Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    513:534 514:533 515:532
	Energy of Broken Structure: -122.8
	Energy of Pseudo-Helices:   -5.5
	Pseudoknot Energy Penalty:  6.9
	Total Free Energy:          -121.4
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -3.7
		Stack = -2.4  for stack of 27-564
		Stack = -1.1  for stack of 28-563
		Stack = -0.9  for stack of 29-562
	Helix total = -4.4
	Internal/bulge = 2.5  for closure of 30-561	Size = 1 BP stack across bulge = -1.3
		Stack = -0.9  for stack of 32-560
		Stack = -2.2  for stack of 33-559
		Stack = -2.4  for stack of 34-558
		Stack = -3.4  for stack of 35-557
		Stack = -2.1  for stack of 36-556
	Helix total = -11.0
	Multiloop = -0.3  for closure of 37-555
		Stack = -3.4  for stack of 508-553
		Stack = -2.1  for stack of 509-552
		Stack = -2.2  for stack of 510-551
		Stack = -3.3  for stack of 511-550
	Helix total = -11.0
	Internal/bulge = 4.4  for closure of 512-549	Size = 6
		Stack = -2.1  for stack of 519-548
		Stack = -2.4  for stack of 520-547
		Stack = -3.3  for stack of 521-546
		Stack = -2.4  for stack of 522-545
	Helix total = -10.2
	Hairpin = 6.1  for closure of 523-544
	Helix total = 0.0
	Internal/bulge = 3.8  for closure of 448-505	Size = 5
		Stack = -2.1  for stack of 450-500
		Stack = -0.6  for stack of 451-499
		Stack = -2.1  for stack of 452-498
		Stack = -3.3  for stack of 453-497
	Helix total = -8.1
	Internal/bulge = 2.4  for closure of 454-496	Size = 7
	Helix total = 0.0
	Internal/bulge = 3.1  for closure of 458-491	Size = 13
		Stack = -2.4  for stack of 465-483
		Stack = -1.1  for stack of 466-482
		Stack = -0.9  for stack of 467-481
		Stack = -2.1  for stack of 468-480
		Stack = -3.3  for stack of 469-479
	Helix total = -9.8
	Hairpin = 5.5  for closure of 470-478
		Stack = -2.2  for stack of 414-444
		Stack = -2.1  for stack of 415-443
		Stack = -2.5  for stack of 416-442
	Helix total = -6.8
	Internal/bulge = 2.6  for closure of 417-441	Size = 11
		Stack = -0.5  for stack of 424-435
		Stack = -2.5  for stack of 425-434
		Stack = -2.1  for stack of 426-433
	Helix total = -5.1
	Hairpin = 5.4  for closure of 427-432
		Stack = -3.4  for stack of 39-411
		Stack = -2.4  for stack of 40-410
		Stack = -3.3  for stack of 41-409
		Stack = -3.4  for stack of 42-408
		Stack = -2.4  for stack of 43-407
	Helix total = -14.9
	Internal/bulge = 1.3  for closure of 44-406	Size = 1 BP stack across bulge = -2.5
		Stack = -1.4  for stack of 45-404
	Helix total = -1.4
	Multiloop = 5.0  for closure of 46-403
	Helix total = 0.0
	Internal/bulge = 2.3  for closure of 375-401	Size = 1 BP stack across bulge = -0.9
		Stack = -2.4  for stack of 377-400
		Stack = -2.4  for stack of 378-399
	Helix total = -4.8
	Internal/bulge = 3.0  for closure of 379-398	Size = 4
		Stack = 0.3  for stack of 383-396
		Stack = -2.1  for stack of 384-395
		Stack = -2.4  for stack of 385-394
		Stack = -2.2  for stack of 386-393
	Helix total = -6.4
	Hairpin = 3.3  for closure of 387-392
		Stack = -1.5  for stack of 52-367
		Stack = -2.5  for stack of 53-366
	Helix total = -4.0
	Internal/bulge = 1.7  for closure of 54-365	Size = 1 BP stack across bulge = -2.1
		Stack = -2.1  for stack of 56-364
		Stack = -3.4  for stack of 57-363
	Helix total = -5.5
	Multiloop = -0.3  for closure of 58-362
		Stack = -2.1  for stack of 347-358
		Stack = -0.9  for stack of 348-357
		Stack = -2.4  for stack of 349-356
	Helix total = -5.4
	Hairpin = 2.8  for closure of 350-355
		Stack = -2.1  for stack of 324-345
		Stack = -2.1  for stack of 325-344
		Stack = -3.3  for stack of 326-343
		Stack = -3.3  for stack of 327-342
	Helix total = -10.8
	Hairpin = 5.4  for closure of 328-341
		Stack = -2.2  for stack of 105-322
		Stack = -0.9  for stack of 106-321
	Helix total = -3.1
	Multiloop = 3.5  for closure of 107-320
