Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:67 50:66 51:65 52:64 150:182 151:181 152:180 153:179
	    154:178 198:224 199:223 200:222 201:221 242:281 243:280 244:279
	    246:276 247:275 248:274
	Energy of Broken Structure: -53.0
	Energy of Pseudo-Helices:   -32.3
	Pseudoknot Energy Penalty:  32.6
	Total Free Energy:          -52.7
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-341
		Stack = -1.5  for stack of 2-340
		Stack = -2.1  for stack of 3-339
		Stack = -3.3  for stack of 4-338
		Stack = -3.4  for stack of 5-337
		Stack = -2.4  for stack of 6-336
	Helix total = -16.0
	Multiloop = 5.2  for closure of 7-335
		Stack = -2.5  for stack of 318-334
		Stack = -1.4  for stack of 319-333
		Stack = -3.3  for stack of 320-332
		Stack = -3.3  for stack of 321-331
	Helix total = -10.5
	Hairpin = 4.4  for closure of 322-330
		Stack = -2.4  for stack of 21-314
		Stack = -2.2  for stack of 22-313
		Stack = -2.4  for stack of 23-312
	Helix total = -7.0
	Internal/bulge = 1.4  for closure of 24-311	Size = 4
	Helix total = 0.0
	Internal/bulge = 2.4  for closure of 27-308	Size = 13
		Stack = -3.3  for stack of 35-301
		Stack = -2.1  for stack of 36-300
	Helix total = -5.4
	Internal/bulge = 3.7  for closure of 37-299	Size = 3
		Stack = -2.1  for stack of 40-297
		Stack = -2.2  for stack of 41-296
		Stack = -1.0  for stack of 42-295
	Helix total = -5.3
	Internal/bulge = 4.1  for closure of 43-294	Size = 4
		Stack = -2.1  for stack of 44-289
		Stack = -1.1  for stack of 45-288
		Stack = -1.3  for stack of 46-287
		Stack = -1.4  for stack of 47-286
	Helix total = -5.9
	Multiloop = 6.5  for closure of 48-285
		Stack = -2.5  for stack of 228-263
		Stack = -2.1  for stack of 229-262
		Stack = -0.9  for stack of 230-261
	Helix total = -5.5
	Internal/bulge = 1.9  for closure of 231-260	Size = 2
	Helix total = 0.0
	Internal/bulge = 4.5  for closure of 233-258	Size = 10
		Stack = -1.5  for stack of 238-251
		Stack = -2.1  for stack of 239-250
	Helix total = -3.6
	Hairpin = 5.4  for closure of 240-249
		Stack = -1.0  for stack of 186-213
		Stack = -2.2  for stack of 187-212
		Stack = -2.1  for stack of 188-211
		Stack = -2.4  for stack of 189-210
		Stack = -2.1  for stack of 190-209
		Stack = -1.3  for stack of 191-208
		Stack = -2.2  for stack of 192-207
	Helix total = -13.3
	Internal/bulge = 1.2  for closure of 193-206	Size = 2
		Stack = -2.1  for stack of 195-204
	Helix total = -2.1
	Hairpin = 4.3  for closure of 196-203
		Stack = -2.1  for stack of 134-169
		Stack = -1.4  for stack of 135-168
		Stack = -2.2  for stack of 136-167
		Stack = -0.9  for stack of 137-166
		Stack = -1.3  for stack of 138-165
		Stack = -1.1  for stack of 139-164
		Stack = -2.4  for stack of 140-163
		Stack = -2.1  for stack of 141-162
	Helix total = -13.5
	Internal/bulge = 0.6  for closure of 142-161	Size = 4
		Stack = -2.1  for stack of 145-158
		Stack = -2.2  for stack of 146-157
	Helix total = -4.3
	Hairpin = 4.0  for closure of 147-156
		Stack = -0.9  for stack of 115-132
		Stack = -2.1  for stack of 116-131
		Stack = -3.3  for stack of 117-130
		Stack = -3.4  for stack of 118-129
		Stack = -2.1  for stack of 119-128
	Helix total = -11.8
	Hairpin = 4.2  for closure of 120-127
		Stack = -1.0  for stack of 55-81
		Stack = -1.3  for stack of 56-80
		Stack = -0.9  for stack of 57-79
		Stack = -2.2  for stack of 58-78
		Stack = -2.1  for stack of 59-77
	Helix total = -7.5
	Hairpin = 6.6  for closure of 60-76


	Total energy = -53.0



