Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    50:65 51:64 52:63 53:62 54:61 157:193 158:192 159:191
	    160:190 161:189 162:188 210:243 211:242 212:241 213:240 214:239
	    215:238 260:297 261:296 262:295 263:294 264:293 265:292 266:291
	Energy of Broken Structure: -66.4
	Energy of Pseudo-Helices:   -39.2
	Pseudoknot Energy Penalty:  37.1
	Total Free Energy:          -68.5
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-358
		Stack = -1.5  for stack of 2-357
		Stack = -2.1  for stack of 3-356
		Stack = -2.4  for stack of 4-355
		Stack = -2.2  for stack of 5-354
		Stack = -2.4  for stack of 6-353
	Helix total = -13.9
	Multiloop = 5.2  for closure of 7-352
		Stack = -3.4  for stack of 335-351
		Stack = -2.4  for stack of 336-350
		Stack = -3.3  for stack of 337-349
		Stack = -3.3  for stack of 338-348
	Helix total = -12.4
	Hairpin = 4.4  for closure of 339-347
		Stack = -2.1  for stack of 21-331
		Stack = -2.1  for stack of 22-330
		Stack = -1.5  for stack of 23-329
		Stack = -2.1  for stack of 24-328
		Stack = -3.3  for stack of 25-327
		Stack = -2.2  for stack of 26-326
		Stack = -2.4  for stack of 27-325
		Stack = -3.3  for stack of 28-324
	Helix total = -19.0
	Internal/bulge = 3.3  for closure of 29-323	Size = 5
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 33-320	Size = 2
		Stack = -2.5  for stack of 35-318
	Helix total = -2.5
	Internal/bulge = 0.3  for closure of 36-317	Size = 4
		Stack = -1.1  for stack of 39-314
		Stack = -1.3  for stack of 40-313
	Helix total = -2.4
	Internal/bulge = 4.9  for closure of 41-312	Size = 9
		Stack = -2.4  for stack of 45-305
		Stack = -2.2  for stack of 46-304
		Stack = -2.1  for stack of 47-303
		Stack = -2.2  for stack of 48-302
	Helix total = -8.9
	Multiloop = 4.9  for closure of 49-301
		Stack = -2.5  for stack of 246-280
		Stack = -1.0  for stack of 247-279
		Stack = -1.1  for stack of 248-278
		Stack = -2.4  for stack of 249-277
		Stack = -2.1  for stack of 250-276
		Stack = -1.1  for stack of 251-275
		Stack = -2.1  for stack of 252-274
		Stack = -2.5  for stack of 253-273
		Stack = -0.6  for stack of 254-272
	Helix total = -15.4
	Internal/bulge = 2.4  for closure of 255-271	Size = 1 BP stack across bulge = -1.0
		Stack = -2.1  for stack of 256-269
		Stack = -2.5  for stack of 257-268
	Helix total = -4.6
	Hairpin = 4.6  for closure of 258-267
		Stack = -2.1  for stack of 198-226
		Stack = -1.3  for stack of 199-225
		Stack = -0.9  for stack of 200-224
		Stack = -0.9  for stack of 201-223
		Stack = -2.2  for stack of 202-222
		Stack = -2.1  for stack of 203-221
	Helix total = -9.5
	Hairpin = 6.7  for closure of 204-220
		Stack = -1.1  for stack of 141-178
		Stack = -2.4  for stack of 142-177
		Stack = -2.4  for stack of 143-176
		Stack = -3.4  for stack of 144-175
	Helix total = -9.3
	Internal/bulge = 1.2  for closure of 145-174	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.1  for closure of 147-172	Size = 1 BP stack across bulge = -1.3
		Stack = -0.9  for stack of 148-170
		Stack = -2.2  for stack of 149-169
		Stack = -2.1  for stack of 150-168
		Stack = -2.1  for stack of 151-167
		Stack = -3.4  for stack of 152-166
		Stack = -2.1  for stack of 153-165
		Stack = -1.4  for stack of 154-164
	Helix total = -14.2
	Hairpin = 5.9  for closure of 155-163
		Stack = -2.5  for stack of 119-140
		Stack = -1.0  for stack of 120-139
		Stack = -2.1  for stack of 121-138
	Helix total = -5.6
	Internal/bulge = 1.2  for closure of 122-137	Size = 4
		Stack = -3.4  for stack of 125-134
	Helix total = -3.4
	Hairpin = 3.1  for closure of 126-133
		Stack = -0.5  for stack of 55-84
		Stack = 1.3  for stack of 56-83
		Stack = -0.5  for stack of 57-82
		Stack = -1.4  for stack of 58-81
		Stack = -1.5  for stack of 59-80
	Helix total = -2.6
	Hairpin = 6.9  for closure of 60-79


	Total energy = -66.4



