Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    53:77 54:76 55:75 230:267 231:266 235:262 236:261 314:339
	    315:338 319:333
	Energy of Broken Structure: 13.0
	Energy of Pseudo-Helices:   -4.5
	Pseudoknot Energy Penalty:  22.8
	Total Free Energy:          31.3
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-420
		Stack = -1.5  for stack of 2-419
		Stack = -2.1  for stack of 3-418
		Stack = -3.3  for stack of 4-417
		Stack = -2.2  for stack of 5-416
		Stack = -2.1  for stack of 6-415
	Helix total = -14.5
	Multiloop = 5.0  for closure of 7-414
		Stack = -2.4  for stack of 397-413
		Stack = -3.3  for stack of 398-412
		Stack = -3.3  for stack of 399-411
		Stack = -3.3  for stack of 400-410
	Helix total = -12.3
	Hairpin = 4.4  for closure of 401-409
		Stack = -2.1  for stack of 20-393
		Stack = -0.9  for stack of 21-392
	Helix total = -3.0
	Internal/bulge = 1.2  for closure of 22-391	Size = 2
		Stack = -1.3  for stack of 24-389
		Stack = -0.9  for stack of 25-388
		Stack = -0.9  for stack of 26-387
		Stack = -0.9  for stack of 27-386
		Stack = -0.9  for stack of 28-385
	Helix total = -4.9
	Internal/bulge = 1.9  for closure of 29-384	Size = 2
		Stack = -0.9  for stack of 31-382
		Stack = -1.1  for stack of 32-381
		Stack = -0.9  for stack of 33-380
	Helix total = -2.9
	Internal/bulge = 1.7  for closure of 34-379	Size = 4
		Stack = -1.3  for stack of 37-376
	Helix total = -1.3
	Internal/bulge = 1.9  for closure of 38-375	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 40-373	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.8  for closure of 42-371	Size = 2
		Stack = -2.5  for stack of 43-368
		Stack = -2.1  for stack of 44-367
		Stack = -2.1  for stack of 45-366
		Stack = -2.2  for stack of 46-365
	Helix total = -8.9
	Multiloop = 3.8  for closure of 47-364
	Helix total = 0.0
	Internal/bulge = 1.4  for closure of 324-360	Size = 8
	Helix total = 0.0
	Internal/bulge = 1.6  for closure of 329-355	Size = 2
		Stack = -0.6  for stack of 331-353
	Helix total = -0.6
	Hairpin = 6.9  for closure of 332-352
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 268-292	Size = 2
		Stack = -0.6  for stack of 270-290
		Stack = -1.3  for stack of 271-289
	Helix total = -1.9
	Internal/bulge = 2.8  for closure of 272-288	Size = 6
	Helix total = 0.0
	Hairpin = 5.5  for closure of 276-284
		Stack = -1.1  for stack of 203-247
		Stack = -0.9  for stack of 204-246
		Stack = -0.9  for stack of 205-245
		Stack = -0.9  for stack of 206-244
	Helix total = -3.8
	Internal/bulge = 6.4  for closure of 207-243	Size = 16
		Stack = -2.4  for stack of 224-242
	Helix total = -2.4
	Internal/bulge = 2.7  for closure of 225-241	Size = 6
	Helix total = 0.0
	Hairpin = 5.8  for closure of 229-237
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 170-201	Size = 2
		Stack = -0.9  for stack of 172-199
		Stack = -1.1  for stack of 173-198
		Stack = -0.9  for stack of 174-197
		Stack = -0.9  for stack of 175-196
	Helix total = -3.8
	Internal/bulge = 1.9  for closure of 176-195	Size = 2
	Helix total = 0.0
	Hairpin = 6.0  for closure of 178-193
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 49-60	Size = 2
		Stack = -1.3  for stack of 51-58
	Helix total = -1.3
	Hairpin = 4.7  for closure of 52-57


	Total energy = 13.0



