Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    551:572 552:571 553:570
	Energy of Broken Structure: -71.9
	Energy of Pseudo-Helices:   -6.7
	Pseudoknot Energy Penalty:  7.2
	Total Free Energy:          -71.4
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -2.8
		Stack = -0.6  for stack of 22-602
		Stack = -1.4  for stack of 23-601
	Helix total = -2.0
	Internal/bulge = 2.5  for closure of 24-600	Size = 1 BP stack across bulge = -1.3
		Stack = -1.1  for stack of 26-599
		Stack = -1.3  for stack of 27-598
		Stack = -1.4  for stack of 28-597
		Stack = -1.4  for stack of 29-596
		Stack = -3.4  for stack of 30-595
		Stack = -2.1  for stack of 31-594
	Helix total = -10.7
	Multiloop = 6.6  for closure of 32-593
		Stack = -0.9  for stack of 545-591
		Stack = -2.1  for stack of 546-590
		Stack = -3.3  for stack of 547-589
		Stack = -2.4  for stack of 548-588
		Stack = -2.1  for stack of 549-587
	Helix total = -10.8
	Internal/bulge = 4.6  for closure of 550-586	Size = 7
		Stack = -2.1  for stack of 558-585
		Stack = -2.1  for stack of 559-584
		Stack = -3.3  for stack of 560-583
	Helix total = -7.5
	Hairpin = 5.6  for closure of 561-582
		Stack = -2.1  for stack of 479-508
		Stack = -0.9  for stack of 480-507
	Helix total = -3.0
	Internal/bulge = 1.6  for closure of 481-506	Size = 1 BP stack across bulge = -2.2
		Stack = -2.1  for stack of 482-504
		Stack = -2.2  for stack of 483-503
		Stack = -2.1  for stack of 484-502
		Stack = -1.0  for stack of 485-501
		Stack = -2.1  for stack of 486-500
		Stack = -2.4  for stack of 487-499
		Stack = -0.9  for stack of 488-498
		Stack = -0.9  for stack of 489-497
	Helix total = -13.7
	Hairpin = 5.6  for closure of 490-496
		Stack = -2.4  for stack of 35-473
		Stack = -2.1  for stack of 36-472
		Stack = -0.9  for stack of 37-471
	Helix total = -5.4
	Multiloop = 6.9  for closure of 38-470
	Helix total = 0.0
	Internal/bulge = 2.1  for closure of 439-464	Size = 1 BP stack across bulge = -1.3
		Stack = -2.2  for stack of 441-463
		Stack = -3.3  for stack of 442-462
	Helix total = -5.5
	Internal/bulge = 3.0  for closure of 443-461	Size = 4
		Stack = -1.5  for stack of 447-459
		Stack = -3.3  for stack of 448-458
		Stack = -2.1  for stack of 449-457
		Stack = -2.1  for stack of 450-456
	Helix total = -9.0
	Hairpin = 5.4  for closure of 451-455
	Helix total = 0.0
	Internal/bulge = 4.4  for closure of 42-433	Size = 6
		Stack = -3.4  for stack of 48-431
		Stack = -3.3  for stack of 49-430
	Helix total = -6.7
	Internal/bulge = 1.7  for closure of 50-429	Size = 1 BP stack across bulge = -2.1
		Stack = -2.1  for stack of 52-428
		Stack = -3.4  for stack of 53-427
	Helix total = -5.5
	Multiloop = 0.1  for closure of 54-426
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 411-422	Size = 2
		Stack = -2.4  for stack of 413-420
	Helix total = -2.4
	Hairpin = 3.6  for closure of 414-419
		Stack = -3.3  for stack of 388-409
	Helix total = -3.3
	Internal/bulge = 1.2  for closure of 389-408	Size = 2
		Stack = -2.1  for stack of 391-406
		Stack = -3.4  for stack of 392-405
	Helix total = -5.5
	Hairpin = 5.5  for closure of 393-404
		Stack = -2.1  for stack of 96-386
		Stack = -2.4  for stack of 97-385
	Helix total = -4.5
	Multiloop = 2.2  for closure of 98-384
		Stack = -2.4  for stack of 361-383
		Stack = -3.3  for stack of 362-382
		Stack = -1.5  for stack of 363-381
	Helix total = -7.2
