Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    452:473 453:472 454:471
	Energy of Broken Structure: -129.1
	Energy of Pseudo-Helices:   -6.7
	Pseudoknot Energy Penalty:  7.2
	Total Free Energy:          -128.6
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -3.7
		Stack = -3.3  for stack of 27-503
		Stack = -2.4  for stack of 28-502
		Stack = -1.1  for stack of 29-501
	Helix total = -6.8
	Internal/bulge = 2.5  for closure of 30-500	Size = 1 BP stack across bulge = -1.3
		Stack = -0.9  for stack of 32-499
		Stack = -2.2  for stack of 33-498
		Stack = -2.4  for stack of 34-497
		Stack = -3.4  for stack of 35-496
		Stack = -2.1  for stack of 36-495
	Helix total = -11.0
	Multiloop = 2.2  for closure of 37-494
		Stack = -3.4  for stack of 447-492
		Stack = -2.1  for stack of 448-491
		Stack = -1.1  for stack of 449-490
		Stack = -2.4  for stack of 450-489
	Helix total = -9.0
	Internal/bulge = 4.4  for closure of 451-488	Size = 6
		Stack = -2.1  for stack of 458-487
		Stack = -2.4  for stack of 459-486
		Stack = -2.1  for stack of 460-485
		Stack = -2.1  for stack of 461-484
		Stack = -2.2  for stack of 462-483
	Helix total = -10.9
	Hairpin = 5.6  for closure of 463-482
		Stack = -2.4  for stack of 412-439
		Stack = -1.4  for stack of 413-438
		Stack = -2.1  for stack of 414-437
		Stack = -2.4  for stack of 415-436
	Helix total = -8.3
	Internal/bulge = 1.4  for closure of 416-435	Size = 7
	Helix total = 0.0
	Hairpin = 5.3  for closure of 420-430
		Stack = -1.5  for stack of 376-406
		Stack = -1.3  for stack of 377-405
		Stack = -2.1  for stack of 378-404
	Helix total = -4.9
	Internal/bulge = 1.2  for closure of 379-403	Size = 11
		Stack = -1.5  for stack of 386-397
		Stack = -2.5  for stack of 387-396
		Stack = -3.3  for stack of 388-395
	Helix total = -7.3
	Hairpin = 2.8  for closure of 389-394
		Stack = -3.4  for stack of 39-373
		Stack = -2.4  for stack of 40-372
		Stack = -3.3  for stack of 41-371
		Stack = -3.4  for stack of 42-370
		Stack = -2.1  for stack of 43-369
	Helix total = -14.6
	Internal/bulge = 2.3  for closure of 44-368	Size = 1 BP stack across bulge = -1.1
		Stack = -2.1  for stack of 45-366
	Helix total = -2.1
	Multiloop = 5.2  for closure of 46-365
	Helix total = 0.0
	Internal/bulge = 0.6  for closure of 337-363	Size = 1 BP stack across bulge = -2.4
		Stack = -3.3  for stack of 339-362
		Stack = -2.4  for stack of 340-361
	Helix total = -5.7
	Internal/bulge = 3.0  for closure of 341-360	Size = 4
		Stack = 0.3  for stack of 345-358
		Stack = -2.1  for stack of 346-357
		Stack = -3.3  for stack of 347-356
		Stack = -3.4  for stack of 348-355
	Helix total = -8.5
	Hairpin = 3.3  for closure of 349-354
	Helix total = 0.0
	Internal/bulge = 3.8  for closure of 47-331	Size = 5
		Stack = -2.1  for stack of 52-329
		Stack = -2.2  for stack of 53-328
	Helix total = -4.3
	Internal/bulge = 1.7  for closure of 54-327	Size = 1 BP stack across bulge = -2.1
		Stack = -2.1  for stack of 56-326
		Stack = -3.4  for stack of 57-325
	Helix total = -5.5
	Multiloop = -0.3  for closure of 58-324
		Stack = -2.1  for stack of 309-320
		Stack = -2.4  for stack of 310-319
		Stack = -3.3  for stack of 311-318
	Helix total = -7.8
	Hairpin = 2.8  for closure of 312-317
		Stack = -2.1  for stack of 286-307
