Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    57:83 58:82 59:81 60:80 167:201 168:200 169:199 170:198
	    171:197 172:196 217:250 218:249 219:248 220:247 221:246 222:245
	    223:244 224:243 271:313 272:312 273:311 274:310 275:309 276:308
	    278:306
	Energy of Broken Structure: -81.5
	Energy of Pseudo-Helices:   -46.8
	Pseudoknot Energy Penalty:  35.9
	Total Free Energy:          -92.4
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-373
		Stack = -1.5  for stack of 2-372
		Stack = -2.1  for stack of 3-371
		Stack = -3.4  for stack of 4-370
		Stack = -2.1  for stack of 5-369
		Stack = -2.1  for stack of 6-368
	Helix total = -14.5
	Multiloop = 5.0  for closure of 7-367
		Stack = -3.3  for stack of 350-366
		Stack = -2.4  for stack of 351-365
		Stack = -3.3  for stack of 352-364
		Stack = -3.3  for stack of 353-363
	Helix total = -12.3
	Hairpin = 4.4  for closure of 354-362
		Stack = -2.1  for stack of 20-346
		Stack = -1.3  for stack of 21-345
		Stack = -2.2  for stack of 22-344
		Stack = -2.4  for stack of 23-343
		Stack = -2.2  for stack of 24-342
		Stack = -1.3  for stack of 25-341
		Stack = 0.3  for stack of 26-340
	Helix total = -11.2
	Internal/bulge = 1.9  for closure of 27-339	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.6  for closure of 29-337	Size = 1 BP stack across bulge = -0.6
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 31-336	Size = 2
		Stack = -3.4  for stack of 33-334
		Stack = -3.3  for stack of 34-333
		Stack = -2.1  for stack of 35-332
		Stack = -2.1  for stack of 36-331
		Stack = -3.3  for stack of 37-330
		Stack = -3.3  for stack of 38-329
	Helix total = -17.5
	Internal/bulge = 1.7  for closure of 39-328	Size = 10
		Stack = -2.4  for stack of 44-321
		Stack = -2.2  for stack of 45-320
		Stack = -2.1  for stack of 46-319
		Stack = -3.4  for stack of 47-318
	Helix total = -10.1
	Multiloop = 3.3  for closure of 48-317
		Stack = -3.3  for stack of 253-291
		Stack = -3.4  for stack of 254-290
		Stack = -2.1  for stack of 255-289
		Stack = -1.5  for stack of 256-288
	Helix total = -10.3
	Internal/bulge = 4.1  for closure of 257-287	Size = 4
		Stack = -2.4  for stack of 262-286
		Stack = -3.3  for stack of 263-285
		Stack = -2.4  for stack of 264-284
		Stack = -3.3  for stack of 265-283
	Helix total = -11.4
	Hairpin = 5.6  for closure of 266-282
		Stack = -2.1  for stack of 205-234
		Stack = -2.1  for stack of 206-233
		Stack = -2.2  for stack of 207-232
		Stack = -0.9  for stack of 208-231
		Stack = -2.4  for stack of 209-230
		Stack = -2.1  for stack of 210-229
		Stack = -0.9  for stack of 211-228
		Stack = -1.4  for stack of 212-227
		Stack = -1.5  for stack of 213-226
	Helix total = -15.6
	Hairpin = 4.1  for closure of 214-225
		Stack = -2.1  for stack of 152-188
		Stack = -2.5  for stack of 153-187
		Stack = -1.5  for stack of 154-186
		Stack = -2.1  for stack of 155-185
		Stack = -2.1  for stack of 156-184
	Helix total = -10.3
	Internal/bulge = 2.3  for closure of 157-183	Size = 4
		Stack = -2.1  for stack of 159-179
		Stack = -1.3  for stack of 160-178
		Stack = -2.1  for stack of 161-177
		Stack = -3.3  for stack of 162-176
	Helix total = -8.8
	Hairpin = 4.1  for closure of 163-175
	Helix total = 0.0
	Internal/bulge = 3.6  for closure of 114-148	Size = 4
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 117-145	Size = 6
	Helix total = 0.0
	Internal/bulge = 0.5  for closure of 121-141	Size = 2
		Stack = -2.1  for stack of 123-139
	Helix total = -2.1
	Internal/bulge = 1.2  for closure of 124-138	Size = 2
		Stack = -3.4  for stack of 126-136
	Helix total = -3.4
	Hairpin = 5.0  for closure of 127-135
		Stack = -2.4  for stack of 49-70
		Stack = -3.3  for stack of 50-69
		Stack = -2.2  for stack of 51-68
		Stack = -2.1  for stack of 52-67
	Helix total = -10.0
	Hairpin = 5.2  for closure of 53-66


	Total energy = -81.5



