Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:68 49:67 50:66 51:65 52:64 195:234 196:233 197:232
	    198:231 199:230 200:229 249:276 250:275 251:274 252:273 296:332
	    297:331 298:330 299:329 300:328
	Energy of Broken Structure: -69.5
	Energy of Pseudo-Helices:   -33.8
	Pseudoknot Energy Penalty:  36.6
	Total Free Energy:          -66.7
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-394
		Stack = -1.5  for stack of 2-393
		Stack = -2.1  for stack of 3-392
		Stack = -2.5  for stack of 4-391
		Stack = -0.6  for stack of 5-390
		Stack = -2.1  for stack of 6-389
	Helix total = -12.1
	Multiloop = 5.0  for closure of 7-388
		Stack = -2.4  for stack of 371-387
		Stack = -2.1  for stack of 372-386
		Stack = -3.3  for stack of 373-385
		Stack = -3.3  for stack of 374-384
	Helix total = -11.1
	Hairpin = 4.4  for closure of 375-383
		Stack = -2.1  for stack of 19-367
		Stack = -0.6  for stack of 20-366
	Helix total = -2.7
	Internal/bulge = 0.8  for closure of 21-365	Size = 4
		Stack = -1.5  for stack of 24-362
	Helix total = -1.5
	Internal/bulge = 3.0  for closure of 25-361	Size = 3
		Stack = -2.4  for stack of 28-359
		Stack = -0.9  for stack of 29-358
		Stack = -0.9  for stack of 30-357
		Stack = -1.1  for stack of 31-356
	Helix total = -5.3
	Internal/bulge = -0.7  for closure of 32-355	Size = 2
		Stack = -1.4  for stack of 34-353
		Stack = -1.0  for stack of 35-352
		Stack = -0.5  for stack of 36-351
		Stack = -2.1  for stack of 37-350
		Stack = -2.5  for stack of 38-349
	Helix total = -7.5
	Internal/bulge = 4.9  for closure of 39-348	Size = 9
		Stack = -2.1  for stack of 43-341
		Stack = -1.1  for stack of 44-340
		Stack = -2.1  for stack of 45-339
		Stack = -3.4  for stack of 46-338
	Helix total = -8.7
	Multiloop = 3.2  for closure of 47-337
		Stack = -3.4  for stack of 282-313
		Stack = -2.1  for stack of 283-312
		Stack = -2.1  for stack of 284-311
		Stack = -3.3  for stack of 285-310
		Stack = -2.4  for stack of 286-309
	Helix total = -13.3
	Internal/bulge = 1.9  for closure of 287-308	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.1  for closure of 289-306	Size = 2
		Stack = -2.4  for stack of 291-304
	Helix total = -2.4
	Hairpin = 5.3  for closure of 292-303
		Stack = -1.4  for stack of 238-263
		Stack = -2.4  for stack of 239-262
		Stack = -2.1  for stack of 240-261
		Stack = -2.1  for stack of 241-260
		Stack = -2.4  for stack of 242-259
		Stack = -0.9  for stack of 243-258
		Stack = -2.1  for stack of 244-257
		Stack = -2.5  for stack of 245-256
		Stack = -1.4  for stack of 246-255
	Helix total = -17.3
	Hairpin = 3.2  for closure of 247-254
		Stack = -2.1  for stack of 176-220
		Stack = -1.4  for stack of 177-219
		Stack = -1.5  for stack of 178-218
		Stack = -2.1  for stack of 179-217
		Stack = -2.2  for stack of 180-216
	Helix total = -9.3
	Internal/bulge = 4.1  for closure of 181-215	Size = 4
		Stack = -1.5  for stack of 182-210
		Stack = -2.4  for stack of 183-209
		Stack = -3.3  for stack of 184-208
		Stack = -2.4  for stack of 185-207
		Stack = -0.9  for stack of 186-206
	Helix total = -10.5
	Internal/bulge = 2.4  for closure of 187-205	Size = 4
	Helix total = 0.0
	Hairpin = 5.7  for closure of 190-202
		Stack = -2.4  for stack of 113-175
		Stack = -2.1  for stack of 114-174
		Stack = -1.3  for stack of 115-173
		Stack = -1.4  for stack of 116-172
	Helix total = -7.2
	Multiloop = 6.4  for closure of 117-171
		Stack = -2.4  for stack of 150-170
		Stack = -3.3  for stack of 151-169
	Helix total = -5.7
	Internal/bulge = 0.9  for closure of 152-168	Size = 2
		Stack = -3.3  for stack of 154-166
		Stack = -3.4  for stack of 155-165
		Stack = -2.1  for stack of 156-164
		Stack = -2.2  for stack of 157-163
	Helix total = -11.0
	Hairpin = 5.4  for closure of 158-162
		Stack = -3.4  for stack of 120-145
		Stack = -2.1  for stack of 121-144
	Helix total = -5.5
	Internal/bulge = 2.1  for closure of 122-143	Size = 1 BP stack across bulge = -1.3
		Stack = -0.9  for stack of 124-142
		Stack = -1.1  for stack of 125-141
		Stack = -2.4  for stack of 126-140
	Helix total = -4.4
	Internal/bulge = 1.2  for closure of 127-139	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 129-137	Size = 2
	Helix total = 0.0
	Hairpin = 5.9  for closure of 131-135
		Stack = -1.5  for stack of 56-83
		Stack = -1.4  for stack of 57-82
		Stack = -1.0  for stack of 58-81
		Stack = -1.3  for stack of 59-80
		Stack = -1.4  for stack of 60-79
		Stack = -0.6  for stack of 61-78
	Helix total = -7.2
	Hairpin = 6.8  for closure of 62-77


	Total energy = -69.5



