Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    498:519 499:518 500:517
	Energy of Broken Structure: -105.1
	Energy of Pseudo-Helices:   -6.7
	Pseudoknot Energy Penalty:  6.9
	Total Free Energy:          -104.9
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -3.1
		Stack = -2.4  for stack of 27-549
		Stack = -0.9  for stack of 28-548
		Stack = -2.2  for stack of 29-547
	Helix total = -5.5
	Internal/bulge = 1.7  for closure of 30-546	Size = 1 BP stack across bulge = -2.1
		Stack = -0.9  for stack of 32-545
		Stack = -2.2  for stack of 33-544
		Stack = -2.4  for stack of 34-543
		Stack = -3.4  for stack of 35-542
		Stack = -2.1  for stack of 36-541
	Helix total = -11.0
	Multiloop = 2.6  for closure of 37-540
		Stack = -3.4  for stack of 493-538
		Stack = -3.3  for stack of 494-537
		Stack = -3.3  for stack of 495-536
		Stack = -3.3  for stack of 496-535
	Helix total = -13.3
	Internal/bulge = 4.9  for closure of 497-534	Size = 6
		Stack = -0.9  for stack of 504-533
		Stack = -1.3  for stack of 505-532
		Stack = -2.2  for stack of 506-531
		Stack = -2.4  for stack of 507-530
	Helix total = -6.8
	Hairpin = 6.1  for closure of 508-529
		Stack = -1.3  for stack of 435-485
		Stack = -0.9  for stack of 436-484
		Stack = -0.9  for stack of 437-483
		Stack = -1.1  for stack of 438-482
	Helix total = -4.2
	Internal/bulge = 1.4  for closure of 439-481	Size = 7
	Helix total = 0.0
	Internal/bulge = 2.2  for closure of 443-476	Size = 10
		Stack = -2.5  for stack of 449-470
		Stack = -2.1  for stack of 450-469
		Stack = -0.9  for stack of 451-468
		Stack = -0.9  for stack of 452-467
		Stack = -2.1  for stack of 453-466
		Stack = -2.2  for stack of 454-465
	Helix total = -10.7
	Hairpin = 5.0  for closure of 455-464
		Stack = -2.4  for stack of 399-429
		Stack = -0.9  for stack of 400-428
		Stack = -1.1  for stack of 401-427
	Helix total = -4.4
	Internal/bulge = 2.6  for closure of 402-426	Size = 11
		Stack = -0.5  for stack of 409-420
		Stack = -1.4  for stack of 410-419
		Stack = -2.4  for stack of 411-418
	Helix total = -4.3
	Hairpin = 3.3  for closure of 412-417
		Stack = -3.4  for stack of 39-396
		Stack = -2.1  for stack of 40-395
		Stack = -2.1  for stack of 41-394
		Stack = -2.2  for stack of 42-393
		Stack = -2.1  for stack of 43-392
	Helix total = -11.9
	Internal/bulge = 0.4  for closure of 44-391	Size = 1 BP stack across bulge = -3.4
		Stack = -2.4  for stack of 45-389
	Helix total = -2.4
	Multiloop = 6.0  for closure of 46-388
	Helix total = 0.0
	Internal/bulge = 1.0  for closure of 363-386	Size = 1 BP stack across bulge = -2.4
		Stack = -3.3  for stack of 365-385
		Stack = -2.4  for stack of 366-384
	Helix total = -5.7
	Internal/bulge = 3.0  for closure of 367-383	Size = 4
		Stack = 0.3  for stack of 371-381
		Stack = -2.1  for stack of 372-380
		Stack = -3.4  for stack of 373-379
	Helix total = -5.2
	Hairpin = 5.4  for closure of 374-378
	Helix total = 0.0
	Internal/bulge = 5.2  for closure of 47-357	Size = 5
		Stack = -2.1  for stack of 52-355
		Stack = -3.4  for stack of 53-354
	Helix total = -5.5
	Internal/bulge = 1.7  for closure of 54-353	Size = 1 BP stack across bulge = -2.1
		Stack = -2.1  for stack of 56-352
		Stack = -3.4  for stack of 57-351
	Helix total = -5.5
	Multiloop = -0.3  for closure of 58-350
		Stack = -2.1  for stack of 335-346
		Stack = -2.4  for stack of 336-345
		Stack = -3.3  for stack of 337-344
	Helix total = -7.8
	Hairpin = 2.8  for closure of 338-343
		Stack = -2.1  for stack of 312-333
		Stack = -2.1  for stack of 313-332
		Stack = -3.3  for stack of 314-331
		Stack = -2.4  for stack of 315-330
	Helix total = -9.9
	Hairpin = 6.4  for closure of 316-329
