Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    512:533 513:532 514:531
	Energy of Broken Structure: -163.7
	Energy of Pseudo-Helices:   -6.7
	Pseudoknot Energy Penalty:  6.9
	Total Free Energy:          -163.5
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -3.7
		Stack = -3.3  for stack of 28-563
		Stack = -2.4  for stack of 29-562
		Stack = -2.2  for stack of 30-561
	Helix total = -7.9
	Internal/bulge = 1.7  for closure of 31-560	Size = 1 BP stack across bulge = -2.1
		Stack = -0.9  for stack of 33-559
		Stack = -2.2  for stack of 34-558
		Stack = -2.4  for stack of 35-557
		Stack = -3.4  for stack of 36-556
		Stack = -2.1  for stack of 37-555
	Helix total = -11.0
	Multiloop = 0.4  for closure of 38-554
		Stack = -3.4  for stack of 507-552
		Stack = -3.3  for stack of 508-551
		Stack = -2.1  for stack of 509-550
		Stack = -2.2  for stack of 510-549
	Helix total = -11.0
	Internal/bulge = 4.4  for closure of 511-548	Size = 6
		Stack = -2.1  for stack of 518-547
		Stack = -1.3  for stack of 519-546
		Stack = -2.2  for stack of 520-545
		Stack = -2.4  for stack of 521-544
	Helix total = -8.0
	Hairpin = 6.1  for closure of 522-543
	Helix total = 0.0
	Internal/bulge = 5.2  for closure of 446-504	Size = 5
		Stack = -0.9  for stack of 448-499
		Stack = -1.3  for stack of 449-498
		Stack = -2.1  for stack of 450-497
		Stack = -3.3  for stack of 451-496
	Helix total = -7.6
	Internal/bulge = 0.7  for closure of 452-495	Size = 7
	Helix total = 0.0
	Internal/bulge = 2.5  for closure of 456-490	Size = 10
		Stack = -2.2  for stack of 462-484
		Stack = -1.3  for stack of 463-483
		Stack = -2.2  for stack of 464-482
		Stack = -3.3  for stack of 465-481
		Stack = -2.4  for stack of 466-480
		Stack = -2.5  for stack of 467-479
		Stack = -0.5  for stack of 468-478
	Helix total = -14.4
	Hairpin = 5.8  for closure of 469-477
		Stack = -2.4  for stack of 412-442
		Stack = -2.1  for stack of 413-441
		Stack = -2.5  for stack of 414-440
	Helix total = -7.0
	Internal/bulge = 1.9  for closure of 415-439	Size = 11
		Stack = -1.5  for stack of 422-433
		Stack = -1.4  for stack of 423-432
		Stack = -1.3  for stack of 424-431
	Helix total = -4.2
	Hairpin = 5.4  for closure of 425-430
		Stack = -3.4  for stack of 40-409
		Stack = -2.4  for stack of 41-408
		Stack = -3.3  for stack of 42-407
		Stack = -3.4  for stack of 43-406
		Stack = -2.4  for stack of 44-405
	Helix total = -14.9
	Internal/bulge = 1.2  for closure of 45-404	Size = 1 BP stack across bulge = -2.2
		Stack = -2.1  for stack of 46-402
	Helix total = -2.1
	Multiloop = 5.0  for closure of 47-401
	Helix total = 0.0
	Internal/bulge = 1.0  for closure of 373-399	Size = 1 BP stack across bulge = -2.4
		Stack = -3.3  for stack of 375-398
		Stack = -2.4  for stack of 376-397
	Helix total = -5.7
	Internal/bulge = 3.0  for closure of 377-396	Size = 4
		Stack = 0.3  for stack of 381-394
		Stack = -2.1  for stack of 382-393
		Stack = -2.4  for stack of 383-392
		Stack = -2.2  for stack of 384-391
	Helix total = -6.4
	Hairpin = 3.3  for closure of 385-390
	Helix total = 0.0
	Internal/bulge = 4.5  for closure of 48-367	Size = 5
		Stack = -1.3  for stack of 53-365
		Stack = -2.2  for stack of 54-364
	Helix total = -3.5
	Internal/bulge = 1.7  for closure of 55-363	Size = 1 BP stack across bulge = -2.1
		Stack = -2.1  for stack of 57-362
		Stack = -3.4  for stack of 58-361
	Helix total = -5.5
	Multiloop = -0.3  for closure of 59-360
		Stack = -2.1  for stack of 345-356
		Stack = -2.4  for stack of 346-355
		Stack = -3.3  for stack of 347-354
	Helix total = -7.8
	Hairpin = 2.8  for closure of 348-353
		Stack = -2.1  for stack of 322-343
		Stack = -2.1  for stack of 323-342
		Stack = -3.3  for stack of 324-341
		Stack = -3.3  for stack of 325-340
	Helix total = -10.8
	Hairpin = 5.4  for closure of 326-339
