Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    55:79 56:78 57:77 58:76 59:75 152:188 153:187 154:186
	    155:185 205:240 207:238 208:237 209:236 210:235 211:234 259:292
	    260:291 261:290 263:288
	Energy of Broken Structure: -66.4
	Energy of Pseudo-Helices:   -18.4
	Pseudoknot Energy Penalty:  41.0
	Total Free Energy:          -43.8
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-354
		Stack = -1.5  for stack of 2-353
		Stack = -2.1  for stack of 3-352
		Stack = -2.4  for stack of 4-351
		Stack = -1.1  for stack of 5-350
		Stack = -2.1  for stack of 6-349
	Helix total = -12.5
	Multiloop = 5.1  for closure of 7-348
		Stack = -3.3  for stack of 331-347
		Stack = -3.4  for stack of 332-346
		Stack = -2.4  for stack of 333-345
		Stack = -3.3  for stack of 334-344
	Helix total = -12.4
	Hairpin = 4.4  for closure of 335-343
		Stack = -2.4  for stack of 20-327
		Stack = -1.5  for stack of 21-326
		Stack = -2.1  for stack of 22-325
		Stack = -1.5  for stack of 23-324
		Stack = -1.3  for stack of 24-323
		Stack = -2.1  for stack of 25-322
		Stack = -2.5  for stack of 26-321
	Helix total = -13.4
	Internal/bulge = 2.6  for closure of 27-320	Size = 9
		Stack = -1.4  for stack of 33-315
		Stack = -0.9  for stack of 34-314
		Stack = -0.9  for stack of 35-313
		Stack = -1.3  for stack of 36-312
		Stack = -0.6  for stack of 37-311
		Stack = -0.5  for stack of 38-310
		Stack = -1.3  for stack of 39-309
		Stack = -1.4  for stack of 40-308
	Helix total = -8.3
	Internal/bulge = 4.5  for closure of 41-307	Size = 5
		Stack = -2.1  for stack of 43-302
		Stack = -1.1  for stack of 44-301
		Stack = -2.1  for stack of 45-300
		Stack = -2.2  for stack of 46-299
	Helix total = -7.5
	Multiloop = 4.6  for closure of 47-298
		Stack = -2.5  for stack of 241-277
		Stack = -2.1  for stack of 242-276
		Stack = -0.9  for stack of 243-275
		Stack = -1.3  for stack of 244-274
	Helix total = -6.8
	Internal/bulge = 4.1  for closure of 245-273	Size = 12
		Stack = -1.5  for stack of 252-266
		Stack = -3.3  for stack of 253-265
	Helix total = -4.8
	Hairpin = 5.3  for closure of 254-264
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 191-226	Size = 2
		Stack = -2.2  for stack of 193-224
		Stack = -2.4  for stack of 194-223
		Stack = -1.4  for stack of 195-222
		Stack = -0.5  for stack of 196-221
		Stack = -2.1  for stack of 197-220
		Stack = -2.2  for stack of 198-219
		Stack = -2.4  for stack of 199-218
		Stack = -2.1  for stack of 200-217
		Stack = -0.9  for stack of 201-216
		Stack = -1.3  for stack of 202-215
		Stack = -1.1  for stack of 203-214
	Helix total = -18.6
	Hairpin = 4.0  for closure of 204-213
		Stack = -1.4  for stack of 137-175
		Stack = -2.5  for stack of 138-174
		Stack = -2.1  for stack of 139-173
		Stack = -2.1  for stack of 140-172
		Stack = -2.4  for stack of 141-171
	Helix total = -10.5
	Internal/bulge = 6.5  for closure of 142-170	Size = 7
		Stack = -2.1  for stack of 144-163
	Helix total = -2.1
	Internal/bulge = 1.5  for closure of 145-162	Size = 4
		Stack = -2.2  for stack of 148-159
	Helix total = -2.2
	Hairpin = 4.4  for closure of 149-158
		Stack = -2.1  for stack of 116-136
		Stack = -1.3  for stack of 117-135
		Stack = -2.1  for stack of 118-134
		Stack = -3.4  for stack of 119-133
		Stack = -2.4  for stack of 120-132
		Stack = -3.3  for stack of 121-131
	Helix total = -14.6
	Hairpin = 5.3  for closure of 122-130
		Stack = -2.4  for stack of 48-66
		Stack = -2.2  for stack of 49-65
		Stack = -2.1  for stack of 50-64
		Stack = -3.4  for stack of 51-63
	Helix total = -10.1
	Hairpin = 5.6  for closure of 52-62


	Total energy = -66.4



