Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:72 50:71 51:70 52:69 53:68 176:237 177:236 178:235
	    179:234 180:233 181:232 182:231 252:281 253:280 254:279 255:278
	    256:277 300:335 301:334 302:333 303:332 304:331 305:330
	Energy of Broken Structure: -86.2
	Energy of Pseudo-Helices:   -39.7
	Pseudoknot Energy Penalty:  33.1
	Total Free Energy:          -92.8
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-397
		Stack = -1.5  for stack of 2-396
		Stack = -2.1  for stack of 3-395
		Stack = -2.4  for stack of 4-394
		Stack = -1.1  for stack of 5-393
		Stack = -2.1  for stack of 6-392
	Helix total = -12.5
	Multiloop = 5.1  for closure of 7-391
		Stack = -3.4  for stack of 374-390
		Stack = -2.4  for stack of 375-389
		Stack = -3.3  for stack of 376-388
		Stack = -3.3  for stack of 377-387
	Helix total = -12.4
	Hairpin = 4.4  for closure of 378-386
		Stack = -2.1  for stack of 20-370
		Stack = -2.1  for stack of 21-369
		Stack = -1.5  for stack of 22-368
		Stack = -0.5  for stack of 23-367
		Stack = -1.4  for stack of 24-366
		Stack = -1.3  for stack of 25-365
	Helix total = -8.9
	Internal/bulge = 2.6  for closure of 26-364	Size = 3
		Stack = -2.1  for stack of 29-362
		Stack = -2.5  for stack of 30-361
	Helix total = -4.6
	Internal/bulge = 1.6  for closure of 31-360	Size = 4
		Stack = -1.5  for stack of 34-357
		Stack = -1.4  for stack of 35-356
		Stack = -1.0  for stack of 36-355
		Stack = -0.5  for stack of 37-354
		Stack = -2.5  for stack of 38-353
		Stack = -2.4  for stack of 39-352
		Stack = -2.5  for stack of 40-351
		Stack = -0.6  for stack of 41-350
		Stack = -1.0  for stack of 42-349
	Helix total = -13.4
	Internal/bulge = 3.7  for closure of 43-348	Size = 3
		Stack = -2.1  for stack of 44-344
		Stack = -2.2  for stack of 45-343
		Stack = -2.1  for stack of 46-342
		Stack = -2.4  for stack of 47-341
	Helix total = -8.8
	Multiloop = 3.6  for closure of 48-340
		Stack = -1.4  for stack of 285-319
		Stack = -1.3  for stack of 286-318
		Stack = -0.9  for stack of 287-317
		Stack = -2.1  for stack of 288-316
		Stack = -2.2  for stack of 289-315
		Stack = -0.9  for stack of 290-314
		Stack = -2.1  for stack of 291-313
	Helix total = -10.9
	Internal/bulge = 3.0  for closure of 292-312	Size = 3
		Stack = -2.2  for stack of 294-309
		Stack = -2.4  for stack of 295-308
	Helix total = -4.6
	Hairpin = 4.9  for closure of 296-307
		Stack = -1.5  for stack of 238-269
		Stack = -3.3  for stack of 239-268
		Stack = -2.4  for stack of 240-267
		Stack = -2.5  for stack of 241-266
		Stack = -0.6  for stack of 242-265
	Helix total = -10.3
	Internal/bulge = 0.3  for closure of 243-264	Size = 4
		Stack = -2.5  for stack of 246-261
		Stack = -1.0  for stack of 247-260
		Stack = -1.4  for stack of 248-259
	Helix total = -4.9
	Hairpin = 4.6  for closure of 249-258
		Stack = -3.4  for stack of 209-229
		Stack = -2.4  for stack of 210-228
		Stack = -3.4  for stack of 211-227
	Helix total = -9.2
	Internal/bulge = 2.8  for closure of 212-226	Size = 2
		Stack = -2.4  for stack of 215-225
		Stack = -2.1  for stack of 216-224
		Stack = -3.4  for stack of 217-223
	Helix total = -7.9
	Hairpin = 5.4  for closure of 218-222
		Stack = -1.4  for stack of 159-199
		Stack = -2.5  for stack of 160-198
		Stack = -2.1  for stack of 161-197
		Stack = -2.4  for stack of 162-196
	Helix total = -8.4
	Internal/bulge = 2.3  for closure of 163-195	Size = 5
		Stack = -2.1  for stack of 166-191
		Stack = -2.1  for stack of 167-190
		Stack = -3.4  for stack of 168-189
	Helix total = -7.6
	Hairpin = 4.7  for closure of 169-188
		Stack = -1.1  for stack of 121-158
		Stack = -2.1  for stack of 122-157
		Stack = -3.3  for stack of 123-156
		Stack = -3.4  for stack of 124-155
		Stack = -2.1  for stack of 125-154
	Helix total = -12.0
	Internal/bulge = 4.0  for closure of 126-153	Size = 5
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 130-150	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.3  for closure of 132-148	Size = 1 BP stack across bulge = -1.1
		Stack = -0.9  for stack of 133-146
		Stack = -1.3  for stack of 134-145
		Stack = -0.6  for stack of 135-144
		Stack = -2.5  for stack of 136-143
	Helix total = -5.3
	Hairpin = 4.1  for closure of 137-142
		Stack = -2.1  for stack of 59-87
		Stack = -1.1  for stack of 60-86
		Stack = -1.0  for stack of 61-85
		Stack = -2.1  for stack of 62-84
		Stack = -2.4  for stack of 63-83
		Stack = -1.4  for stack of 64-82
	Helix total = -10.1
	Hairpin = 6.0  for closure of 65-81


	Total energy = -86.2



