Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    13:331 14:330 15:329 16:328 17:327 18:326 19:325 62:289
	    63:288 64:287 65:286
	Energy of Broken Structure: -95.5
	Energy of Pseudo-Helices:   -23.7
	Pseudoknot Energy Penalty:  17.6
	Total Free Energy:          -101.6
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = 0.5
		Stack = -0.9  for stack of 1-381
		Stack = -0.9  for stack of 2-380
		Stack = -2.2  for stack of 3-379
		Stack = -3.3  for stack of 4-378
		Stack = -2.4  for stack of 5-377
	Helix total = -9.7
	Internal/bulge = 1.4  for closure of 6-376	Size = 1 BP stack across bulge = -2.4
		Stack = -0.9  for stack of 8-375
		Stack = -2.1  for stack of 9-374
		Stack = -2.5  for stack of 10-373
	Helix total = -5.5
	Internal/bulge = 2.4  for closure of 11-372	Size = 1 BP stack across bulge = -1.4
	Helix total = 0.0
	Multiloop = 5.4  for closure of 12-370
		Stack = -0.9  for stack of 46-368
		Stack = -2.1  for stack of 47-367
	Helix total = -3.0
	Internal/bulge = 0.4  for closure of 48-366	Size = 1 BP stack across bulge = -3.4
		Stack = -3.3  for stack of 50-365
		Stack = -2.4  for stack of 51-364
		Stack = -2.4  for stack of 52-363
		Stack = -0.9  for stack of 53-362
	Helix total = -9.0
	Multiloop = 5.2  for closure of 54-361
		Stack = -2.1  for stack of 333-353
		Stack = -1.1  for stack of 334-352
		Stack = -2.4  for stack of 335-351
		Stack = -2.1  for stack of 336-350
		Stack = -2.2  for stack of 337-349
		Stack = -2.1  for stack of 338-348
		Stack = -1.0  for stack of 339-347
	Helix total = -13.0
	Hairpin = 5.6  for closure of 340-346
		Stack = -3.3  for stack of 246-311
		Stack = -3.4  for stack of 247-310
		Stack = -3.3  for stack of 248-309
	Helix total = -10.0
	Internal/bulge = 2.2  for closure of 249-308	Size = 11
		Stack = -3.3  for stack of 256-302
		Stack = -2.4  for stack of 257-301
		Stack = -0.9  for stack of 258-300
		Stack = -0.6  for stack of 259-299
		Stack = -2.5  for stack of 260-298
		Stack = -2.1  for stack of 261-297
	Helix total = -11.8
	Multiloop = 6.6  for closure of 262-296
		Stack = -3.3  for stack of 281-293
		Stack = -3.3  for stack of 282-292
		Stack = -2.5  for stack of 283-291
	Helix total = -9.1
	Hairpin = 5.6  for closure of 284-290
		Stack = -0.6  for stack of 263-278
		Stack = -0.9  for stack of 264-277
		Stack = -2.4  for stack of 265-276
		Stack = -3.3  for stack of 266-275
		Stack = -2.1  for stack of 267-274
	Helix total = -9.3
	Hairpin = 4.7  for closure of 268-273
		Stack = -2.1  for stack of 55-242
		Stack = -0.9  for stack of 56-241
		Stack = -2.4  for stack of 57-240
	Helix total = -5.4
	Internal/bulge = 4.7  for closure of 58-239	Size = 8
		Stack = -3.3  for stack of 67-238
		Stack = -3.3  for stack of 68-237
	Helix total = -6.6
	Internal/bulge = 0.5  for closure of 69-236	Size = 1 BP stack across bulge = -3.3
	Helix total = 0.0
	Multiloop = 1.7  for closure of 71-235
		Stack = -2.1  for stack of 126-234
	Helix total = -2.1
	Internal/bulge = 3.2  for closure of 127-233	Size = 3
		Stack = -2.2  for stack of 131-232
	Helix total = -2.2
	Multiloop = 4.7  for closure of 132-231
		Stack = -3.4  for stack of 202-221
		Stack = -2.1  for stack of 203-220
		Stack = -2.1  for stack of 204-219
		Stack = -3.3  for stack of 205-218
	Helix total = -10.9
	Internal/bulge = 0.5  for closure of 206-217	Size = 2
		Stack = -2.1  for stack of 208-215
	Helix total = -2.1
	Hairpin = 4.4  for closure of 209-214
		Stack = -3.3  for stack of 181-199
	Helix total = -3.3
	Internal/bulge = 0.5  for closure of 182-198	Size = 2
		Stack = -3.3  for stack of 184-196
		Stack = -2.2  for stack of 185-195
	Helix total = -5.5
	Hairpin = 4.5  for closure of 186-194
		Stack = -3.3  for stack of 148-173
	Helix total = -3.3
	Internal/bulge = 3.3  for closure of 149-172	Size = 2
		Stack = -2.5  for stack of 150-169
		Stack = -2.1  for stack of 151-168
		Stack = -2.4  for stack of 152-167
		Stack = -3.3  for stack of 153-166
		Stack = -2.4  for stack of 154-165
		Stack = -3.3  for stack of 155-164
	Helix total = -16.0
	Hairpin = 4.3  for closure of 156-163
	Helix total = 0.0
	Internal/bulge = 0.5  for closure of 100-125	Size = 1 BP stack across bulge = -3.3
		Stack = -1.5  for stack of 101-123
		Stack = -2.5  for stack of 102-122
		Stack = -2.1  for stack of 103-121
		Stack = -2.1  for stack of 104-120
	Helix total = -8.2
	Internal/bulge = 0.4  for closure of 105-119	Size = 1 BP stack across bulge = -3.4
		Stack = -1.4  for stack of 106-117
		Stack = -2.1  for stack of 107-116
		Stack = -3.4  for stack of 108-115
	Helix total = -6.9
	Hairpin = 3.3  for closure of 109-114
		Stack = -3.3  for stack of 72-99
		Stack = -2.4  for stack of 73-98
		Stack = -3.3  for stack of 74-97
		Stack = -2.2  for stack of 75-96
		Stack = -2.4  for stack of 76-95
	Helix total = -13.6
	Internal/bulge = 2.8  for closure of 77-94	Size = 2
		Stack = -2.4  for stack of 78-91
		Stack = -0.6  for stack of 79-90
	Helix total = -3.0
	Hairpin = 5.2  for closure of 80-89
		Stack = -2.1  for stack of 21-41
		Stack = -2.1  for stack of 22-40
		Stack = -2.5  for stack of 23-39
		Stack = -1.0  for stack of 24-38
		Stack = -1.1  for stack of 25-37
		Stack = -2.1  for stack of 26-36
		Stack = -3.3  for stack of 27-35
		Stack = -2.2  for stack of 28-34
	Helix total = -16.4
	Hairpin = 5.9  for closure of 29-33


	Total energy = -95.5



