Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:65 51:63 184:212 185:211 186:210 187:209 188:208 228:257
	    229:256 230:255 231:254 232:253 233:252 276:312 277:311 278:310
	    279:309 280:308 281:307 282:306 283:305 284:304
	Energy of Broken Structure: -33.4
	Energy of Pseudo-Helices:   -23.4
	Pseudoknot Energy Penalty:  30.3
	Total Free Energy:          -26.5
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-372
		Stack = -1.5  for stack of 2-371
		Stack = -2.1  for stack of 3-370
		Stack = -1.5  for stack of 4-369
		Stack = -1.4  for stack of 5-368
		Stack = -2.1  for stack of 6-367
	Helix total = -11.9
	Multiloop = 5.0  for closure of 7-366
		Stack = -3.3  for stack of 349-365
		Stack = -2.4  for stack of 350-364
		Stack = -3.3  for stack of 351-363
		Stack = -3.3  for stack of 352-362
	Helix total = -12.3
	Hairpin = 4.4  for closure of 353-361
		Stack = -2.1  for stack of 20-345
		Stack = -1.4  for stack of 21-344
		Stack = 0.3  for stack of 22-343
		Stack = -2.5  for stack of 23-342
		Stack = -2.1  for stack of 24-341
		Stack = -1.1  for stack of 25-340
		Stack = -1.3  for stack of 26-339
		Stack = -0.9  for stack of 27-338
	Helix total = -11.1
	Internal/bulge = 3.4  for closure of 28-337	Size = 6
		Stack = -0.9  for stack of 32-333
		Stack = -1.3  for stack of 33-332
	Helix total = -2.2
	Internal/bulge = 1.4  for closure of 34-331	Size = 4
		Stack = -2.1  for stack of 37-328
		Stack = -2.4  for stack of 38-327
		Stack = -2.2  for stack of 39-326
	Helix total = -6.7
	Internal/bulge = 4.5  for closure of 40-325	Size = 5
		Stack = -2.5  for stack of 42-320
		Stack = -2.1  for stack of 43-319
		Stack = -2.1  for stack of 44-318
		Stack = -2.2  for stack of 45-317
	Helix total = -8.9
	Multiloop = 5.6  for closure of 46-316
		Stack = -1.3  for stack of 259-297
		Stack = -0.9  for stack of 260-296
		Stack = -1.1  for stack of 261-295
		Stack = -1.3  for stack of 262-294
	Helix total = -4.6
	Internal/bulge = 3.7  for closure of 263-293	Size = 3
		Stack = -0.9  for stack of 266-291
	Helix total = -0.9
	Internal/bulge = 1.6  for closure of 267-290	Size = 2
		Stack = -1.4  for stack of 269-288
		Stack = -1.3  for stack of 270-287
	Helix total = -2.7
	Hairpin = 6.8  for closure of 271-286
		Stack = -2.2  for stack of 218-242
		Stack = -1.3  for stack of 219-241
		Stack = -0.6  for stack of 220-240
		Stack = -0.9  for stack of 221-239
		Stack = -1.3  for stack of 222-238
		Stack = -1.1  for stack of 223-237
	Helix total = -7.4
	Hairpin = 5.1  for closure of 224-236
		Stack = -1.4  for stack of 169-201
		Stack = -2.5  for stack of 170-200
		Stack = -2.1  for stack of 171-199
		Stack = -0.9  for stack of 172-198
	Helix total = -6.9
	Internal/bulge = 1.9  for closure of 173-197	Size = 2
		Stack = -1.3  for stack of 175-195
		Stack = -0.9  for stack of 176-194
		Stack = -0.6  for stack of 177-193
		Stack = -1.4  for stack of 178-192
		Stack = -2.1  for stack of 179-191
	Helix total = -6.3
	Hairpin = 3.9  for closure of 180-190
		Stack = -2.1  for stack of 142-167
		Stack = -1.3  for stack of 143-166
		Stack = -0.6  for stack of 144-165
		Stack = -1.4  for stack of 145-164
		Stack = -0.9  for stack of 146-163
		Stack = -0.9  for stack of 147-162
		Stack = -0.9  for stack of 148-161
		Stack = -0.9  for stack of 149-160
		Stack = -1.0  for stack of 150-159
	Helix total = -10.0
	Hairpin = 5.2  for closure of 151-158
		Stack = -0.6  for stack of 55-76
	Helix total = -0.6
	Internal/bulge = 2.1  for closure of 56-75	Size = 4
	Helix total = 0.0
	Hairpin = 6.2  for closure of 59-72


	Total energy = -33.4



