142.4
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-352
		Stack = -1.5  for stack of 2-351
		Stack = -2.1  for stack of 3-350
		Stack = -3.3  for stack of 4-349
		Stack = -3.4  for stack of 5-348
		Stack = -2.4  for stack of 6-347
	Helix total = -16.0
	Multiloop = 5.0  for closure of 7-346
		Stack = -3.3  for stack of 329-345
		Stack = -3.3  for stack of 330-344
		Stack = -3.3  for stack of 331-343
		Stack = -3.3  for stack of 332-342
	Helix total = -13.2
	Hairpin = 4.4  for closure of 333-341
		Stack = -2.4  for stack of 19-325
		Stack = -1.5  for stack of 20-324
		Stack = -0.5  for stack of 21-323
		Stack = -2.1  for stack of 22-322
		Stack = -2.4  for stack of 23-321
		Stack = -1.1  for stack of 24-320
		Stack = -2.1  for stack of 25-319
		Stack = -3.3  for stack of 26-318
		Stack = -2.4  for stack of 27-317
		Stack = -2.1  for stack of 28-316
	Helix total = -19.9
	Internal/bulge = 0.5  for closure of 29-315	Size = 2
		Stack = -3.3  for stack of 31-313
		Stack = -3.3  for stack of 32-312
		Stack = -3.3  for stack of 33-311
		Stack = -2.1  for stack of 34-310
		Stack = -2.1  for stack of 35-309
		Stack = -3.3  for stack of 36-308
		Stack = -3.3  for stack of 37-307
	Helix total = -20.7
	Internal/bulge = 2.4  for closure of 38-306	Size = 9
		Stack = -2.4  for stack of 42-299
		Stack = -2.4  for stack of 43-298
		Stack = -2.1  for stack of 44-297
		Stack = -3.4  for stack of 45-296
	Helix total = -10.3
	Multiloop = 2.2  for closure of 46-295
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 236-276	Size = 2
		Stack = -1.4  for stack of 238-274
		Stack = -3.3  for stack of 239-273
		Stack = -3.3  for stack of 240-272
		Stack = -2.4  for stack of 241-271
		Stack = -2.1  for stack of 242-270
	Helix total = -12.5
	Internal/bulge = 0.3  for closure of 243-269	Size = 2
		Stack = -1.5  for stack of 245-267
	Helix total = -1.5
	Internal/bulge = 1.2  for closure of 246-266	Size = 2
	Helix total = 0.0
	Internal/bulge = 0.9  for closure of 248-264	Size = 2
	Helix total = 0.0
	Hairpin = 5.6  for closure of 250-262
		Stack = -3.3  for stack of 188-219
		Stack = -2.4  for stack of 189-218
		Stack = -2.4  for stack of 190-217
		Stack = -1.1  for stack of 191-216
		Stack = -0.9  for stack of 192-215
		Stack = -2.4  for stack of 193-214
		Stack = -2.1  for stack of 194-213
		Stack = -2.1  for stack of 195-212
	Helix total = -16.7
	Internal/bulge = 1.2  for closure of 196-211	Size = 2
		Stack = -0.5  for stack of 198-209
	Helix total = -0.5
	Hairpin = 5.4  for closure of 199-208
		Stack = -2.4  for stack of 134-171
		Stack = -2.5  for stack of 135-170
		Stack = -1.5  for stack of 136-169
		Stack = -3.3  for stack of 137-168
	Helix total = -9.7
	Internal/bulge = 1.7  for closure of 138-167	Size = 1 BP stack across bulge = -2.1
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 139-165	Size = 2
		Stack = -2.4  for stack of 141-163
		Stack = -3.3  for stack of 142-162
		Stack = -2.4  for stack of 143-161
		Stack = -2.4  for stack of 144-160
		Stack = -0.9  for stack of 145-159
		Stack = -2.1  for stack of 146-158
	Helix total = -13.5
	Hairpin = 5.3  for closure of 147-157
		Stack = -3.4  for stack of 113-133
		Stack = -3.3  for stack of 114-132
		Stack = -2.4  for stack of 115-131
		Stack = -3.4  for stack of 116-130
		Stack = -2.1  for stack of 117-129
		Stack = -0.9  for stack of 118-128
		Stack = -1.3  for stack of 119-127
	Helix total = -16.8
	Hairpin = 5.4  for closure of 120-126
		Stack = -3.3  for stack of 54-78
		Stack = -3.3  for stack of 55-77
		Stack = -2.1  for stack of 56-76
		Stack = -2.2  for stack of 57-75
		Stack = -3.3  for stack of 58-74
		Stack = -2.1  for stack of 59-73
	Helix total = -16.3
	Hairpin = 6.4  for closure of 60-72


	Total energy = -117.6



