Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    51:70 53:68 54:67 55:66 222:253 223:252 224:251 225:250
	    226:249 227:248 268:303 270:301 271:300 272:299 273:298 274:297
	    275:296 320:357 321:356 322:355 323:354 324:353 325:352 326:351
	    327:350 328:349
	Energy of Broken Structure: -39.0
	Energy of Pseudo-Helices:   -29.9
	Pseudoknot Energy Penalty:  32.7
	Total Free Energy:          -36.2
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-419
		Stack = -1.5  for stack of 2-418
		Stack = -2.1  for stack of 3-417
		Stack = -2.4  for stack of 4-416
		Stack = -1.1  for stack of 5-415
		Stack = -2.1  for stack of 6-414
	Helix total = -12.5
	Multiloop = 7.1  for closure of 7-413
		Stack = -1.1  for stack of 396-412
		Stack = -2.1  for stack of 397-411
		Stack = -3.3  for stack of 398-410
		Stack = -3.3  for stack of 399-409
	Helix total = -9.8
	Hairpin = 4.4  for closure of 400-408
		Stack = -2.1  for stack of 20-392
		Stack = -0.6  for stack of 21-391
		Stack = -0.5  for stack of 22-390
	Helix total = -3.2
	Internal/bulge = 1.6  for closure of 23-389	Size = 1 BP stack across bulge = -1.4
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 24-387	Size = 2
		Stack = -2.2  for stack of 26-385
	Helix total = -2.2
	Internal/bulge = 2.2  for closure of 27-384	Size = 5
		Stack = -0.9  for stack of 30-380
		Stack = -1.1  for stack of 31-379
		Stack = -0.9  for stack of 32-378
		Stack = -0.9  for stack of 33-377
		Stack = -1.3  for stack of 34-376
		Stack = -1.1  for stack of 35-375
		Stack = -1.3  for stack of 36-374
		Stack = -1.1  for stack of 37-373
		Stack = -1.3  for stack of 38-372
	Helix total = -9.9
	Internal/bulge = 5.1  for closure of 39-371	Size = 6
		Stack = -2.1  for stack of 41-365
		Stack = -1.1  for stack of 42-364
		Stack = -1.3  for stack of 43-363
		Stack = -1.1  for stack of 44-362
	Helix total = -5.6
	Multiloop = 4.2  for closure of 45-361
		Stack = -2.5  for stack of 304-340
		Stack = -1.0  for stack of 305-339
		Stack = -0.9  for stack of 306-338
		Stack = -1.1  for stack of 307-337
	Helix total = -5.5
	Internal/bulge = 2.3  for closure of 308-336	Size = 1 BP stack across bulge = -0.9
	Helix total = 0.0
	Internal/bulge = 3.3  for closure of 310-335	Size = 5
		Stack = -1.5  for stack of 313-331
		Stack = -1.3  for stack of 314-330
	Helix total = -2.8
	Hairpin = 5.6  for closure of 315-329
		Stack = -0.9  for stack of 254-289
		Stack = -0.9  for stack of 255-288
		Stack = -2.1  for stack of 256-287
		Stack = -3.4  for stack of 257-286
		Stack = -2.1  for stack of 258-285
		Stack = -1.3  for stack of 259-284
		Stack = -0.9  for stack of 260-283
	Helix total = -11.6
	Internal/bulge = 3.0  for closure of 261-282	Size = 3
		Stack = -2.1  for stack of 264-280
		Stack = -1.5  for stack of 265-279
	Helix total = -3.6
	Hairpin = 4.1  for closure of 266-278
		Stack = -3.3  for stack of 208-240
	Helix total = -3.3
	Internal/bulge = 0.0  for closure of 209-239	Size = 6
		Stack = -2.1  for stack of 213-235
		Stack = -0.9  for stack of 214-234
		Stack = -1.3  for stack of 215-233
		Stack = -0.9  for stack of 216-232
		Stack = -0.9  for stack of 217-231
		Stack = -1.1  for stack of 218-230
		Stack = -1.3  for stack of 219-229
	Helix total = -8.5
	Hairpin = 5.7  for closure of 220-228
		Stack = -0.9  for stack of 183-206
		Stack = -0.9  for stack of 184-205
		Stack = -0.9  for stack of 185-204
		Stack = -2.1  for stack of 186-203
		Stack = -3.4  for stack of 187-202
		Stack = -2.1  for stack of 188-201
		Stack = -0.9  for stack of 189-200
		Stack = -1.3  for stack of 190-199
	Helix total = -12.5
	Hairpin = 5.1  for closure of 191-198
		Stack = -2.1  for stack of 46-59
		Stack = -0.9  for stack of 47-58
		Stack = -2.1  for stack of 48-57
	Helix total = -5.1
	Hairpin = 3.2  for closure of 49-56


	Total energy = -39.0