		Stack = -2.1  for stack of 287-306
		Stack = -3.3  for stack of 288-305
		Stack = -3.3  for stack of 289-304
	Helix total = -10.8
	Hairpin = 5.4  for closure of 290-303
		Stack = -2.2  for stack of 96-284
		Stack = -2.1  for stack of 97-283
	Helix total = -4.3
	Multiloop = 4.4  for closure of 98-282
		Stack = -3.4  for stack of 259-281
		Stack = -2.1  for stack of 260-280
		Stack = -2.1  for stack of 261-279
	Helix total = -7.6
	Internal/bulge = 3.7  for closure of 262-278	Size = 3
		Stack = -1.4  for stack of 263-274
		Stack = -2.4  for stack of 264-273
		Stack = -3.3  for stack of 265-272
	Helix total = -7.1
	Hairpin = 3.3  for closure of 266-271
		Stack = -2.1  for stack of 210-256
		Stack = -2.1  for stack of 211-255
	Helix total = -4.2
	Internal/bulge = 2.7  for closure of 212-254	Size = 10
		Stack = -3.4  for stack of 217-247
		Stack = -2.1  for stack of 218-246
	Helix total = -5.5
	Internal/bulge = 3.8  for closure of 219-245	Size = 2
		Stack = -0.9  for stack of 222-244
		Stack = -2.1  for stack of 223-243
		Stack = -3.3  for stack of 224-242
		Stack = -2.2  for stack of 225-241
		Stack = -1.0  for stack of 226-240
		Stack = -1.3  for stack of 227-239
		Stack = -2.1  for stack of 228-238
	Helix total = -12.9
	Hairpin = 3.8  for closure of 229-237
		Stack = -2.5  for stack of 105-209
		Stack = -2.4  for stack of 106-208
		Stack = -2.5  for stack of 107-207
	Helix total = -7.4
	Internal/bulge = 1.9  for closure of 108-206	Size = 2
		Stack = -2.1  for stack of 110-204
	Helix total = -2.1
	Internal/bulge = 1.1  for closure of 111-203	Size = 3
		Stack = -3.3  for stack of 114-201
	Helix total = -3.3
	Internal/bulge = 2.6  for closure of 115-200	Size = 5
		Stack = -3.3  for stack of 119-197
		Stack = -2.1  for stack of 120-196
		Stack = -0.9  for stack of 121-195
		Stack = -2.1  for stack of 122-194
		Stack = -3.3  for stack of 123-193
		Stack = -3.3  for stack of 124-192
	Helix total = -15.0
	Multiloop = 1.5  for closure of 125-191
		Stack = -3.3  for stack of 180-189
		Stack = -2.4  for stack of 181-188
	Helix total = -5.7
	Hairpin = 4.4  for closure of 182-187
		Stack = -3.4  for stack of 166-175
		Stack = -2.1  for stack of 167-174
	Helix total = -5.5
	Hairpin = 4.1  for closure of 168-173
		Stack = -3.3  for stack of 127-161
		Stack = -3.3  for stack of 128-160
		Stack = -3.3  for stack of 129-159
	Helix total = -9.9
	Internal/bulge = 3.2  for closure of 130-158	Size = 11
		Stack = -2.1  for stack of 136-151
		Stack = -0.9  for stack of 137-150
		Stack = -2.2  for stack of 138-149
		Stack = -2.1  for stack of 139-148
		Stack = -1.4  for stack of 140-147
	Helix total = -8.7
	Hairpin = 3.1  for closure of 141-146
		Stack = -2.5  for stack of 61-89
		Stack = -1.5  for stack of 62-88
	Helix total = -4.0
	Internal/bulge = 3.3  for closure of 63-87	Size = 2
		Stack = -2.2  for stack of 66-86
	Helix total = -2.2
	Internal/bulge = 0.5  for closure of 67-85	Size = 2
		Stack = -3.3  for stack of 69-83
		Stack = -2.4  for stack of 70-82
		Stack = -0.9  for stack of 71-81
		Stack = -0.6  for stack of 72-80
	Helix total = -7.2
	Hairpin = 5.6  for closure of 73-79
		Stack = -2.4  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 = -7.5
	Hairpin = 6.0  for closure of 13-21


	Total energy = -129.1