	Internal/bulge = 3.7  for closure of 364-380	Size = 3
		Stack = -2.4  for stack of 365-376
		Stack = -0.9  for stack of 366-375
		Stack = -1.4  for stack of 367-374
	Helix total = -4.7
	Hairpin = 5.4  for closure of 368-373
		Stack = -3.3  for stack of 309-357
		Stack = -2.1  for stack of 310-356
	Helix total = -5.4
	Internal/bulge = 4.4  for closure of 311-355	Size = 10
		Stack = -3.4  for stack of 316-348
		Stack = -2.1  for stack of 317-347
	Helix total = -5.5
	Internal/bulge = 4.6  for closure of 318-346	Size = 4
		Stack = -2.2  for stack of 323-345
		Stack = -2.4  for stack of 324-344
		Stack = -3.3  for stack of 325-343
		Stack = -2.2  for stack of 326-342
		Stack = -1.3  for stack of 327-341
	Helix total = -11.4
	Internal/bulge = 1.9  for closure of 328-340	Size = 2
	Helix total = 0.0
	Hairpin = 4.5  for closure of 330-338
		Stack = -2.1  for stack of 106-307
		Stack = -2.1  for stack of 107-306
	Helix total = -4.2
	Internal/bulge = 0.3  for closure of 108-305	Size = 4
	Helix total = 0.0
	Internal/bulge = 3.7  for closure of 111-302	Size = 4
		Stack = -0.9  for stack of 115-300
	Helix total = -0.9
	Internal/bulge = 3.5  for closure of 116-299	Size = 7
		Stack = -2.1  for stack of 121-295
		Stack = -2.4  for stack of 122-294
		Stack = -1.1  for stack of 123-293
	Helix total = -5.6
	Multiloop = 7.3  for closure of 124-292
		Stack = -2.4  for stack of 267-288
		Stack = -2.4  for stack of 268-287
		Stack = -3.4  for stack of 269-286
	Helix total = -8.2
	Internal/bulge = 2.3  for closure of 270-285	Size = 4
		Stack = -2.4  for stack of 274-283
		Stack = -2.2  for stack of 275-282
	Helix total = -4.6
	Hairpin = 3.7  for closure of 276-281
		Stack = -0.9  for stack of 203-257
		Stack = -1.3  for stack of 204-256
		Stack = -1.4  for stack of 205-255
		Stack = -0.6  for stack of 206-254
		Stack = -1.3  for stack of 207-253
	Helix total = -5.5
	Internal/bulge = 3.5  for closure of 208-252	Size = 14
		Stack = -2.2  for stack of 217-245
		Stack = -3.3  for stack of 218-244
	Helix total = -5.5
	Internal/bulge = 4.2  for closure of 219-243	Size = 9
		Stack = -3.3  for stack of 223-236
		Stack = -2.1  for stack of 224-235
		Stack = -2.2  for stack of 225-234
		Stack = -3.3  for stack of 226-233
	Helix total = -10.9
	Hairpin = 4.2  for closure of 227-232
		Stack = -2.1  for stack of 178-198
		Stack = -3.4  for stack of 179-197
		Stack = -3.3  for stack of 180-196
		Stack = -2.1  for stack of 181-195
	Helix total = -10.9
	Internal/bulge = 2.9  for closure of 182-194	Size = 1 BP stack across bulge = -0.9
		Stack = -1.3  for stack of 184-193
		Stack = -1.5  for stack of 185-192
	Helix total = -2.8
	Hairpin = 4.8  for closure of 186-191
		Stack = -2.1  for stack of 136-171
		Stack = -1.1  for stack of 137-170
		Stack = -2.1  for stack of 138-169
	Helix total = -5.3
	Internal/bulge = 2.2  for closure of 139-168	Size = 11
		Stack = -3.3  for stack of 145-161
		Stack = -1.4  for stack of 146-160
		Stack = -1.4  for stack of 147-159
		Stack = -1.0  for stack of 148-158
		Stack = -2.1  for stack of 149-157
	Helix total = -9.2
	Hairpin = 4.1  for closure of 150-156
		Stack = -2.5  for stack of 57-89
	Helix total = -2.5
	Internal/bulge = 4.2  for closure of 58-88	Size = 3
		Stack = -2.1  for stack of 62-87
		Stack = -2.2  for stack of 63-86
	Helix total = -4.3
	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 = -71.9



