Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    55:80 56:79 57:78 58:77 149:196 150:195 151:194 152:193
	    153:192 154:191 211:244 212:243 213:242 214:241 215:240 216:239
	    217:238 218:237 261:303 262:302 263:301 264:300 265:298
	Energy of Broken Structure: 1318.9
	Energy of Pseudo-Helices:   -33.3
	Pseudoknot Energy Penalty:  35.9
	Total Free Energy:          1321.5
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-363
		Stack = -1.5  for stack of 2-362
		Stack = -2.1  for stack of 3-361
		Stack = -3.4  for stack of 4-360
		Stack = -3.3  for stack of 5-359
		Stack = -2.4  for stack of 6-358
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-357
		Stack = -3.4  for stack of 340-356
		Stack = -2.4  for stack of 341-355
		Stack = -3.3  for stack of 342-354
		Stack = -3.3  for stack of 343-353
	Helix total = -12.4
	Hairpin = 4.4  for closure of 344-352
		Stack = -2.4  for stack of 20-336
		Stack = -2.5  for stack of 21-335
		Stack = 0.3  for stack of 22-334
		Stack = -0.5  for stack of 23-333
		Stack = -2.1  for stack of 24-332
		Stack = -2.5  for stack of 25-331
		Stack = -1.5  for stack of 26-330
	Helix total = -11.2
	Internal/bulge = 2.7  for closure of 27-329	Size = 9
		Stack = -2.5  for stack of 33-324
		Stack = -2.1  for stack of 34-323
		Stack = -2.1  for stack of 35-322
	Helix total = -6.7
	Internal/bulge = 0.5  for closure of 36-321	Size = 1 BP stack across bulge = -3.3
		Stack = -2.5  for stack of 38-320
		Stack = -1.0  for stack of 39-319
		Stack = -2.1  for stack of 40-318
	Helix total = -5.6
	Internal/bulge = 2.9  for closure of 41-317	Size = 7
		Stack = -2.1  for stack of 44-311
		Stack = -1.1  for stack of 45-310
		Stack = -1.3  for stack of 46-309
		Stack = -2.2  for stack of 47-308
	Helix total = -6.7
	Multiloop = 3.6  for closure of 48-307
		Stack = -2.1  for stack of 246-282
		Stack = -3.4  for stack of 247-281
	Helix total = -5.5
	Internal/bulge = 0.7  for closure of 248-280	Size = 6
		Stack = -1.1  for stack of 252-276
		Stack = -2.4  for stack of 253-275
	Helix total = -3.5
	Internal/bulge = 1.7  for closure of 254-274	Size = 7
		Stack = -3.3  for stack of 258-269
	Helix total = -3.3
	Hairpin = 4.1  for closure of 259-268
		Stack = -3.4  for stack of 200-228
		Stack = -1.4  for stack of 201-227
		Stack = -2.5  for stack of 202-226
		Stack = -2.1  for stack of 203-225
		Stack = -0.6  for stack of 204-224
		Stack = -2.1  for stack of 205-223
		Stack = -2.5  for stack of 206-222
		Stack = -1.5  for stack of 207-221
		Stack = -3.3  for stack of 208-220
	Helix total = -19.4
	Hairpin = 4.9  for closure of 209-219
		Stack = -2.2  for stack of 134-183
		Stack = -2.1  for stack of 135-182
		Stack = -2.4  for stack of 136-181
		Stack = -2.1  for stack of 137-180
		Stack = -2.2  for stack of 138-179
	Helix total = -11.0
	Multiloop = 2.8  for closure of 139-178
		Stack = -3.3  for stack of 162-175
		Stack = -2.4  for stack of 163-174
		Stack = -3.3  for stack of 164-173
	Helix total = -9.0
	Internal/bulge = 1.2  for closure of 165-172	Size = 2
	Helix total = 0.0
	Hairpin = 1400.5  for closure of 167-170
		Stack = -2.1  for stack of 141-160
		Stack = -1.3  for stack of 142-159
		Stack = -2.1  for stack of 143-158
		Stack = -3.4  for stack of 144-157
		Stack = -3.3  for stack of 145-156
	Helix total = -12.2
	Hairpin = 4.5  for closure of 146-155
	Helix total = 0.0
	Internal/bulge = 3.6  for closure of 113-133	Size = 4
	Helix total = 0.0
	Internal/bulge = 0.5  for closure of 118-132	Size = 2
	Helix total = 0.0
	Hairpin = 5.7  for closure of 120-130
		Stack = -2.4  for stack of 49-67
		Stack = -2.4  for stack of 50-66
		Stack = -2.1  for stack of 51-65
		Stack = -3.3  for stack of 52-64
	Helix total = -10.2
	Hairpin = 3.9  for closure of 53-63


	Total energy = 1318.9



