Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    17:339 18:338 19:337 20:336 21:335 22:334 23:333 71:269
	    72:268 73:267 74:266
	Energy of Broken Structure: -181.3
	Energy of Pseudo-Helices:   -25.1
	Pseudoknot Energy Penalty:  17.5
	Total Free Energy:          -188.9
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -3.5
		Stack = -3.3  for stack of 375-394
		Stack = -3.3  for stack of 376-393
		Stack = -3.3  for stack of 377-392
		Stack = -2.4  for stack of 378-391
		Stack = -2.4  for stack of 379-390
		Stack = -2.1  for stack of 380-389
		Stack = -3.4  for stack of 381-388
	Helix total = -20.2
	Hairpin = 3.2  for closure of 382-387
		Stack = -3.3  for stack of 3-373
		Stack = -3.3  for stack of 4-372
		Stack = -3.3  for stack of 5-371
		Stack = -2.1  for stack of 6-370
		Stack = -2.1  for stack of 7-369
		Stack = -3.3  for stack of 8-368
		Stack = -2.4  for stack of 9-367
		Stack = -1.1  for stack of 10-366
		Stack = -1.3  for stack of 11-365
		Stack = -2.1  for stack of 12-364
		Stack = -3.3  for stack of 13-363
		Stack = -3.3  for stack of 14-362
	Helix total = -30.9
	Internal/bulge = 0.5  for closure of 15-361	Size = 1 BP stack across bulge = -3.3
	Helix total = 0.0
	Multiloop = 5.4  for closure of 16-359
		Stack = -0.9  for stack of 55-357
		Stack = -2.1  for stack of 56-356
	Helix total = -3.0
	Internal/bulge = 0.4  for closure of 57-355	Size = 1 BP stack across bulge = -3.4
		Stack = -3.3  for stack of 59-354
		Stack = -2.4  for stack of 60-353
		Stack = -3.3  for stack of 61-352
		Stack = -3.3  for stack of 62-351
	Helix total = -12.3
	Multiloop = 4.3  for closure of 63-350
		Stack = -1.5  for stack of 303-322
		Stack = -2.5  for stack of 304-321
		Stack = -3.3  for stack of 305-320
		Stack = -2.4  for stack of 306-319
		Stack = -3.3  for stack of 307-318
		Stack = -2.2  for stack of 308-317
		Stack = -2.1  for stack of 309-316
	Helix total = -17.3
	Hairpin = 3.1  for closure of 310-315
		Stack = -3.3  for stack of 243-296
		Stack = -3.4  for stack of 244-295
		Stack = -3.3  for stack of 245-294
	Helix total = -10.0
	Internal/bulge = 1.7  for closure of 246-293	Size = 12
		Stack = -3.4  for stack of 253-286
		Stack = -2.1  for stack of 254-285
		Stack = -2.1  for stack of 255-284
		Stack = -3.3  for stack of 256-283
	Helix total = -10.9
	Internal/bulge = 4.4  for closure of 257-282	Size = 9
		Stack = -3.3  for stack of 260-274
		Stack = -3.3  for stack of 261-273
		Stack = -3.4  for stack of 262-272
		Stack = -2.1  for stack of 263-271
	Helix total = -12.1
	Hairpin = 5.6  for closure of 264-270
		Stack = -2.1  for stack of 64-239
		Stack = -2.2  for stack of 65-238
		Stack = -3.3  for stack of 66-237
	Helix total = -7.6
	Internal/bulge = 4.7  for closure of 67-236	Size = 8
		Stack = -3.3  for stack of 76-235
		Stack = -3.3  for stack of 77-234
		Stack = -2.2  for stack of 78-233
		Stack = -2.1  for stack of 79-232
	Helix total = -10.9
	Multiloop = 0.3  for closure of 80-231
		Stack = -3.3  for stack of 111-230
	Helix total = -3.3
	Internal/bulge = 3.2  for closure of 112-229	Size = 3
		Stack = -2.2  for stack of 116-228
	Helix total = -2.2
	Multiloop = 4.0  for closure of 117-227
		Stack = -3.3  for stack of 196-217
		Stack = -2.1  for stack of 197-216
		Stack = 0.3  for stack of 198-215
		Stack = -2.1  for stack of 199-214
		Stack = -3.4  for stack of 200-213
		Stack = -3.3  for stack of 201-212
		Stack = -2.1  for stack of 202-211
		Stack = -2.1  for stack of 203-210
	Helix total = -18.1
	Hairpin = 3.1  for closure of 204-209
		Stack = -3.3  for stack of 176-194
		Stack = -2.2  for stack of 177-193
		Stack = -2.1  for stack of 178-192
		Stack = -3.3  for stack of 179-191
		Stack = -3.3  for stack of 180-190
	Helix total = -14.2
	Hairpin = 3.8  for closure of 181-189
		Stack = -3.3  for stack of 133-168
	Helix total = -3.3
	Internal/bulge = 2.8  for closure of 134-167	Size = 2
		Stack = -3.4  for stack of 135-164
		Stack = -3.3  for stack of 136-163
	Helix total = -6.7
	Internal/bulge = 0.5  for closure of 137-162	Size = 2
		Stack = -3.4  for stack of 139-160
	Helix total = -3.4
	Internal/bulge = 2.0  for closure of 140-159	Size = 1 BP stack across bulge = -1.4
		Stack = -2.5  for stack of 142-158
		Stack = -3.3  for stack of 143-157
		Stack = -2.4  for stack of 144-156
		Stack = -3.3  for stack of 145-155
		Stack = -3.3  for stack of 146-154
		Stack = -3.3  for stack of 147-153
	Helix total = -18.1
	Hairpin = 5.4  for closure of 148-152
	Helix total = 0.0
	Internal/bulge = 0.4  for closure of 96-110	Size = 1 BP stack across bulge = -3.4
		Stack = -2.4  for stack of 97-108
		Stack = -3.3  for stack of 98-107
		Stack = -3.3  for stack of 99-106
	Helix total = -9.0
	Hairpin = 3.1  for closure of 100-105
		Stack = -3.3  for stack of 81-95
		Stack = -2.1  for stack of 82-94
		Stack = -2.1  for stack of 83-93
		Stack = -3.4  for stack of 84-92
	Helix total = -10.9
	Hairpin = 4.7  for closure of 85-91
		Stack = -1.4  for stack of 25-50
		Stack = -2.5  for stack of 26-49
		Stack = -3.3  for stack of 27-48
		Stack = -3.3  for stack of 28-47
		Stack = -1.4  for stack of 29-46
		Stack = -2.1  for stack of 30-45
		Stack = -3.3  for stack of 31-44
		Stack = -3.3  for stack of 32-43
		Stack = -3.3  for stack of 33-42
	Helix total = -23.9
	Hairpin = 3.9  for closure of 34-41


	Total energy = -181.3



