Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:66 49:65 50:64 51:63 52:62 154:186 155:185 157:183
	    158:182 159:181 160:180 203:236 207:232 255:295 256:294 257:293
	    258:292 259:291 260:290 261:289
	Energy of Broken Structure: -83.9
	Energy of Pseudo-Helices:   -30.8
	Pseudoknot Energy Penalty:  31.3
	Total Free Energy:          -83.4
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-356
		Stack = -1.5  for stack of 2-355
		Stack = -2.1  for stack of 3-354
		Stack = -3.3  for stack of 4-353
		Stack = -3.4  for stack of 5-352
		Stack = -2.4  for stack of 6-351
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-350
		Stack = -3.4  for stack of 333-349
		Stack = -2.4  for stack of 334-348
		Stack = -3.3  for stack of 335-347
		Stack = -3.3  for stack of 336-346
	Helix total = -12.4
	Hairpin = 4.4  for closure of 337-345
		Stack = -2.4  for stack of 20-329
		Stack = -1.5  for stack of 21-328
		Stack = -2.1  for stack of 22-327
		Stack = -1.5  for stack of 23-326
		Stack = -1.3  for stack of 24-325
		Stack = -1.4  for stack of 25-324
		Stack = -1.0  for stack of 26-323
	Helix total = -11.2
	Internal/bulge = 3.4  for closure of 27-322	Size = 9
		Stack = -2.5  for stack of 33-317
	Helix total = -2.5
	Internal/bulge = 3.3  for closure of 34-316	Size = 5
		Stack = -1.3  for stack of 37-312
		Stack = -2.1  for stack of 38-311
		Stack = -2.5  for stack of 39-310
	Helix total = -5.9
	Internal/bulge = 3.6  for closure of 40-309	Size = 7
		Stack = -2.1  for stack of 43-303
		Stack = -2.1  for stack of 44-302
		Stack = -3.3  for stack of 45-301
		Stack = -2.2  for stack of 46-300
	Helix total = -9.7
	Multiloop = 5.3  for closure of 47-299
		Stack = -1.4  for stack of 240-278
		Stack = -3.4  for stack of 241-277
		Stack = -3.3  for stack of 242-276
		Stack = -1.4  for stack of 243-275
	Helix total = -9.5
	Internal/bulge = 1.2  for closure of 244-274	Size = 2
	Helix total = 0.0
	Internal/bulge = -1.4  for closure of 246-272	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.9  for closure of 248-270	Size = 7
		Stack = -3.4  for stack of 251-264
		Stack = -3.3  for stack of 252-263
	Helix total = -6.7
	Hairpin = 4.5  for closure of 253-262
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 188-221	Size = 2
		Stack = -2.5  for stack of 190-219
		Stack = -2.1  for stack of 191-218
		Stack = -2.2  for stack of 192-217
		Stack = -3.3  for stack of 193-216
		Stack = -3.3  for stack of 194-215
	Helix total = -13.4
	Internal/bulge = 2.0  for closure of 195-214	Size = 6
		Stack = -3.4  for stack of 199-210
	Helix total = -3.4
	Hairpin = 4.4  for closure of 200-209
		Stack = -2.1  for stack of 138-172
		Stack = -2.2  for stack of 139-171
		Stack = -2.1  for stack of 140-170
		Stack = -2.1  for stack of 141-169
	Helix total = -8.5
	Internal/bulge = 1.2  for closure of 142-168	Size = 2
		Stack = -1.3  for stack of 144-166
		Stack = -1.4  for stack of 145-165
		Stack = -3.3  for stack of 146-164
		Stack = -3.4  for stack of 147-163
	Helix total = -9.4
	Hairpin = 5.4  for closure of 148-162
		Stack = -1.4  for stack of 115-137
		Stack = -3.3  for stack of 116-136
		Stack = -3.4  for stack of 117-135
	Helix total = -8.1
	Internal/bulge = 1.3  for closure of 118-134	Size = 1 BP stack across bulge = -2.1
		Stack = -2.1  for stack of 119-132
		Stack = -3.4  for stack of 120-131
		Stack = -3.3  for stack of 121-130
		Stack = -2.1  for stack of 122-129
	Helix total = -10.9
	Hairpin = 5.3  for closure of 123-128
		Stack = -3.4  for stack of 54-77
		Stack = -3.3  for stack of 55-76
		Stack = -2.4  for stack of 56-75
		Stack = -3.4  for stack of 57-74
		Stack = -2.1  for stack of 58-73
	Helix total = -14.6
	Hairpin = 5.2  for closure of 59-72


	Total energy = -83.9



