Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    54:73 56:71 58:69 143:179 144:178 145:177 146:176 147:175
	    148:174 149:173 194:223 195:222 196:221 197:220 198:219 199:218
	    200:217 201:216 241:278 242:277 243:276 244:275 245:274 246:273
	    248:271
	Energy of Broken Structure: -43.1
	Energy of Pseudo-Helices:   -29.0
	Pseudoknot Energy Penalty:  32.0
	Total Free Energy:          -40.1
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-340
		Stack = -1.5  for stack of 2-339
		Stack = -2.1  for stack of 3-338
		Stack = -2.4  for stack of 4-337
		Stack = -1.1  for stack of 5-336
		Stack = -2.1  for stack of 6-335
	Helix total = -12.5
	Multiloop = 6.5  for closure of 7-334
		Stack = -2.2  for stack of 317-333
		Stack = -2.4  for stack of 318-332
		Stack = -2.4  for stack of 319-331
		Stack = -2.1  for stack of 320-330
	Helix total = -9.1
	Hairpin = 4.4  for closure of 321-329
		Stack = -2.4  for stack of 20-313
		Stack = -1.5  for stack of 21-312
		Stack = -0.5  for stack of 22-311
		Stack = -0.5  for stack of 23-310
		Stack = -1.4  for stack of 24-309
		Stack = -1.3  for stack of 25-308
		Stack = 0.3  for stack of 26-307
	Helix total = -7.3
	Internal/bulge = 3.0  for closure of 27-306	Size = 3
	Helix total = 0.0
	Internal/bulge = -0.2  for closure of 29-303	Size = 2
		Stack = -1.5  for stack of 31-301
		Stack = 1.3  for stack of 32-300
		Stack = -0.5  for stack of 33-299
		Stack = -1.0  for stack of 34-298
		Stack = -1.1  for stack of 35-297
		Stack = -1.3  for stack of 36-296
		Stack = -0.6  for stack of 37-295
		Stack = -2.1  for stack of 38-294
		Stack = -2.5  for stack of 39-293
	Helix total = -9.3
	Internal/bulge = 4.6  for closure of 40-292	Size = 7
		Stack = -2.1  for stack of 43-286
		Stack = -0.9  for stack of 44-285
		Stack = -2.1  for stack of 45-284
		Stack = -2.2  for stack of 46-283
	Helix total = -7.3
	Multiloop = 4.7  for closure of 47-282
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 224-263	Size = 2
		Stack = -2.2  for stack of 226-261
	Helix total = -2.2
	Internal/bulge = 0.8  for closure of 227-260	Size = 4
		Stack = -1.3  for stack of 230-257
		Stack = -0.6  for stack of 231-256
		Stack = -1.4  for stack of 232-255
		Stack = -0.9  for stack of 233-254
		Stack = -1.3  for stack of 234-253
	Helix total = -5.5
	Internal/bulge = 0.1  for closure of 235-252	Size = 4
	Helix total = 0.0
	Hairpin = 5.5  for closure of 238-249
		Stack = -3.3  for stack of 183-209
		Stack = -2.1  for stack of 184-208
		Stack = -1.1  for stack of 185-207
		Stack = -1.3  for stack of 186-206
		Stack = -0.9  for stack of 187-205
		Stack = -0.9  for stack of 188-204
		Stack = -1.4  for stack of 189-203
	Helix total = -11.0
	Hairpin = 5.7  for closure of 190-202
		Stack = -2.1  for stack of 126-165
		Stack = -2.2  for stack of 127-164
		Stack = -3.3  for stack of 128-163
		Stack = -2.1  for stack of 129-162
	Helix total = -9.7
	Internal/bulge = 2.3  for closure of 130-161	Size = 1 BP stack across bulge = -0.9
		Stack = -2.1  for stack of 131-159
		Stack = -1.5  for stack of 132-158
		Stack = -1.3  for stack of 133-157
	Helix total = -4.9
	Internal/bulge = 1.5  for closure of 134-156	Size = 2
		Stack = -0.9  for stack of 136-154
		Stack = -2.2  for stack of 137-153
		Stack = -2.1  for stack of 138-152
		Stack = -0.5  for stack of 139-151
	Helix total = -5.7
	Hairpin = 6.1  for closure of 140-150
		Stack = -1.3  for stack of 107-125
		Stack = -2.1  for stack of 108-124
		Stack = -3.4  for stack of 109-123
		Stack = -2.1  for stack of 110-122
		Stack = -2.1  for stack of 111-121
	Helix total = -11.0
	Hairpin = 5.5  for closure of 112-120
		Stack = -2.1  for stack of 48-63
	Helix total = -2.1
	Internal/bulge = -0.7  for closure of 49-62	Size = 2
	Helix total = 0.0
	Hairpin = 5.2  for closure of 51-60


	Total energy = -43.1



