Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    12:340 13:339 14:338 15:337 16:336 17:335 18:334 80:277
	    81:276 82:275 83:274
	Energy of Broken Structure: -122.7
	Energy of Pseudo-Helices:   -23.4
	Pseudoknot Energy Penalty:  17.4
	Total Free Energy:          -128.7
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -2.4  for stack of 1-371
		Stack = -0.9  for stack of 2-370
		Stack = -0.6  for stack of 3-369
		Stack = -2.5  for stack of 4-368
		Stack = -2.1  for stack of 5-367
		Stack = -2.1  for stack of 6-366
		Stack = -2.4  for stack of 7-365
		Stack = -2.2  for stack of 8-364
		Stack = -3.3  for stack of 9-363
	Helix total = -18.5
	Internal/bulge = 1.7  for closure of 10-362	Size = 1 BP stack across bulge = -2.1
	Helix total = 0.0
	Multiloop = 6.3  for closure of 11-360
		Stack = -0.9  for stack of 64-358
		Stack = -2.1  for stack of 65-357
	Helix total = -3.0
	Internal/bulge = 0.4  for closure of 66-356	Size = 1 BP stack across bulge = -3.4
		Stack = -3.3  for stack of 68-355
		Stack = -2.4  for stack of 69-354
		Stack = -3.3  for stack of 70-353
		Stack = -3.3  for stack of 71-352
	Helix total = -12.3
	Multiloop = 5.8  for closure of 72-351
		Stack = -3.4  for stack of 304-323
		Stack = -3.3  for stack of 305-322
		Stack = -2.1  for stack of 306-321
		Stack = -2.1  for stack of 307-320
		Stack = -2.5  for stack of 308-319
		Stack = 0.3  for stack of 309-318
		Stack = -1.3  for stack of 310-317
	Helix total = -14.4
	Hairpin = 4.4  for closure of 311-316
		Stack = -2.1  for stack of 248-297
		Stack = -3.4  for stack of 249-296
		Stack = -3.3  for stack of 250-295
	Helix total = -8.8
	Internal/bulge = 2.2  for closure of 251-294	Size = 11
		Stack = -3.3  for stack of 258-288
		Stack = -3.3  for stack of 259-287
		Stack = -2.2  for stack of 260-286
		Stack = -0.9  for stack of 261-285
		Stack = -2.4  for stack of 262-284
	Helix total = -12.1
	Internal/bulge = 4.1  for closure of 263-283	Size = 4
		Stack = -2.1  for stack of 268-282
		Stack = -2.2  for stack of 269-281
		Stack = -1.3  for stack of 270-280
		Stack = -2.2  for stack of 271-279
	Helix total = -7.8
	Hairpin = 4.2  for closure of 272-278
		Stack = -2.1  for stack of 73-244
		Stack = -2.4  for stack of 74-243
		Stack = -3.3  for stack of 75-242
	Helix total = -7.8
	Internal/bulge = 4.7  for closure of 76-241	Size = 8
		Stack = -3.3  for stack of 85-240
		Stack = -3.3  for stack of 86-239
		Stack = -2.2  for stack of 87-238
		Stack = -2.1  for stack of 88-237
	Helix total = -10.9
	Multiloop = 0.3  for closure of 89-236
		Stack = -2.4  for stack of 118-235
	Helix total = -2.4
	Internal/bulge = 3.7  for closure of 119-234	Size = 3
		Stack = -2.2  for stack of 123-233
	Helix total = -2.2
	Multiloop = 4.2  for closure of 124-232
		Stack = -1.4  for stack of 202-222
		Stack = -2.5  for stack of 203-221
		Stack = -2.4  for stack of 204-220
		Stack = -3.3  for stack of 205-219
	Helix total = -9.6
	Internal/bulge = 0.4  for closure of 206-218	Size = 1 BP stack across bulge = -3.4
		Stack = -2.1  for stack of 207-216
		Stack = -2.1  for stack of 208-215
	Helix total = -4.2
	Hairpin = 3.1  for closure of 209-214
		Stack = -3.3  for stack of 182-200
		Stack = -2.2  for stack of 183-199
		Stack = -2.1  for stack of 184-198
		Stack = -3.4  for stack of 185-197
		Stack = -2.4  for stack of 186-196
	Helix total = -13.4
	Hairpin = 3.8  for closure of 187-195
		Stack = -3.3  for stack of 140-174
	Helix total = -3.3
	Internal/bulge = 3.3  for closure of 141-173	Size = 2
		Stack = -2.5  for stack of 142-170
		Stack = -3.3  for stack of 143-169
	Helix total = -5.8
	Internal/bulge = 3.3  for closure of 144-168	Size = 2
		Stack = -2.1  for stack of 147-167
		Stack = -1.5  for stack of 148-166
	Helix total = -3.6
	Internal/bulge = 1.3  for closure of 149-165	Size = 1 BP stack across bulge = -2.5
		Stack = -3.3  for stack of 150-163
		Stack = -3.3  for stack of 151-162
		Stack = -2.1  for stack of 152-161
		Stack = -2.2  for stack of 153-160
	Helix total = -10.9
	Hairpin = 3.3  for closure of 154-159
	Helix total = 0.0
	Internal/bulge = 0.5  for closure of 105-117	Size = 1 BP stack across bulge = -3.3
		Stack = -3.3  for stack of 106-115
		Stack = -3.3  for stack of 107-114
	Helix total = -6.6
	Hairpin = 3.1  for closure of 108-113
		Stack = -3.3  for stack of 90-104
		Stack = -2.1  for stack of 91-103
		Stack = -2.1  for stack of 92-102
		Stack = -3.3  for stack of 93-101
	Helix total = -10.8
	Hairpin = 4.6  for closure of 94-100
		Stack = -3.3  for stack of 20-59
	Helix total = -3.3
	Internal/bulge = -2.2  for closure of 21-58	Size = 2
		Stack = -2.1  for stack of 23-56
		Stack = -1.3  for stack of 24-55
		Stack = -1.5  for stack of 25-54
		Stack = -2.4  for stack of 26-53
		Stack = -2.5  for stack of 27-52
	Helix total = -9.8
	Internal/bulge = 1.7  for closure of 28-51	Size = 1 BP stack across bulge = -1.5
		Stack = -2.4  for stack of 29-49
		Stack = -2.2  for stack of 30-48
		Stack = -2.4  for stack of 31-47
	Helix total = -7.0
	Internal/bulge = 1.7  for closure of 32-46	Size = 1 BP stack across bulge = -2.1
		Stack = -2.4  for stack of 34-45
		Stack = -3.3  for stack of 35-44
		Stack = -2.1  for stack of 36-43
	Helix total = -7.8
	Hairpin = 5.4  for closure of 37-42


	Total energy = -122.7



