Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:64 49:63 50:62 51:61 52:60 160:195 161:194 162:193
	    163:192 164:191 213:242 214:241 215:240 216:239 217:238 261:302
	    262:301 263:300 264:299 265:297 266:296 267:295
	Energy of Broken Structure: -59.6
	Energy of Pseudo-Helices:   -38.1
	Pseudoknot Energy Penalty:  32.7
	Total Free Energy:          -65.0
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 = -2.4  for stack of 4-360
		Stack = -2.2  for stack of 5-359
		Stack = -2.4  for stack of 6-358
	Helix total = -13.9
	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 = -2.1  for stack of 20-336
		Stack = -0.6  for stack of 21-335
		Stack = -0.5  for stack of 22-334
		Stack = -2.5  for stack of 23-333
		Stack = -2.1  for stack of 24-332
		Stack = -2.2  for stack of 25-331
		Stack = -2.1  for stack of 26-330
	Helix total = -12.1
	Internal/bulge = 1.9  for closure of 27-329	Size = 10
		Stack = -2.5  for stack of 33-323
		Stack = -2.1  for stack of 34-322
		Stack = -0.9  for stack of 35-321
		Stack = -1.0  for stack of 36-320
		Stack = -1.3  for stack of 37-319
		Stack = -0.9  for stack of 38-318
	Helix total = -8.7
	Internal/bulge = 4.3  for closure of 39-317	Size = 9
		Stack = -2.4  for stack of 43-310
		Stack = -2.2  for stack of 44-309
		Stack = -0.9  for stack of 45-308
		Stack = -1.3  for stack of 46-307
	Helix total = -6.8
	Multiloop = 6.0  for closure of 47-306
		Stack = -2.5  for stack of 245-282
	Helix total = -2.5
	Internal/bulge = 1.0  for closure of 246-281	Size = 4
	Helix total = 0.0
	Internal/bulge = 2.9  for closure of 249-278	Size = 5
	Helix total = 0.0
	Internal/bulge = 4.0  for closure of 253-275	Size = 5
		Stack = -2.1  for stack of 256-271
		Stack = -3.4  for stack of 257-270
		Stack = -3.3  for stack of 258-269
	Helix total = -8.8
	Hairpin = 4.1  for closure of 259-268
		Stack = -0.9  for stack of 201-227
		Stack = -0.9  for stack of 202-226
		Stack = -2.4  for stack of 203-225
		Stack = -2.1  for stack of 204-224
		Stack = -0.9  for stack of 205-223
		Stack = -2.2  for stack of 206-222
		Stack = -2.1  for stack of 207-221
		Stack = -0.9  for stack of 208-220
	Helix total = -12.4
	Hairpin = 5.5  for closure of 209-219
		Stack = -2.4  for stack of 144-181
		Stack = -1.4  for stack of 145-180
		Stack = -1.5  for stack of 146-179
		Stack = -3.3  for stack of 147-178
		Stack = -2.1  for stack of 148-177
	Helix total = -10.7
	Internal/bulge = 3.3  for closure of 149-176	Size = 2
		Stack = -2.1  for stack of 150-173
		Stack = -2.4  for stack of 151-172
		Stack = -2.4  for stack of 152-171
	Helix total = -6.9
	Internal/bulge = 0.5  for closure of 153-170	Size = 1 BP stack across bulge = -3.3
		Stack = -3.4  for stack of 154-168
		Stack = -2.1  for stack of 155-167
		Stack = -1.4  for stack of 156-166
	Helix total = -6.9
	Hairpin = 6.0  for closure of 157-165
	Helix total = 0.0
	Internal/bulge = 1.0  for closure of 116-141	Size = 2
		Stack = -0.6  for stack of 118-139
		Stack = -1.3  for stack of 119-138
		Stack = -0.6  for stack of 120-137
		Stack = -2.5  for stack of 121-136
		Stack = -2.1  for stack of 122-135
		Stack = -2.1  for stack of 123-134
	Helix total = -9.2
	Hairpin = 4.4  for closure of 124-133
		Stack = -2.2  for stack of 53-76
	Helix total = -2.2
	Internal/bulge = 1.7  for closure of 54-75	Size = 2
		Stack = -2.2  for stack of 56-73
		Stack = -2.4  for stack of 57-72
		Stack = -2.2  for stack of 58-71
	Helix total = -6.8
	Hairpin = 6.3  for closure of 59-70


	Total energy = -59.6



