Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    55:84 56:83 57:82 58:81 59:80 159:195 160:194 161:193
	    162:192 163:191 164:190 165:189 210:241 211:240 212:239 213:238
	    214:237 259:296 260:295 261:294 263:291 264:290 265:289
	Energy of Broken Structure: -73.9
	Energy of Pseudo-Helices:   -38.3
	Pseudoknot Energy Penalty:  31.5
	Total Free Energy:          -80.7
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-356
		Stack = -1.5  for stack of 2-355
		Stack = -2.1  for stack of 3-354
		Stack = -3.3  for stack of 4-353
		Stack = -3.4  for stack of 5-352
		Stack = -2.4  for stack of 6-351
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-350
		Stack = -3.4  for stack of 333-349
		Stack = -2.4  for stack of 334-348
		Stack = -3.3  for stack of 335-347
		Stack = -3.3  for stack of 336-346
	Helix total = -12.4
	Hairpin = 4.4  for closure of 337-345
		Stack = -2.4  for stack of 20-329
		Stack = -2.2  for stack of 21-328
		Stack = -1.0  for stack of 22-327
		Stack = -0.5  for stack of 23-326
		Stack = -1.3  for stack of 24-325
		Stack = -1.1  for stack of 25-324
		Stack = -2.4  for stack of 26-323
	Helix total = -10.9
	Internal/bulge = 1.2  for closure of 27-322	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.2  for closure of 29-320	Size = 8
		Stack = -3.3  for stack of 35-316
		Stack = -2.4  for stack of 36-315
	Helix total = -5.7
	Internal/bulge = 2.5  for closure of 37-314	Size = 3
		Stack = -2.4  for stack of 39-311
		Stack = -2.2  for stack of 40-310
		Stack = -1.4  for stack of 41-309
	Helix total = -6.0
	Internal/bulge = 3.7  for closure of 42-308	Size = 3
		Stack = -2.1  for stack of 43-304
		Stack = -1.1  for stack of 44-303
		Stack = -2.1  for stack of 45-302
		Stack = -2.5  for stack of 46-301
	Helix total = -7.8
	Multiloop = 5.8  for closure of 47-300
		Stack = -2.1  for stack of 244-278
		Stack = -2.1  for stack of 245-277
		Stack = -2.2  for stack of 246-276
		Stack = -2.4  for stack of 247-275
	Helix total = -8.8
	Internal/bulge = 1.3  for closure of 248-274	Size = 1 BP stack across bulge = -2.1
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 250-273	Size = 2
		Stack = -1.3  for stack of 252-271
	Helix total = -1.3
	Internal/bulge = 1.2  for closure of 253-270	Size = 2
		Stack = -3.3  for stack of 255-268
		Stack = -3.3  for stack of 256-267
	Helix total = -6.6
	Hairpin = 4.1  for closure of 257-266
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 196-229	Size = 2
		Stack = -2.5  for stack of 198-227
		Stack = -3.3  for stack of 199-226
	Helix total = -5.8
	Internal/bulge = 1.2  for closure of 200-225	Size = 2
		Stack = -2.4  for stack of 202-223
		Stack = -2.1  for stack of 203-222
	Helix total = -4.5
	Internal/bulge = 3.3  for closure of 204-221	Size = 5
		Stack = -2.1  for stack of 207-217
		Stack = -1.1  for stack of 208-216
	Helix total = -3.2
	Hairpin = 5.4  for closure of 209-215
		Stack = -3.3  for stack of 144-180
		Stack = -2.4  for stack of 145-179
		Stack = -2.2  for stack of 146-178
		Stack = -0.9  for stack of 147-177
		Stack = -2.1  for stack of 148-176
	Helix total = -10.9
	Internal/bulge = 2.3  for closure of 149-175	Size = 5
		Stack = -3.3  for stack of 152-171
		Stack = -3.3  for stack of 153-170
		Stack = -2.4  for stack of 154-169
		Stack = -1.1  for stack of 155-168
		Stack = -1.3  for stack of 156-167
	Helix total = -11.4
	Hairpin = 5.3  for closure of 157-166
		Stack = -0.9  for stack of 119-143
		Stack = -2.1  for stack of 120-142
		Stack = -2.4  for stack of 121-141
		Stack = -0.9  for stack of 122-140
		Stack = -2.1  for stack of 123-139
		Stack = -3.4  for stack of 124-138
		Stack = -2.1  for stack of 125-137
		Stack = -0.9  for stack of 126-136
	Helix total = -14.8
	Hairpin = 5.5  for closure of 127-135
		Stack = -2.4  for stack of 48-68
		Stack = -2.4  for stack of 49-67
		Stack = -2.1  for stack of 50-66
		Stack = -3.4  for stack of 51-65
	Helix total = -10.3
	Hairpin = 5.6  for closure of 52-64


	Total energy = -73.9



