Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    54:76 55:75 194:228 195:227 196:226 197:225 198:224 199:223
	    200:222 241:273 242:272 243:271 244:270 245:269 246:268 248:266
	    276:313 278:311 279:310 282:308 283:307 285:305 288:302 290:300
	Energy of Broken Structure: -43.3
	Energy of Pseudo-Helices:   -20.2
	Pseudoknot Energy Penalty:  43.9
	Total Free Energy:          -19.6
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-390
		Stack = -1.5  for stack of 2-389
		Stack = -2.1  for stack of 3-388
		Stack = -1.5  for stack of 4-387
		Stack = -1.4  for stack of 5-386
		Stack = -2.1  for stack of 6-385
	Helix total = -11.9
	Multiloop = 5.0  for closure of 7-384
		Stack = -2.4  for stack of 367-383
		Stack = -3.3  for stack of 368-382
		Stack = -3.3  for stack of 369-381
		Stack = -3.3  for stack of 370-380
	Helix total = -12.3
	Hairpin = 4.4  for closure of 371-379
		Stack = -2.1  for stack of 20-363
	Helix total = -2.1
	Internal/bulge = -0.7  for closure of 21-362	Size = 2
		Stack = -2.5  for stack of 23-360
		Stack = -2.1  for stack of 24-359
		Stack = -2.2  for stack of 25-358
		Stack = -2.1  for stack of 26-357
	Helix total = -8.9
	Internal/bulge = 2.1  for closure of 27-356	Size = 8
		Stack = -0.9  for stack of 32-351
		Stack = -1.3  for stack of 33-350
		Stack = -0.9  for stack of 34-349
		Stack = -1.1  for stack of 35-348
		Stack = -1.3  for stack of 36-347
		Stack = -0.9  for stack of 37-346
		Stack = -0.9  for stack of 38-345
		Stack = -1.1  for stack of 39-344
	Helix total = -8.4
	Internal/bulge = 5.2  for closure of 40-343	Size = 5
		Stack = -2.5  for stack of 42-338
		Stack = -2.1  for stack of 43-337
		Stack = -0.6  for stack of 44-336
	Helix total = -5.2
	Multiloop = 3.7  for closure of 45-335
		Stack = -2.2  for stack of 291-329
		Stack = -0.9  for stack of 292-328
		Stack = -1.3  for stack of 293-327
		Stack = -0.9  for stack of 294-326
		Stack = -1.1  for stack of 295-325
		Stack = -0.9  for stack of 296-324
		Stack = -1.3  for stack of 297-323
		Stack = -0.6  for stack of 298-322
	Helix total = -9.2
	Hairpin = 6.8  for closure of 299-321
		Stack = -2.5  for stack of 230-258
	Helix total = -2.5
	Internal/bulge = 0.5  for closure of 231-257	Size = 1 BP stack across bulge = -3.3
		Stack = -2.1  for stack of 232-255
		Stack = -0.9  for stack of 233-254
		Stack = -1.3  for stack of 234-253
		Stack = -0.9  for stack of 235-252
		Stack = -2.2  for stack of 236-251
		Stack = -2.1  for stack of 237-250
	Helix total = -9.5
	Hairpin = 6.0  for closure of 238-249
		Stack = -2.1  for stack of 181-214
		Stack = -0.6  for stack of 182-213
	Helix total = -2.7
	Internal/bulge = 1.1  for closure of 183-212	Size = 1 BP stack across bulge = -2.1
		Stack = -3.4  for stack of 184-210
		Stack = -1.4  for stack of 185-209
		Stack = -1.3  for stack of 186-208
		Stack = -0.9  for stack of 187-207
		Stack = -1.1  for stack of 188-206
		Stack = -1.3  for stack of 189-205
		Stack = -1.1  for stack of 190-204
	Helix total = -10.5
	Internal/bulge = 1.9  for closure of 191-203	Size = 2
	Helix total = 0.0
	Hairpin = 5.9  for closure of 193-201
		Stack = -2.1  for stack of 155-179
		Stack = -1.3  for stack of 156-178
		Stack = -2.2  for stack of 157-177
	Helix total = -5.6
	Internal/bulge = 1.2  for closure of 158-176	Size = 2
		Stack = -1.1  for stack of 160-174
		Stack = -0.9  for stack of 161-173
		Stack = -0.9  for stack of 162-172
		Stack = -1.0  for stack of 163-171
	Helix total = -3.9
	Hairpin = 5.6  for closure of 164-170
		Stack = -1.5  for stack of 47-67
		Stack = -1.4  for stack of 48-66
	Helix total = -2.9
	Internal/bulge = 1.2  for closure of 49-65	Size = 2
	Helix total = 0.0
	Hairpin = 4.1  for closure of 51-63


	Total energy = -43.3



