Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    50:69 51:68 53:66 54:65 152:186 153:185 154:184 155:183
	    156:182 157:181 202:233 203:232 204:231 205:230 206:229 207:228
	    208:227 236:271 240:267 242:266 244:264 246:260 248:258
	Energy of Broken Structure: -85.6
	Energy of Pseudo-Helices:   -27.6
	Pseudoknot Energy Penalty:  48.4
	Total Free Energy:          -64.8
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 = 6.6  for closure of 7-345
		Stack = -2.1  for stack of 328-344
		Stack = -3.3  for stack of 329-343
		Stack = -3.3  for stack of 330-342
		Stack = -3.3  for stack of 331-341
	Helix total = -12.0
	Hairpin = 4.4  for closure of 332-340
		Stack = -2.4  for stack of 21-324
		Stack = -1.5  for stack of 22-323
		Stack = -0.5  for stack of 23-322
		Stack = -0.5  for stack of 24-321
		Stack = -2.1  for stack of 25-320
		Stack = -3.4  for stack of 26-319
		Stack = -2.1  for stack of 27-318
	Helix total = -12.5
	Internal/bulge = 3.5  for closure of 28-317	Size = 7
		Stack = -2.5  for stack of 33-313
		Stack = -2.1  for stack of 34-312
		Stack = -1.5  for stack of 35-311
		Stack = -3.3  for stack of 36-310
		Stack = -2.1  for stack of 37-309
		Stack = -2.1  for stack of 38-308
		Stack = -2.4  for stack of 39-307
		Stack = -2.1  for stack of 40-306
	Helix total = -18.1
	Internal/bulge = 1.2  for closure of 41-305	Size = 2
	Helix total = 0.0
	Internal/bulge = 4.5  for closure of 43-303	Size = 5
		Stack = -2.4  for stack of 45-298
		Stack = -2.4  for stack of 46-297
		Stack = -2.1  for stack of 47-296
		Stack = -2.2  for stack of 48-295
	Helix total = -9.1
	Multiloop = 5.5  for closure of 49-294
		Stack = -2.2  for stack of 251-290
		Stack = -0.9  for stack of 252-289
		Stack = -0.9  for stack of 253-288
		Stack = -1.3  for stack of 254-287
		Stack = -1.4  for stack of 255-286
		Stack = -1.5  for stack of 256-285
	Helix total = -8.2
	Hairpin = 5.2  for closure of 257-284
		Stack = -3.3  for stack of 189-220
		Stack = -2.4  for stack of 190-219
	Helix total = -5.7
	Internal/bulge = 0.1  for closure of 191-218	Size = 4
		Stack = -2.1  for stack of 194-215
		Stack = -2.4  for stack of 195-214
		Stack = -2.1  for stack of 196-213
		Stack = -1.3  for stack of 197-212
		Stack = -2.2  for stack of 198-211
	Helix total = -10.1
	Hairpin = 5.0  for closure of 199-210
		Stack = -2.4  for stack of 137-173
		Stack = -2.5  for stack of 138-172
		Stack = -1.5  for stack of 139-171
		Stack = -3.3  for stack of 140-170
		Stack = -2.1  for stack of 141-169
		Stack = -1.3  for stack of 142-168
	Helix total = -13.1
	Internal/bulge = 1.6  for closure of 143-167	Size = 1 BP stack across bulge = -2.2
		Stack = -2.1  for stack of 144-165
		Stack = -0.9  for stack of 145-164
		Stack = -1.0  for stack of 146-163
		Stack = -2.1  for stack of 147-162
		Stack = -3.3  for stack of 148-161
	Helix total = -9.4
	Hairpin = 5.4  for closure of 149-160
		Stack = -2.1  for stack of 116-136
		Stack = -3.4  for stack of 117-135
		Stack = -2.1  for stack of 118-134
		Stack = -2.1  for stack of 119-133
		Stack = -3.4  for stack of 120-132
	Helix total = -13.1
	Hairpin = 5.6  for closure of 121-131
		Stack = -2.4  for stack of 57-83
		Stack = -3.3  for stack of 58-82
		Stack = -2.1  for stack of 59-81
		Stack = 0.3  for stack of 60-80
		Stack = -2.1  for stack of 61-79
	Helix total = -9.6
	Hairpin = 4.4  for closure of 62-78


	Total energy = -85.6



