Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:67 49:66 50:65 51:64 52:63 153:186 154:185 155:184
	    156:183 157:182 158:181 203:236 204:235 205:234 206:233 207:232
	    208:231 209:230 254:290 255:289 256:288 257:287 258:286 259:285
	    260:284
	Energy of Broken Structure: -116.2
	Energy of Pseudo-Helices:   -54.0
	Pseudoknot Energy Penalty:  43.4
	Total Free Energy:          -126.8
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-351
		Stack = -1.5  for stack of 2-350
		Stack = -2.1  for stack of 3-349
		Stack = -3.3  for stack of 4-348
		Stack = -3.4  for stack of 5-347
		Stack = -2.4  for stack of 6-346
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-345
		Stack = -3.4  for stack of 328-344
		Stack = -2.4  for stack of 329-343
		Stack = -3.3  for stack of 330-342
		Stack = -3.3  for stack of 331-341
	Helix total = -12.4
	Hairpin = 4.4  for closure of 332-340
		Stack = -2.4  for stack of 20-324
		Stack = -3.3  for stack of 21-323
		Stack = -1.5  for stack of 22-322
		Stack = -2.1  for stack of 23-321
		Stack = -2.4  for stack of 24-320
		Stack = -1.1  for stack of 25-319
		Stack = -1.3  for stack of 26-318
		Stack = -2.1  for stack of 27-317
	Helix total = -16.2
	Internal/bulge = 1.2  for closure of 28-316	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 30-314	Size = 2
		Stack = -2.1  for stack of 32-312
		Stack = -2.4  for stack of 33-311
		Stack = -1.1  for stack of 34-310
		Stack = -0.9  for stack of 35-309
		Stack = -1.3  for stack of 36-308
		Stack = -0.9  for stack of 37-307
		Stack = -0.9  for stack of 38-306
		Stack = -2.2  for stack of 39-305
	Helix total = -11.8
	Internal/bulge = 0.5  for closure of 40-304	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.2  for closure of 42-302	Size = 3
		Stack = -2.1  for stack of 43-298
		Stack = -2.1  for stack of 44-297
		Stack = -3.3  for stack of 45-296
		Stack = -3.4  for stack of 46-295
	Helix total = -10.9
	Multiloop = 3.6  for closure of 47-294
		Stack = -2.2  for stack of 239-273
		Stack = -1.3  for stack of 240-272
	Helix total = -3.5
	Internal/bulge = 1.1  for closure of 241-271	Size = 1 BP stack across bulge = -2.1
		Stack = -3.3  for stack of 243-270
	Helix total = -3.3
	Internal/bulge = 1.2  for closure of 244-269	Size = 2
		Stack = -2.1  for stack of 246-267
		Stack = -3.4  for stack of 247-266
		Stack = -2.1  for stack of 248-265
		Stack = -0.9  for stack of 249-264
		Stack = -2.1  for stack of 250-263
	Helix total = -10.6
	Hairpin = 4.0  for closure of 251-262
		Stack = -1.4  for stack of 189-221
		Stack = -3.3  for stack of 190-220
		Stack = -3.3  for stack of 191-219
		Stack = -2.4  for stack of 192-218
		Stack = -2.1  for stack of 193-217
		Stack = -3.3  for stack of 194-216
		Stack = -3.4  for stack of 195-215
		Stack = -2.1  for stack of 196-214
		Stack = -0.9  for stack of 197-213
		Stack = -1.3  for stack of 198-212
		Stack = -0.9  for stack of 199-211
	Helix total = -24.4
	Hairpin = 6.3  for closure of 200-210
		Stack = -1.4  for stack of 137-173
		Stack = -2.5  for stack of 138-172
		Stack = -2.1  for stack of 139-171
		Stack = -2.2  for stack of 140-170
		Stack = -3.3  for stack of 141-169
		Stack = -2.1  for stack of 142-168
		Stack = -0.9  for stack of 143-167
		Stack = -0.9  for stack of 144-166
		Stack = -1.3  for stack of 145-165
	Helix total = -16.7
	Internal/bulge = 1.9  for closure of 146-164	Size = 2
		Stack = -2.2  for stack of 148-162
		Stack = -3.3  for stack of 149-161
		Stack = -2.1  for stack of 150-160
	Helix total = -7.6
	Hairpin = 5.1  for closure of 151-159
		Stack = -2.1  for stack of 115-136
		Stack = -3.3  for stack of 116-135
		Stack = -3.4  for stack of 117-134
		Stack = -2.1  for stack of 118-133
		Stack = -2.1  for stack of 119-132
		Stack = -3.4  for stack of 120-131
	Helix total = -16.4
	Hairpin = 4.7  for closure of 121-130
		Stack = -3.4  for stack of 55-80
		Stack = -2.1  for stack of 56-79
		Stack = -2.2  for stack of 57-78
		Stack = -3.3  for stack of 58-77
		Stack = -3.3  for stack of 59-76
	Helix total = -14.3
	Hairpin = 5.4  for closure of 60-75


	Total energy = -116.2



