Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    56:82 57:81 58:80 59:79 61:77 210:252 211:251 212:250
	    213:249 214:248 215:247 216:246 268:297 269:296 270:295 271:294
	    272:293 316:356 317:355 318:354 319:353 321:350 322:349
	Energy of Broken Structure: -52.8
	Energy of Pseudo-Helices:   -31.8
	Pseudoknot Energy Penalty:  34.1
	Total Free Energy:          -50.5
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-417
		Stack = -1.5  for stack of 2-416
		Stack = -2.1  for stack of 3-415
		Stack = -3.3  for stack of 4-414
		Stack = -3.4  for stack of 5-413
		Stack = -2.4  for stack of 6-412
	Helix total = -16.0
	Multiloop = 5.2  for closure of 7-411
		Stack = -3.4  for stack of 394-410
		Stack = -2.4  for stack of 395-409
		Stack = -3.3  for stack of 396-408
		Stack = -3.3  for stack of 397-407
	Helix total = -12.4
	Hairpin = 4.4  for closure of 398-406
		Stack = -2.1  for stack of 21-390
		Stack = -1.4  for stack of 22-389
		Stack = 0.3  for stack of 23-388
		Stack = -1.3  for stack of 24-387
		Stack = -0.9  for stack of 25-386
		Stack = -1.4  for stack of 26-385
	Helix total = -6.8
	Internal/bulge = 1.9  for closure of 27-384	Size = 2
	Helix total = 0.0
	Internal/bulge = 4.1  for closure of 29-382	Size = 7
		Stack = -1.1  for stack of 34-378
		Stack = -2.4  for stack of 35-377
		Stack = -2.1  for stack of 36-376
	Helix total = -5.6
	Internal/bulge = 2.0  for closure of 37-375	Size = 4
		Stack = -3.3  for stack of 40-372
	Helix total = -3.3
	Internal/bulge = 3.3  for closure of 41-371	Size = 7
		Stack = -2.1  for stack of 44-365
		Stack = -1.1  for stack of 45-364
		Stack = -2.1  for stack of 46-363
		Stack = -3.4  for stack of 47-362
	Helix total = -8.7
	Multiloop = 2.8  for closure of 48-361
		Stack = -3.4  for stack of 300-337
		Stack = -2.1  for stack of 301-336
	Helix total = -5.5
	Internal/bulge = 3.7  for closure of 302-335	Size = 3
		Stack = -2.2  for stack of 304-332
		Stack = -2.1  for stack of 305-331
		Stack = -1.3  for stack of 306-330
		Stack = -1.1  for stack of 307-329
		Stack = -0.9  for stack of 308-328
	Helix total = -7.6
	Internal/bulge = 1.4  for closure of 309-327	Size = 1 BP stack across bulge = -2.4
		Stack = -3.3  for stack of 311-326
		Stack = -3.3  for stack of 312-325
		Stack = -2.1  for stack of 313-324
	Helix total = -8.7
	Hairpin = 5.2  for closure of 314-323
		Stack = -1.4  for stack of 253-285
		Stack = -2.1  for stack of 254-284
		Stack = -2.5  for stack of 255-283
		Stack = -1.5  for stack of 256-282
		Stack = -2.1  for stack of 257-281
		Stack = -0.9  for stack of 258-280
	Helix total = -10.5
	Internal/bulge = 1.9  for closure of 259-279	Size = 2
		Stack = -2.5  for stack of 261-277
		Stack = -2.1  for stack of 262-276
		Stack = -1.3  for stack of 263-275
		Stack = -0.5  for stack of 264-274
	Helix total = -6.4
	Hairpin = 5.8  for closure of 265-273
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 191-237	Size = 2
		Stack = -2.2  for stack of 193-235
		Stack = -2.4  for stack of 194-234
		Stack = -3.3  for stack of 195-233
	Helix total = -7.9
	Internal/bulge = 3.3  for closure of 196-232	Size = 2
		Stack = -1.1  for stack of 199-231
		Stack = -2.1  for stack of 200-230
	Helix total = -3.2
	Internal/bulge = 5.8  for closure of 201-229	Size = 7
		Stack = -1.3  for stack of 203-222
		Stack = -2.1  for stack of 204-221
		Stack = -2.2  for stack of 205-220
	Helix total = -5.6
	Internal/bulge = 1.9  for closure of 206-219	Size = 2
	Helix total = 0.0
	Hairpin = 5.3  for closure of 208-217
	Helix total = 0.0
	Internal/bulge = 1.1  for closure of 147-187	Size = 6
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 151-183	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.1  for closure of 153-181	Size = 4
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 156-178	Size = 2
		Stack = -0.9  for stack of 158-176
		Stack = -2.1  for stack of 159-175
		Stack = -3.4  for stack of 160-174
		Stack = -2.1  for stack of 161-173
		Stack = -1.0  for stack of 162-172
	Helix total = -9.5
	Hairpin = 5.8  for closure of 163-171
		Stack = -2.4  for stack of 49-69
		Stack = -2.4  for stack of 50-68
		Stack = -2.1  for stack of 51-67
		Stack = -3.3  for stack of 52-66
	Helix total = -10.2
	Hairpin = 5.5  for closure of 53-65


	Total energy = -52.8



