Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    53:77 54:76 55:75 230:267 231:266 235:262 236:261 268:298
	    276:290 320:349 325:344 326:343
	Energy of Broken Structure: 17.0
	Energy of Pseudo-Helices:   -5.2
	Pseudoknot Energy Penalty:  30.8
	Total Free Energy:          42.6
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-429
		Stack = -1.5  for stack of 2-428
		Stack = -2.1  for stack of 3-427
		Stack = -3.3  for stack of 4-426
		Stack = -2.2  for stack of 5-425
		Stack = -2.1  for stack of 6-424
	Helix total = -14.5
	Multiloop = 5.0  for closure of 7-423
		Stack = -2.4  for stack of 406-422
		Stack = -3.3  for stack of 407-421
		Stack = -3.3  for stack of 408-420
		Stack = -3.3  for stack of 409-419
	Helix total = -12.3
	Hairpin = 4.4  for closure of 410-418
		Stack = -2.1  for stack of 20-402
		Stack = -0.9  for stack of 21-401
	Helix total = -3.0
	Internal/bulge = 1.2  for closure of 22-400	Size = 2
		Stack = -1.3  for stack of 24-398
		Stack = -0.9  for stack of 25-397
		Stack = -0.9  for stack of 26-396
		Stack = -0.9  for stack of 27-395
		Stack = -0.9  for stack of 28-394
	Helix total = -4.9
	Internal/bulge = 1.9  for closure of 29-393	Size = 2
		Stack = -0.9  for stack of 31-391
		Stack = -1.1  for stack of 32-390
		Stack = -0.9  for stack of 33-389
	Helix total = -2.9
	Internal/bulge = 1.7  for closure of 34-388	Size = 4
		Stack = -1.3  for stack of 37-385
	Helix total = -1.3
	Internal/bulge = 1.9  for closure of 38-384	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 40-382	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.8  for closure of 42-380	Size = 2
		Stack = -2.5  for stack of 43-377
		Stack = -2.1  for stack of 44-376
		Stack = -2.1  for stack of 45-375
		Stack = -2.2  for stack of 46-374
	Helix total = -8.9
	Multiloop = 4.7  for closure of 47-373
	Helix total = 0.0
	Internal/bulge = 2.8  for closure of 333-369	Size = 6
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 337-365	Size = 2
		Stack = -1.4  for stack of 339-363
		Stack = 0.3  for stack of 340-362
	Helix total = -1.1
	Hairpin = 6.9  for closure of 341-361
	Helix total = 0.0
	Internal/bulge = 3.4  for closure of 280-311	Size = 6
		Stack = -0.6  for stack of 284-307
	Helix total = -0.6
	Hairpin = 7.4  for closure of 285-306
		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 = 17.0