		Stack = -3.3  for stack of 297-319
		Stack = -3.4  for stack of 298-318
		Stack = -2.4  for stack of 299-317
	Helix total = -9.1
	Internal/bulge = 3.7  for closure of 300-316	Size = 3
		Stack = -1.3  for stack of 301-312
		Stack = -1.1  for stack of 302-311
		Stack = -1.3  for stack of 303-310
	Helix total = -3.7
	Hairpin = 4.7  for closure of 304-309
		Stack = -2.4  for stack of 248-294
		Stack = -1.4  for stack of 249-293
	Helix total = -3.8
	Internal/bulge = 4.4  for closure of 250-292	Size = 10
		Stack = -3.4  for stack of 255-285
		Stack = -2.1  for stack of 256-284
	Helix total = -5.5
	Internal/bulge = 3.8  for closure of 257-283	Size = 2
		Stack = -0.9  for stack of 260-282
		Stack = -2.1  for stack of 261-281
		Stack = -3.3  for stack of 262-280
		Stack = -2.2  for stack of 263-279
		Stack = -1.0  for stack of 264-278
		Stack = -2.1  for stack of 265-277
		Stack = -3.3  for stack of 266-276
	Helix total = -14.9
	Hairpin = 3.8  for closure of 267-275
		Stack = -2.1  for stack of 115-246
		Stack = -1.1  for stack of 116-245
		Stack = -1.3  for stack of 117-244
		Stack = -2.1  for stack of 118-243
		Stack = -2.4  for stack of 119-242
		Stack = -1.4  for stack of 120-241
	Helix total = -10.4
	Internal/bulge = 3.8  for closure of 121-240	Size = 2
		Stack = -2.4  for stack of 124-239
	Helix total = -2.4
	Internal/bulge = 2.6  for closure of 125-238	Size = 5
		Stack = -3.3  for stack of 129-235
		Stack = -2.1  for stack of 130-234
		Stack = -2.4  for stack of 131-233
		Stack = -2.1  for stack of 132-232
		Stack = -0.9  for stack of 133-231
		Stack = -2.2  for stack of 134-230
	Helix total = -13.0
	Multiloop = 4.2  for closure of 135-229
		Stack = -2.4  for stack of 206-227
		Stack = -0.9  for stack of 207-226
		Stack = -0.6  for stack of 208-225
		Stack = -2.1  for stack of 209-224
		Stack = -3.3  for stack of 210-223
	Helix total = -9.3
	Internal/bulge = 3.3  for closure of 211-222	Size = 2
		Stack = -2.4  for stack of 214-221
	Helix total = -2.4
	Hairpin = 3.7  for closure of 215-220
		Stack = -1.4  for stack of 177-201
		Stack = -1.3  for stack of 178-200
		Stack = -1.1  for stack of 179-199
		Stack = -2.1  for stack of 180-198
		Stack = -2.2  for stack of 181-197
		Stack = -0.9  for stack of 182-196
	Helix total = -9.0
	Internal/bulge = 2.1  for closure of 183-195	Size = 1 BP stack across bulge = -0.9
		Stack = -1.3  for stack of 184-193
		Stack = -2.1  for stack of 185-192
	Helix total = -3.4
	Hairpin = 4.1  for closure of 186-191
	Helix total = 0.0
	Internal/bulge = -1.4  for closure of 137-171	Size = 2
		Stack = -3.3  for stack of 139-169
	Helix total = -3.3
	Internal/bulge = 3.2  for closure of 140-168	Size = 11
		Stack = -2.4  for stack of 146-161
		Stack = -3.3  for stack of 147-160
		Stack = -2.2  for stack of 148-159
		Stack = -1.3  for stack of 149-158
		Stack = -1.4  for stack of 150-157
	Helix total = -10.6
	Hairpin = 3.1  for closure of 151-156
		Stack = -2.5  for stack of 61-98
		Stack = -1.5  for stack of 62-97
	Helix total = -4.0
	Internal/bulge = 3.3  for closure of 63-96	Size = 2
		Stack = -2.2  for stack of 66-95
	Helix total = -2.2
	Internal/bulge = 1.2  for closure of 67-94	Size = 2
		Stack = -1.3  for stack of 69-92
		Stack = -0.9  for stack of 70-91
		Stack = -1.1  for stack of 71-90
		Stack = -1.3  for stack of 72-89
		Stack = -0.9  for stack of 73-88
		Stack = -1.4  for stack of 74-87
		Stack = 0.3  for stack of 75-86
		Stack = -1.3  for stack of 76-85
		Stack = -2.2  for stack of 77-84
	Helix total = -10.1
	Hairpin = 3.7  for closure of 78-83
		Stack = -2.4  for stack of 9-25
		Stack = -0.9  for stack of 10-24
		Stack = -1.4  for stack of 11-23
		Stack = -0.5  for stack of 12-22
	Helix total = -5.2
	Hairpin = 5.1  for closure of 13-21


	Total energy = -122.8



