Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    51:71 52:70 53:69 54:68 158:192 159:191 160:190 161:189
	    162:188 163:187 211:243 212:242 213:241 214:240 215:239 263:304
	    264:303 265:302 266:301 267:300 268:299 269:298
	Energy of Broken Structure: -116.9
	Energy of Pseudo-Helices:   -37.1
	Pseudoknot Energy Penalty:  38.6
	Total Free Energy:          -115.4
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-365
		Stack = -1.5  for stack of 2-364
		Stack = -2.1  for stack of 3-363
		Stack = -2.4  for stack of 4-362
		Stack = -1.1  for stack of 5-361
		Stack = -2.1  for stack of 6-360
	Helix total = -12.5
	Multiloop = 5.0  for closure of 7-359
		Stack = -3.3  for stack of 342-358
		Stack = -2.4  for stack of 343-357
		Stack = -3.3  for stack of 344-356
		Stack = -3.3  for stack of 345-355
	Helix total = -12.3
	Hairpin = 4.4  for closure of 346-354
		Stack = -2.4  for stack of 20-338
		Stack = -2.2  for stack of 21-337
		Stack = -2.1  for stack of 22-336
		Stack = -2.2  for stack of 23-335
		Stack = -1.3  for stack of 24-334
		Stack = -2.1  for stack of 25-333
		Stack = -2.5  for stack of 26-332
	Helix total = -14.8
	Internal/bulge = 3.7  for closure of 27-331	Size = 3
		Stack = -2.4  for stack of 31-330
		Stack = -2.5  for stack of 32-329
		Stack = 0.3  for stack of 33-328
		Stack = -2.5  for stack of 34-327
		Stack = -2.1  for stack of 35-326
		Stack = -2.1  for stack of 36-325
	Helix total = -11.3
	Internal/bulge = -0.9  for closure of 37-324	Size = 1 BP stack across bulge = -3.4
		Stack = -2.1  for stack of 38-322
		Stack = -0.6  for stack of 39-321
		Stack = -1.3  for stack of 40-320
		Stack = -2.2  for stack of 41-319
		Stack = -2.1  for stack of 42-318
	Helix total = -8.3
	Internal/bulge = 2.9  for closure of 43-317	Size = 6
		Stack = -3.3  for stack of 46-312
		Stack = -2.1  for stack of 47-311
		Stack = -2.1  for stack of 48-310
		Stack = -3.4  for stack of 49-309
	Helix total = -10.9
	Multiloop = 6.1  for closure of 50-308
		Stack = -2.5  for stack of 247-285
		Stack = -2.4  for stack of 248-284
	Helix total = -4.9
	Internal/bulge = 0.5  for closure of 249-283	Size = 2
		Stack = -2.4  for stack of 251-281
		Stack = -3.4  for stack of 252-280
		Stack = -3.3  for stack of 253-279
		Stack = -3.3  for stack of 254-278
	Helix total = -12.4
	Internal/bulge = 1.7  for closure of 255-277	Size = 1 BP stack across bulge = -2.1
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 256-275	Size = 3
		Stack = -3.4  for stack of 258-272
		Stack = -3.3  for stack of 259-271
	Helix total = -6.7
	Hairpin = 5.4  for closure of 260-270
		Stack = -2.5  for stack of 196-228
		Stack = -3.3  for stack of 197-227
		Stack = -2.4  for stack of 198-226
	Helix total = -8.2
	Internal/bulge = 0.5  for closure of 199-225	Size = 2
		Stack = -2.4  for stack of 201-223
		Stack = -3.4  for stack of 202-222
		Stack = -1.4  for stack of 203-221
		Stack = -1.4  for stack of 204-220
		Stack = -1.3  for stack of 205-219
		Stack = -1.5  for stack of 206-218
	Helix total = -11.4
	Hairpin = 5.0  for closure of 207-217
		Stack = -2.1  for stack of 140-178
		Stack = -2.2  for stack of 141-177
		Stack = -2.4  for stack of 142-176
		Stack = -2.1  for stack of 143-175
		Stack = -2.4  for stack of 144-174
		Stack = -1.4  for stack of 145-173
		Stack = -2.5  for stack of 146-172
		Stack = -2.4  for stack of 147-171
		Stack = -2.5  for stack of 148-170
	Helix total = -20.0
	Internal/bulge = 3.0  for closure of 149-169	Size = 3
		Stack = -2.1  for stack of 152-167
		Stack = -1.5  for stack of 153-166
		Stack = -3.3  for stack of 154-165
	Helix total = -6.9
	Hairpin = 3.4  for closure of 155-164
		Stack = -2.4  for stack of 116-139
		Stack = -1.1  for stack of 117-138
		Stack = -2.1  for stack of 118-137
		Stack = -3.3  for stack of 119-136
	Helix total = -8.9
	Internal/bulge = 0.5  for closure of 120-135	Size = 2
		Stack = -3.3  for stack of 122-133
		Stack = -3.4  for stack of 123-132
	Helix total = -6.7
	Hairpin = 3.1  for closure of 124-131
		Stack = -3.3  for stack of 58-85
		Stack = -2.1  for stack of 59-84
		Stack = -2.1  for stack of 60-83
		Stack = -2.4  for stack of 61-82
		Stack = -1.4  for stack of 62-81
	Helix total = -11.3
	Hairpin = 6.1  for closure of 63-80


	Total energy = -116.9