		Stack = -2.2  for stack of 99-310
		Stack = -2.1  for stack of 100-309
	Helix total = -4.3
	Multiloop = 5.8  for closure of 101-308
		Stack = -2.2  for stack of 285-307
		Stack = -3.3  for stack of 286-306
		Stack = -2.4  for stack of 287-305
	Helix total = -7.9
	Internal/bulge = 3.7  for closure of 288-304	Size = 3
		Stack = -2.5  for stack of 289-300
		Stack = -3.3  for stack of 290-299
		Stack = -2.1  for stack of 291-298
	Helix total = -7.9
	Hairpin = 4.7  for closure of 292-297
		Stack = -2.1  for stack of 236-282
		Stack = -0.9  for stack of 237-281
	Helix total = -3.0
	Internal/bulge = 4.4  for closure of 238-280	Size = 10
		Stack = -3.4  for stack of 243-273
		Stack = -2.1  for stack of 244-272
	Helix total = -5.5
	Internal/bulge = 3.8  for closure of 245-271	Size = 2
		Stack = -0.9  for stack of 248-270
		Stack = -2.1  for stack of 249-269
		Stack = -3.3  for stack of 250-268
		Stack = -2.2  for stack of 251-267
		Stack = -1.3  for stack of 252-266
		Stack = -2.1  for stack of 253-265
		Stack = -3.3  for stack of 254-264
	Helix total = -15.2
	Hairpin = 3.8  for closure of 255-263
		Stack = -2.5  for stack of 108-235
		Stack = -2.4  for stack of 109-234
		Stack = -2.5  for stack of 110-233
		Stack = 0.3  for stack of 111-232
		Stack = -2.1  for stack of 112-231
		Stack = -2.4  for stack of 113-230
		Stack = -1.4  for stack of 114-229
	Helix total = -13.0
	Internal/bulge = 3.8  for closure of 115-228	Size = 2
		Stack = -2.4  for stack of 118-227
	Helix total = -2.4
	Internal/bulge = 2.3  for closure of 119-226	Size = 5
		Stack = -2.1  for stack of 123-223
		Stack = -1.3  for stack of 124-222
		Stack = -1.4  for stack of 125-221
		Stack = 0.3  for stack of 126-220
		Stack = -1.3  for stack of 127-219
		Stack = -2.1  for stack of 128-218
	Helix total = -7.9
	Multiloop = 4.6  for closure of 129-217
		Stack = -2.4  for stack of 198-215
	Helix total = -2.4
	Internal/bulge = 2.9  for closure of 199-214	Size = 1 BP stack across bulge = -0.9
		Stack = -2.1  for stack of 200-212
		Stack = -3.4  for stack of 201-211
	Helix total = -5.5
	Hairpin = 5.0  for closure of 202-210
		Stack = -1.4  for stack of 171-192
		Stack = -2.4  for stack of 172-191
		Stack = -2.1  for stack of 173-190
		Stack = -0.6  for stack of 174-189
		Stack = -1.4  for stack of 175-188
		Stack = -0.9  for stack of 176-187
		Stack = -1.3  for stack of 177-186
		Stack = -0.9  for stack of 178-185
	Helix total = -11.0
	Hairpin = 5.5  for closure of 179-184
	Helix total = 0.0
	Internal/bulge = -1.4  for closure of 131-165	Size = 2
		Stack = -3.3  for stack of 133-163
	Helix total = -3.3
	Internal/bulge = 2.2  for closure of 134-162	Size = 11
		Stack = -2.1  for stack of 140-155
		Stack = -1.3  for stack of 141-154
		Stack = -1.4  for stack of 142-153
		Stack = -0.6  for stack of 143-152
		Stack = -1.3  for stack of 144-151
	Helix total = -6.7
	Hairpin = 4.4  for closure of 145-150
		Stack = -2.5  for stack of 61-92
		Stack = -1.5  for stack of 62-91
	Helix total = -4.0
	Internal/bulge = 3.3  for closure of 63-90	Size = 2
		Stack = -2.2  for stack of 66-89
	Helix total = -2.2
	Internal/bulge = 0.5  for closure of 67-88	Size = 2
		Stack = -1.5  for stack of 69-86
		Stack = -1.3  for stack of 70-85
		Stack = -1.1  for stack of 71-84
		Stack = -2.1  for stack of 72-83
		Stack = -2.2  for stack of 73-82
		Stack = -1.3  for stack of 74-81
	Helix total = -9.5
	Hairpin = 4.4  for closure of 75-80
		Stack = -1.3  for stack of 9-25
		Stack = -2.1  for stack of 10-24
		Stack = -2.5  for stack of 11-23
		Stack = -0.5  for stack of 12-22
	Helix total = -6.4
	Hairpin = 5.1  for closure of 13-21


	Total energy = -105.1



