Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    560:581 561:580 562:579
	Energy of Broken Structure: -65.0
	Energy of Pseudo-Helices:   -6.7
	Pseudoknot Energy Penalty:  7.2
	Total Free Energy:          -64.5
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -2.8
		Stack = -0.6  for stack of 22-611
		Stack = -1.4  for stack of 23-610
	Helix total = -2.0
	Internal/bulge = 2.1  for closure of 24-609	Size = 1 BP stack across bulge = -1.3
		Stack = -1.1  for stack of 26-608
		Stack = -1.3  for stack of 27-607
		Stack = -1.4  for stack of 28-606
		Stack = -1.4  for stack of 29-605
		Stack = -3.4  for stack of 30-604
		Stack = -2.1  for stack of 31-603
	Helix total = -10.7
	Multiloop = 3.6  for closure of 32-602
		Stack = -0.9  for stack of 554-600
		Stack = -2.1  for stack of 555-599
		Stack = -3.3  for stack of 556-598
		Stack = -2.4  for stack of 557-597
		Stack = -2.1  for stack of 558-596
	Helix total = -10.8
	Internal/bulge = 4.6  for closure of 559-595	Size = 7
		Stack = -2.1  for stack of 567-594
		Stack = -2.1  for stack of 568-593
		Stack = -3.3  for stack of 569-592
	Helix total = -7.5
	Hairpin = 5.6  for closure of 570-591
		Stack = -2.2  for stack of 524-544
	Helix total = -2.2
	Hairpin = 6.6  for closure of 525-543
		Stack = -2.1  for stack of 484-517
		Stack = -0.9  for stack of 485-516
	Helix total = -3.0
	Internal/bulge = 2.3  for closure of 486-515	Size = 1 BP stack across bulge = -1.1
		Stack = -1.3  for stack of 487-513
		Stack = -2.2  for stack of 488-512
		Stack = -2.1  for stack of 489-511
		Stack = -2.1  for stack of 490-510
		Stack = -3.3  for stack of 491-509
	Helix total = -11.0
	Internal/bulge = 1.1  for closure of 492-508	Size = 3
		Stack = -2.1  for stack of 494-505
		Stack = -2.4  for stack of 495-504
	Helix total = -4.5
	Hairpin = 3.9  for closure of 496-503
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 35-478	Size = 2
		Stack = -2.4  for stack of 37-476
	Helix total = -2.4
	Multiloop = 5.5  for closure of 38-475
	Helix total = 0.0
	Internal/bulge = 2.1  for closure of 444-469	Size = 1 BP stack across bulge = -1.3
		Stack = -2.2  for stack of 446-468
		Stack = -3.3  for stack of 447-467
	Helix total = -5.5
	Internal/bulge = 3.0  for closure of 448-466	Size = 4
		Stack = -1.5  for stack of 452-464
		Stack = -3.3  for stack of 453-463
		Stack = -3.3  for stack of 454-462
	Helix total = -8.1
	Hairpin = 4.2  for closure of 455-461
	Helix total = 0.0
	Internal/bulge = 4.4  for closure of 42-438	Size = 6
		Stack = -3.4  for stack of 48-436
		Stack = -3.3  for stack of 49-435
	Helix total = -6.7
	Internal/bulge = 1.7  for closure of 50-434	Size = 1 BP stack across bulge = -2.1
		Stack = -2.1  for stack of 52-433
		Stack = -3.4  for stack of 53-432
	Helix total = -5.5
	Multiloop = 0.1  for closure of 54-431
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 416-427	Size = 2
		Stack = -2.4  for stack of 418-425
	Helix total = -2.4
	Hairpin = 3.6  for closure of 419-424
		Stack = -3.3  for stack of 393-414
	Helix total = -3.3
	Internal/bulge = 1.2  for closure of 394-413	Size = 2
		Stack = -2.1  for stack of 396-411
		Stack = -3.4  for stack of 397-410
	Helix total = -5.5
	Hairpin = 5.5  for closure of 398-409
		Stack = -2.1  for stack of 96-391
		Stack = -2.4  for stack of 97-390
	Helix total = -4.5
	Multiloop = 2.6  for closure of 98-389
		Stack = -2.4  for stack of 366-388
		Stack = -3.3  for stack of 367-387
		Stack = -1.5  for stack of 368-386
	Helix total = -7.2
	Internal/bulge = 3.7  for closure of 369-385	Size = 3
		Stack = -2.4  for stack of 370-381
