Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    12:346 13:345 14:344 15:343 16:342 17:341 18:340 69:282
	    70:281 71:280 72:279 73:278 74:277 75:276
	Energy of Broken Structure: -149.4
	Energy of Pseudo-Helices:   -28.9
	Pseudoknot Energy Penalty:  17.7
	Total Free Energy:          -160.6
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -0.4
		Stack = -3.3  for stack of 1-398
		Stack = -2.1  for stack of 2-397
		Stack = -2.1  for stack of 3-396
		Stack = -2.2  for stack of 4-395
		Stack = -0.9  for stack of 5-394
		Stack = -2.1  for stack of 6-393
		Stack = -3.3  for stack of 7-392
		Stack = -3.4  for stack of 8-391
		Stack = -3.3  for stack of 9-390
	Helix total = -22.7
	Internal/bulge = 1.4  for closure of 10-389	Size = 1 BP stack across bulge = -2.4
	Helix total = 0.0
	Multiloop = 5.2  for closure of 11-387
		Stack = -0.9  for stack of 55-385
		Stack = -2.1  for stack of 56-384
	Helix total = -3.0
	Internal/bulge = 0.4  for closure of 57-383	Size = 1 BP stack across bulge = -3.4
		Stack = -3.3  for stack of 59-382
		Stack = -2.4  for stack of 60-381
		Stack = -3.3  for stack of 61-380
		Stack = -3.3  for stack of 62-379
	Helix total = -12.3
	Multiloop = 4.1  for closure of 63-378
		Stack = -2.5  for stack of 349-368
		Stack = -0.5  for stack of 350-367
		Stack = -1.5  for stack of 351-366
		Stack = -3.3  for stack of 352-365
		Stack = -2.4  for stack of 353-364
		Stack = -3.3  for stack of 354-363
	Helix total = -13.5
	Hairpin = 2.9  for closure of 355-362
		Stack = -1.5  for stack of 310-329
		Stack = -2.5  for stack of 311-328
		Stack = -2.4  for stack of 312-327
		Stack = -3.3  for stack of 313-326
		Stack = -3.4  for stack of 314-325
		Stack = -2.1  for stack of 315-324
		Stack = -1.1  for stack of 316-323
	Helix total = -16.3
	Hairpin = 4.1  for closure of 317-322
		Stack = -1.3  for stack of 229-303
		Stack = -2.2  for stack of 230-302
		Stack = -3.3  for stack of 231-301
	Helix total = -6.8
	Internal/bulge = 1.2  for closure of 232-300	Size = 11
		Stack = -3.3  for stack of 239-294
		Stack = -2.4  for stack of 240-293
		Stack = -1.1  for stack of 241-292
		Stack = -2.1  for stack of 242-291
		Stack = -2.4  for stack of 243-290
		Stack = -2.2  for stack of 244-289
	Helix total = -13.5
	Multiloop = 3.7  for closure of 245-288
		Stack = -3.4  for stack of 272-285
		Stack = -3.3  for stack of 273-284
	Helix total = -6.7
	Hairpin = 3.1  for closure of 274-283
		Stack = -1.5  for stack of 249-268
		Stack = -0.5  for stack of 250-267
		Stack = -2.5  for stack of 251-266
		Stack = -1.4  for stack of 252-265
		Stack = -2.1  for stack of 253-264
		Stack = -3.3  for stack of 254-263
		Stack = -3.4  for stack of 255-262
	Helix total = -14.7
	Hairpin = 3.3  for closure of 256-261
		Stack = -2.1  for stack of 64-225
		Stack = -2.4  for stack of 65-224
		Stack = -3.3  for stack of 66-223
	Helix total = -7.8
	Internal/bulge = 4.8  for closure of 67-222	Size = 9
		Stack = -2.4  for stack of 77-221
		Stack = -3.3  for stack of 78-220
		Stack = -2.2  for stack of 79-219
		Stack = -2.1  for stack of 80-218
	Helix total = -10.0
	Multiloop = 0.2  for closure of 81-217
		Stack = -3.3  for stack of 112-216
	Helix total = -3.3
	Internal/bulge = 3.2  for closure of 113-215	Size = 3
		Stack = -2.2  for stack of 117-214
	Helix total = -2.2
	Multiloop = 4.2  for closure of 118-213
		Stack = -1.4  for stack of 184-203
		Stack = -2.5  for stack of 185-202
		Stack = -3.3  for stack of 186-201
		Stack = -1.4  for stack of 187-200
		Stack = -2.5  for stack of 188-199
		Stack = -2.1  for stack of 189-198
		Stack = -2.1  for stack of 190-197
	Helix total = -15.3
	Hairpin = 3.1  for closure of 191-196
		Stack = -3.3  for stack of 164-182
		Stack = -2.2  for stack of 165-181
		Stack = -2.1  for stack of 166-180
		Stack = -3.3  for stack of 167-179
		Stack = -3.3  for stack of 168-178
	Helix total = -14.2
	Hairpin = 3.8  for closure of 169-177
		Stack = -3.3  for stack of 134-156
	Helix total = -3.3
	Internal/bulge = 3.3  for closure of 135-155	Size = 2
		Stack = -2.5  for stack of 136-152
		Stack = -3.3  for stack of 137-151
		Stack = -2.1  for stack of 138-150
		Stack = -1.1  for stack of 139-149
		Stack = -2.1  for stack of 140-148
		Stack = -3.4  for stack of 141-147
	Helix total = -14.5
	Hairpin = 5.4  for closure of 142-146
	Helix total = 0.0
	Internal/bulge = 1.4  for closure of 97-111	Size = 1 BP stack across bulge = -2.4
		Stack = -3.3  for stack of 98-109
		Stack = -3.3  for stack of 99-108
		Stack = -3.3  for stack of 100-107
	Helix total = -9.9
	Hairpin = 3.1  for closure of 101-106
		Stack = -3.3  for stack of 82-96
		Stack = -2.4  for stack of 83-95
		Stack = -3.3  for stack of 84-94
		Stack = -2.4  for stack of 85-93
	Helix total = -11.4
	Hairpin = 5.6  for closure of 86-92
		Stack = -1.4  for stack of 20-50
		Stack = -2.5  for stack of 21-49
		Stack = -3.3  for stack of 22-48
		Stack = -2.1  for stack of 23-47
		Stack = -0.9  for stack of 24-46
		Stack = -1.3  for stack of 25-45
		Stack = -2.2  for stack of 26-44
		Stack = -3.3  for stack of 27-43
	Helix total = -17.0
	Internal/bulge = 3.2  for closure of 28-42	Size = 3
		Stack = -2.2  for stack of 32-41
		Stack = -2.4  for stack of 33-40
	Helix total = -4.6
	Hairpin = 3.3  for closure of 34-39


	Total energy = -149.4



