Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:68 49:67 50:66 51:65 52:64 197:236 198:235 199:234
	    200:233 201:232 202:231 252:279 253:278 254:277 255:276 299:334
	    300:333 301:332 302:331 303:330
	Energy of Broken Structure: -71.7
	Energy of Pseudo-Helices:   -35.3
	Pseudoknot Energy Penalty:  36.5
	Total Free Energy:          -70.5
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-396
		Stack = -1.5  for stack of 2-395
		Stack = -2.1  for stack of 3-394
		Stack = -3.4  for stack of 4-393
		Stack = -2.1  for stack of 5-392
		Stack = -2.1  for stack of 6-391
	Helix total = -14.5
	Multiloop = 5.0  for closure of 7-390
		Stack = -2.4  for stack of 373-389
		Stack = -2.1  for stack of 374-388
		Stack = -2.4  for stack of 375-387
		Stack = -2.1  for stack of 376-386
	Helix total = -9.0
	Hairpin = 4.4  for closure of 377-385
		Stack = -2.1  for stack of 19-369
		Stack = -0.6  for stack of 20-368
	Helix total = -2.7
	Internal/bulge = 0.8  for closure of 21-367	Size = 4
		Stack = -1.5  for stack of 24-364
	Helix total = -1.5
	Internal/bulge = 3.0  for closure of 25-363	Size = 3
		Stack = -2.4  for stack of 28-361
		Stack = -0.9  for stack of 29-360
	Helix total = -3.3
	Internal/bulge = -0.7  for closure of 30-359	Size = 2
		Stack = -1.0  for stack of 32-357
		Stack = -0.5  for stack of 33-356
		Stack = -1.4  for stack of 34-355
		Stack = -0.9  for stack of 35-354
		Stack = -0.9  for stack of 36-353
		Stack = -2.1  for stack of 37-352
		Stack = -2.5  for stack of 38-351
	Helix total = -9.3
	Internal/bulge = 4.9  for closure of 39-350	Size = 9
		Stack = -2.1  for stack of 43-343
		Stack = -1.1  for stack of 44-342
		Stack = -2.1  for stack of 45-341
		Stack = -3.4  for stack of 46-340
	Helix total = -8.7
	Multiloop = 6.1  for closure of 47-339
	Helix total = 0.0
	Internal/bulge = 1.1  for closure of 281-320	Size = 6
		Stack = -2.5  for stack of 285-316
		Stack = -0.6  for stack of 286-315
		Stack = -2.1  for stack of 287-314
		Stack = -3.4  for stack of 288-313
		Stack = -2.4  for stack of 289-312
		Stack = -3.3  for stack of 290-311
		Stack = -2.5  for stack of 291-310
		Stack = 0.3  for stack of 292-309
		Stack = -0.5  for stack of 293-308
		Stack = -2.1  for stack of 294-307
	Helix total = -19.1
	Hairpin = 4.9  for closure of 295-306
		Stack = -2.5  for stack of 240-266
		Stack = -2.1  for stack of 241-265
		Stack = -0.9  for stack of 242-264
		Stack = -2.1  for stack of 243-263
	Helix total = -7.6
	Internal/bulge = 0.5  for closure of 244-262	Size = 2
		Stack = -2.4  for stack of 246-260
	Helix total = -2.4
	Internal/bulge = 1.2  for closure of 247-259	Size = 2
		Stack = -1.4  for stack of 249-257
	Helix total = -1.4
	Hairpin = 5.4  for closure of 250-256
		Stack = -2.1  for stack of 178-222
		Stack = -1.4  for stack of 179-221
		Stack = -1.5  for stack of 180-220
		Stack = -2.1  for stack of 181-219
		Stack = -2.2  for stack of 182-218
	Helix total = -9.3
	Internal/bulge = 4.4  for closure of 183-217	Size = 6
		Stack = -2.4  for stack of 185-211
		Stack = -3.3  for stack of 186-210
		Stack = -2.4  for stack of 187-209
	Helix total = -8.1
	Internal/bulge = 3.0  for closure of 188-208	Size = 3
		Stack = -3.4  for stack of 190-205
		Stack = -3.3  for stack of 191-204
	Helix total = -6.7
	Hairpin = 4.2  for closure of 192-203
		Stack = -2.4  for stack of 113-177
		Stack = -2.1  for stack of 114-176
		Stack = -2.4  for stack of 115-175
		Stack = -2.4  for stack of 116-174
	Helix total = -9.3
	Multiloop = 6.4  for closure of 117-173
		Stack = -2.4  for stack of 152-172
		Stack = -3.3  for stack of 153-171
	Helix total = -5.7
	Internal/bulge = 0.3  for closure of 154-170	Size = 4
		Stack = -2.2  for stack of 157-167
		Stack = -2.1  for stack of 158-166
		Stack = -2.2  for stack of 159-165
	Helix total = -6.5
	Hairpin = 5.4  for closure of 160-164
		Stack = -3.4  for stack of 120-147
		Stack = -2.1  for stack of 121-146
	Helix total = -5.5
	Internal/bulge = 2.1  for closure of 122-145	Size = 1 BP stack across bulge = -1.3
		Stack = -1.0  for stack of 123-143
		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 = -5.4
	Internal/bulge = 1.2  for closure of 127-139	Size = 2
	Helix total = 0.0
	Hairpin = 5.7  for closure of 129-137
		Stack = -1.4  for stack of 56-83
		Stack = -1.3  for stack of 57-82
		Stack = 0.3  for stack of 58-81
		Stack = -0.5  for stack of 59-80
		Stack = -2.5  for stack of 60-79
		Stack = -3.3  for stack of 61-78
	Helix total = -8.7
	Hairpin = 5.4  for closure of 62-77


	Total energy = -71.7