		Stack = -0.9  for stack of 371-380
		Stack = -1.4  for stack of 372-379
	Helix total = -4.7
	Hairpin = 5.4  for closure of 373-378
		Stack = -3.3  for stack of 314-362
		Stack = -2.1  for stack of 315-361
	Helix total = -5.4
	Internal/bulge = 5.1  for closure of 316-360	Size = 10
		Stack = -2.2  for stack of 321-353
		Stack = -2.1  for stack of 322-352
	Helix total = -4.3
	Internal/bulge = 4.6  for closure of 323-351	Size = 4
		Stack = -1.1  for stack of 328-350
		Stack = -2.1  for stack of 329-349
		Stack = -3.3  for stack of 330-348
		Stack = -2.2  for stack of 331-347
		Stack = -1.3  for stack of 332-346
		Stack = -2.1  for stack of 333-345
		Stack = -2.2  for stack of 334-344
	Helix total = -14.3
	Hairpin = 5.5  for closure of 335-343
		Stack = -2.1  for stack of 106-312
		Stack = -2.1  for stack of 107-311
	Helix total = -4.2
	Internal/bulge = 1.5  for closure of 108-310	Size = 2
		Stack = -1.0  for stack of 110-308
	Helix total = -1.0
	Internal/bulge = 3.7  for closure of 111-307	Size = 4
		Stack = -0.9  for stack of 115-305
	Helix total = -0.9
	Internal/bulge = 3.5  for closure of 116-304	Size = 7
		Stack = -2.1  for stack of 121-300
		Stack = -2.4  for stack of 122-299
		Stack = -1.1  for stack of 123-298
		Stack = -2.4  for stack of 124-297
	Helix total = -8.0
	Multiloop = 6.0  for closure of 125-296
		Stack = -2.4  for stack of 272-293
		Stack = -2.4  for stack of 273-292
		Stack = -2.2  for stack of 274-291
	Helix total = -7.0
	Internal/bulge = 2.5  for closure of 275-290	Size = 1 BP stack across bulge = -1.3
		Stack = -1.4  for stack of 277-289
		Stack = -3.3  for stack of 278-288
		Stack = -2.2  for stack of 279-287
	Helix total = -6.9
	Hairpin = 5.7  for closure of 280-286
		Stack = -0.9  for stack of 207-263
		Stack = -1.3  for stack of 208-262
		Stack = -1.1  for stack of 209-261
		Stack = -1.3  for stack of 210-260
	Helix total = -4.6
	Internal/bulge = 3.9  for closure of 211-259	Size = 15
		Stack = -0.9  for stack of 219-250
		Stack = -2.2  for stack of 220-249
		Stack = -3.3  for stack of 221-248
		Stack = -2.1  for stack of 222-247
		Stack = -0.9  for stack of 223-246
	Helix total = -9.4
	Internal/bulge = 5.1  for closure of 224-245	Size = 6
		Stack = -2.4  for stack of 226-239
		Stack = -2.4  for stack of 227-238
		Stack = -1.1  for stack of 228-237
		Stack = -2.4  for stack of 229-236
	Helix total = -8.3
	Hairpin = 3.3  for closure of 230-235
		Stack = -2.2  for stack of 181-202
		Stack = -2.1  for stack of 182-201
		Stack = -1.4  for stack of 183-200
		Stack = -1.4  for stack of 184-199
	Helix total = -7.1
	Internal/bulge = -0.5  for closure of 185-198	Size = 4
		Stack = -3.3  for stack of 188-195
	Helix total = -3.3
	Hairpin = 3.5  for closure of 189-194
	Helix total = 0.0
	Internal/bulge = 0.8  for closure of 137-172	Size = 2
		Stack = -2.1  for stack of 139-170
	Helix total = -2.1
	Internal/bulge = 2.2  for closure of 140-169	Size = 11
		Stack = -2.1  for stack of 146-162
	Helix total = -2.1
	Internal/bulge = -0.7  for closure of 147-161	Size = 2
		Stack = -1.0  for stack of 149-159
		Stack = -2.1  for stack of 150-158
	Helix total = -3.1
	Hairpin = 4.1  for closure of 151-157
		Stack = -2.5  for stack of 57-89
	Helix total = -2.5
	Internal/bulge = 4.5  for closure of 58-88	Size = 5
		Stack = -2.2  for stack of 63-86
	Helix total = -2.2
	Hairpin = 6.7  for closure of 64-85
		Stack = -2.1  for stack of 4-20
		Stack = -2.1  for stack of 5-19
		Stack = -3.3  for stack of 6-18
		Stack = -2.5  for stack of 7-17
	Helix total = -10.0
	Hairpin = 5.1  for closure of 8-16


	Total energy = -65.0



