Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    54:77 55:76 56:75 57:74 149:185 150:184 151:183 152:182
	    153:181 154:180 155:179 200:235 202:233 203:232 204:231 205:230
	    206:229 252:288 253:287 254:286 255:285 256:284 257:283 258:282
	Energy of Broken Structure: -110.7
	Energy of Pseudo-Helices:   -52.6
	Pseudoknot Energy Penalty:  33.3
	Total Free Energy:          -130.0
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-349
		Stack = -1.5  for stack of 2-348
		Stack = -2.1  for stack of 3-347
		Stack = -2.4  for stack of 4-346
		Stack = -1.1  for stack of 5-345
		Stack = -2.1  for stack of 6-344
	Helix total = -12.5
	Multiloop = 5.0  for closure of 7-343
		Stack = -3.3  for stack of 326-342
		Stack = -3.3  for stack of 327-341
		Stack = -3.3  for stack of 328-340
		Stack = -3.3  for stack of 329-339
	Helix total = -13.2
	Hairpin = 4.4  for closure of 330-338
		Stack = -2.1  for stack of 19-322
		Stack = -2.1  for stack of 20-321
		Stack = -1.5  for stack of 21-320
		Stack = -2.1  for stack of 22-319
		Stack = -3.4  for stack of 23-318
	Helix total = -11.2
	Internal/bulge = 2.3  for closure of 24-317	Size = 4
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 27-314	Size = 2
		Stack = -2.1  for stack of 29-312
		Stack = -2.5  for stack of 30-311
	Helix total = -4.6
	Internal/bulge = 2.3  for closure of 31-310	Size = 1 BP stack across bulge = -1.5
		Stack = -2.4  for stack of 33-309
		Stack = -2.4  for stack of 34-308
		Stack = -2.1  for stack of 35-307
		Stack = -3.3  for stack of 36-306
		Stack = -2.4  for stack of 37-305
		Stack = -1.1  for stack of 38-304
	Helix total = -13.7
	Internal/bulge = 4.8  for closure of 39-303	Size = 8
		Stack = -2.1  for stack of 42-296
		Stack = -2.1  for stack of 43-295
		Stack = -3.3  for stack of 44-294
		Stack = -2.5  for stack of 45-293
	Helix total = -10.0
	Multiloop = 4.9  for closure of 46-292
		Stack = -3.4  for stack of 237-271
		Stack = -2.1  for stack of 238-270
		Stack = -2.1  for stack of 239-269
	Helix total = -7.6
	Internal/bulge = 0.4  for closure of 240-268	Size = 1 BP stack across bulge = -3.4
		Stack = -3.3  for stack of 242-267
		Stack = -1.4  for stack of 243-266
		Stack = -2.1  for stack of 244-265
		Stack = -3.3  for stack of 245-264
	Helix total = -10.1
	Internal/bulge = 1.2  for closure of 246-263	Size = 2
		Stack = -2.4  for stack of 248-261
		Stack = -3.3  for stack of 249-260
	Helix total = -5.7
	Hairpin = 4.5  for closure of 250-259
		Stack = -3.3  for stack of 190-217
		Stack = -2.1  for stack of 191-216
		Stack = -2.1  for stack of 192-215
		Stack = -3.3  for stack of 193-214
		Stack = -3.4  for stack of 194-213
		Stack = -3.3  for stack of 195-212
		Stack = -3.3  for stack of 196-211
	Helix total = -20.8
	Hairpin = 5.2  for closure of 197-210
		Stack = -2.4  for stack of 132-171
		Stack = -2.5  for stack of 133-170
		Stack = -1.5  for stack of 134-169
		Stack = -2.1  for stack of 135-168
	Helix total = -8.5
	Internal/bulge = 3.3  for closure of 136-167	Size = 5
		Stack = -3.3  for stack of 139-163
		Stack = -2.4  for stack of 140-162
		Stack = -1.5  for stack of 141-161
		Stack = -1.3  for stack of 142-160
		Stack = -2.2  for stack of 143-159
		Stack = -3.3  for stack of 144-158
		Stack = -3.3  for stack of 145-157
	Helix total = -17.3
	Hairpin = 4.3  for closure of 146-156
		Stack = -2.1  for stack of 109-131
		Stack = -3.3  for stack of 110-130
		Stack = -3.4  for stack of 111-129
		Stack = -2.1  for stack of 112-128
		Stack = -2.1  for stack of 113-127
		Stack = -3.4  for stack of 114-126
		Stack = -2.4  for stack of 115-125
		Stack = -2.2  for stack of 116-124
	Helix total = -21.0
	Hairpin = 5.4  for closure of 117-123
		Stack = -2.4  for stack of 47-66
		Stack = -2.4  for stack of 48-65
		Stack = -2.1  for stack of 49-64
	Helix total = -6.9
	Hairpin = 4.2  for closure of 50-63


	Total energy = -110.7