		Stack = -2.2  for stack of 109-320
		Stack = -2.1  for stack of 110-319
	Helix total = -4.3
	Multiloop = 1.8  for closure of 111-318
		Stack = -3.4  for stack of 295-317
		Stack = -3.3  for stack of 296-316
		Stack = -2.4  for stack of 297-315
	Helix total = -9.1
	Internal/bulge = 3.7  for closure of 298-314	Size = 3
		Stack = -2.2  for stack of 299-310
		Stack = -3.3  for stack of 300-309
		Stack = -2.1  for stack of 301-308
	Helix total = -7.6
	Hairpin = 4.7  for closure of 302-307
		Stack = -2.4  for stack of 246-292
		Stack = -3.4  for stack of 247-291
	Helix total = -5.8
	Internal/bulge = 3.7  for closure of 248-290	Size = 10
		Stack = -3.4  for stack of 253-283
		Stack = -2.1  for stack of 254-282
	Helix total = -5.5
	Internal/bulge = 3.8  for closure of 255-281	Size = 2
		Stack = -0.9  for stack of 258-280
		Stack = -2.1  for stack of 259-279
		Stack = -3.3  for stack of 260-278
		Stack = -2.2  for stack of 261-277
		Stack = -2.1  for stack of 262-276
		Stack = -2.4  for stack of 263-275
		Stack = -2.1  for stack of 264-274
	Helix total = -15.1
	Hairpin = 3.8  for closure of 265-273
		Stack = -2.4  for stack of 119-244
		Stack = -2.5  for stack of 120-243
		Stack = -1.4  for stack of 121-242
		Stack = -3.3  for stack of 122-241
		Stack = -3.3  for stack of 123-240
		Stack = -2.2  for stack of 124-239
	Helix total = -15.1
	Internal/bulge = 3.3  for closure of 125-238	Size = 2
		Stack = -3.3  for stack of 128-237
	Helix total = -3.3
	Internal/bulge = 2.3  for closure of 129-236	Size = 5
		Stack = -2.1  for stack of 133-233
		Stack = -2.1  for stack of 134-232
		Stack = -2.2  for stack of 135-231
		Stack = -1.3  for stack of 136-230
		Stack = -0.9  for stack of 137-229
		Stack = -2.1  for stack of 138-228
	Helix total = -10.7
	Multiloop = 3.8  for closure of 139-227
		Stack = -3.3  for stack of 210-225
		Stack = -2.2  for stack of 211-224
		Stack = -1.0  for stack of 212-223
		Stack = -2.1  for stack of 213-222
		Stack = -3.4  for stack of 214-221
	Helix total = -12.0
	Hairpin = 3.7  for closure of 215-220
		Stack = -2.1  for stack of 181-204
		Stack = -2.2  for stack of 182-203
		Stack = -0.9  for stack of 183-202
		Stack = -0.9  for stack of 184-201
		Stack = -2.1  for stack of 185-200
		Stack = -2.4  for stack of 186-199
		Stack = -0.9  for stack of 187-198
		Stack = -2.2  for stack of 188-197
		Stack = -3.3  for stack of 189-196
	Helix total = -17.0
	Hairpin = 4.1  for closure of 190-195
		Stack = -2.1  for stack of 141-175
		Stack = -1.4  for stack of 142-174
		Stack = -3.3  for stack of 143-173
	Helix total = -6.8
	Internal/bulge = 2.2  for closure of 144-172	Size = 11
		Stack = -2.1  for stack of 150-165
		Stack = -1.5  for stack of 151-164
		Stack = -3.3  for stack of 152-163
		Stack = -2.4  for stack of 153-162
		Stack = -3.3  for stack of 154-161
	Helix total = -12.6
	Hairpin = 3.1  for closure of 155-160
		Stack = -2.5  for stack of 62-102
		Stack = -1.5  for stack of 63-101
	Helix total = -4.0
	Internal/bulge = 2.8  for closure of 64-100	Size = 2
		Stack = -3.4  for stack of 67-99
	Helix total = -3.4
	Internal/bulge = 1.2  for closure of 68-98	Size = 2
		Stack = -1.3  for stack of 70-96
		Stack = -2.2  for stack of 71-95
	Helix total = -3.5
	Internal/bulge = 2.4  for closure of 72-94	Size = 1 BP stack across bulge = -1.4
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 74-93	Size = 2
		Stack = -1.4  for stack of 76-91
		Stack = -3.3  for stack of 77-90
		Stack = -3.3  for stack of 78-89
		Stack = -2.4  for stack of 79-88
		Stack = -2.1  for stack of 80-87
	Helix total = -12.5
	Hairpin = 4.5  for closure of 81-86
		Stack = -2.4  for stack of 10-26
		Stack = -2.1  for stack of 11-25
		Stack = -2.5  for stack of 12-24
		Stack = -0.5  for stack of 13-23
	Helix total = -7.5
	Hairpin = 5.1  for closure of 14-22


	Total energy = -163.7



