Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    55:71 56:70 57:69 155:194 156:193 157:192 158:191 159:190
	    160:189 161:188 209:242 210:241 211:240 212:239 213:238 214:237
	    215:236 260:298 261:297 262:296 263:295 264:294 265:293 266:292
	    267:291 268:290
	Energy of Broken Structure: -50.3
	Energy of Pseudo-Helices:   -35.7
	Pseudoknot Energy Penalty:  32.3
	Total Free Energy:          -53.7
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-359
		Stack = -1.5  for stack of 2-358
		Stack = -2.1  for stack of 3-357
		Stack = -2.4  for stack of 4-356
		Stack = -1.1  for stack of 5-355
		Stack = -2.1  for stack of 6-354
	Helix total = -12.5
	Multiloop = 5.1  for closure of 7-353
		Stack = -3.4  for stack of 336-352
		Stack = -2.4  for stack of 337-351
		Stack = -3.3  for stack of 338-350
		Stack = -3.3  for stack of 339-349
	Helix total = -12.4
	Hairpin = 4.4  for closure of 340-348
		Stack = -2.1  for stack of 20-332
		Stack = -1.0  for stack of 21-331
		Stack = -1.3  for stack of 22-330
		Stack = -0.9  for stack of 23-329
		Stack = -0.9  for stack of 24-328
		Stack = -0.9  for stack of 25-327
		Stack = -1.4  for stack of 26-326
	Helix total = -8.5
	Internal/bulge = 4.2  for closure of 27-325	Size = 3
		Stack = -0.9  for stack of 31-324
		Stack = -1.1  for stack of 32-323
		Stack = -1.3  for stack of 33-322
		Stack = -1.1  for stack of 34-321
		Stack = -0.9  for stack of 35-320
		Stack = -1.0  for stack of 36-319
		Stack = -1.4  for stack of 37-318
		Stack = -1.3  for stack of 38-317
		Stack = -0.9  for stack of 39-316
		Stack = -2.1  for stack of 40-315
		Stack = -2.5  for stack of 41-314
		Stack = -0.6  for stack of 42-313
	Helix total = -15.1
	Internal/bulge = 4.5  for closure of 43-312	Size = 5
		Stack = -2.1  for stack of 45-307
		Stack = -0.6  for stack of 46-306
		Stack = -2.1  for stack of 47-305
		Stack = -3.4  for stack of 48-304
	Helix total = -8.2
	Multiloop = 6.3  for closure of 49-303
		Stack = -3.4  for stack of 244-282
		Stack = -2.1  for stack of 245-281
		Stack = -0.9  for stack of 246-280
		Stack = -1.1  for stack of 247-279
	Helix total = -7.5
	Internal/bulge = 4.2  for closure of 248-278	Size = 3
		Stack = -1.4  for stack of 252-277
		Stack = -2.1  for stack of 253-276
		Stack = -3.3  for stack of 254-275
		Stack = -2.2  for stack of 255-274
		Stack = -0.9  for stack of 256-273
		Stack = -0.9  for stack of 257-272
		Stack = -2.1  for stack of 258-271
	Helix total = -12.9
	Hairpin = 5.8  for closure of 259-270
	Helix total = 0.0
	Internal/bulge = -1.4  for closure of 195-228	Size = 2
		Stack = -2.1  for stack of 197-226
		Stack = -0.6  for stack of 198-225
		Stack = -1.3  for stack of 199-224
		Stack = -0.9  for stack of 200-223
		Stack = -0.9  for stack of 201-222
		Stack = -0.9  for stack of 202-221
		Stack = -0.9  for stack of 203-220
		Stack = -1.1  for stack of 204-219
	Helix total = -8.7
	Hairpin = 5.2  for closure of 205-218
		Stack = -0.6  for stack of 136-180
		Stack = -1.3  for stack of 137-179
		Stack = -2.1  for stack of 138-178
		Stack = -2.4  for stack of 139-177
		Stack = -2.1  for stack of 140-176
	Helix total = -8.5
	Internal/bulge = 2.2  for closure of 141-175	Size = 3
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 143-172	Size = 4
		Stack = -2.2  for stack of 146-169
	Helix total = -2.2
	Internal/bulge = 1.9  for closure of 147-168	Size = 2
		Stack = -1.3  for stack of 149-166
	Helix total = -1.3
	Internal/bulge = 1.9  for closure of 150-165	Size = 2
		Stack = -0.6  for stack of 152-163
	Helix total = -0.6
	Hairpin = 5.3  for closure of 153-162
		Stack = -1.0  for stack of 119-133
		Stack = -0.5  for stack of 120-132
		Stack = -2.5  for stack of 121-131
		Stack = -2.1  for stack of 122-130
	Helix total = -6.1
	Hairpin = 4.2  for closure of 123-129
		Stack = -0.9  for stack of 98-118
		Stack = -1.3  for stack of 99-117
		Stack = -2.2  for stack of 100-116
		Stack = -2.1  for stack of 101-115
		Stack = -0.9  for stack of 102-114
		Stack = -2.1  for stack of 103-113
	Helix total = -9.5
	Internal/bulge = 1.2  for closure of 104-112	Size = 2
	Helix total = 0.0
	Hairpin = 5.9  for closure of 106-110
		Stack = -0.6  for stack of 50-63
	Helix total = -0.6
	Internal/bulge = 1.9  for closure of 51-62	Size = 2
		Stack = -2.1  for stack of 53-60
	Helix total = -2.1
	Hairpin = 4.1  for closure of 54-59


	Total energy = -50.3



