Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    50:71 51:70 52:69 53:68 54:67 166:198 167:197 168:196
	    169:194 170:193 171:192 215:259 216:258 217:257 218:256 219:255
	    220:254 223:251 280:315 283:312 284:311 285:310
	Energy of Broken Structure: -59.6
	Energy of Pseudo-Helices:   -35.3
	Pseudoknot Energy Penalty:  33.2
	Total Free Energy:          -61.7
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-376
		Stack = -1.5  for stack of 2-375
		Stack = -2.1  for stack of 3-374
		Stack = -3.3  for stack of 4-373
		Stack = -3.4  for stack of 5-372
		Stack = -2.4  for stack of 6-371
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-370
		Stack = -3.3  for stack of 353-369
		Stack = -3.3  for stack of 354-368
		Stack = -2.4  for stack of 355-367
		Stack = -2.1  for stack of 356-366
	Helix total = -11.1
	Hairpin = 5.0  for closure of 357-365
		Stack = -3.3  for stack of 20-349
		Stack = -2.4  for stack of 21-348
	Helix total = -5.7
	Internal/bulge = 0.5  for closure of 22-347	Size = 1 BP stack across bulge = -3.3
		Stack = -2.4  for stack of 23-345
		Stack = -1.1  for stack of 24-344
		Stack = -2.1  for stack of 25-343
	Helix total = -5.6
	Internal/bulge = 3.0  for closure of 26-342	Size = 4
	Helix total = 0.0
	Internal/bulge = 1.4  for closure of 30-340	Size = 6
		Stack = -2.5  for stack of 34-336
		Stack = -2.4  for stack of 35-335
	Helix total = -4.9
	Internal/bulge = 1.4  for closure of 36-334	Size = 1 BP stack across bulge = -2.4
		Stack = -1.1  for stack of 38-333
		Stack = -2.1  for stack of 39-332
		Stack = -3.4  for stack of 40-331
		Stack = -3.3  for stack of 41-330
	Helix total = -9.9
	Internal/bulge = 3.9  for closure of 42-329	Size = 7
		Stack = -1.4  for stack of 45-323
		Stack = -1.4  for stack of 46-322
		Stack = -2.1  for stack of 47-321
		Stack = -2.2  for stack of 48-320
	Helix total = -7.1
	Multiloop = 6.4  for closure of 49-319
	Helix total = 0.0
	Internal/bulge = 2.7  for closure of 264-304	Size = 6
	Helix total = 0.0
	Internal/bulge = 3.2  for closure of 268-300	Size = 10
		Stack = -1.4  for stack of 274-294
		Stack = -2.4  for stack of 275-293
		Stack = -0.9  for stack of 276-292
		Stack = -2.1  for stack of 277-291
	Helix total = -6.8
	Hairpin = 6.1  for closure of 278-290
		Stack = -3.3  for stack of 199-245
		Stack = -2.4  for stack of 200-244
		Stack = -2.5  for stack of 201-243
	Helix total = -8.2
	Internal/bulge = 3.7  for closure of 202-242	Size = 5
		Stack = -2.2  for stack of 206-239
		Stack = -2.1  for stack of 207-238
		Stack = -2.4  for stack of 208-237
		Stack = -2.1  for stack of 209-236
		Stack = -0.9  for stack of 210-235
		Stack = -0.6  for stack of 211-234
	Helix total = -10.3
	Internal/bulge = 1.9  for closure of 212-233	Size = 2
	Helix total = 0.0
	Hairpin = 4.7  for closure of 214-231
		Stack = -2.1  for stack of 146-181
		Stack = -2.4  for stack of 147-180
		Stack = -1.4  for stack of 148-179
		Stack = -1.4  for stack of 149-178
		Stack = -3.3  for stack of 150-177
		Stack = -1.5  for stack of 151-176
	Helix total = -12.1
	Internal/bulge = -0.7  for closure of 152-175	Size = 2
		Stack = -1.1  for stack of 154-173
	Helix total = -1.1
	Hairpin = 6.8  for closure of 155-172
	Helix total = 0.0
	Internal/bulge = -0.8  for closure of 114-145	Size = 4
	Helix total = 0.0
	Internal/bulge = 0.5  for closure of 117-142	Size = 2
		Stack = -3.3  for stack of 119-140
		Stack = -3.4  for stack of 120-139
	Helix total = -6.7
	Internal/bulge = 1.2  for closure of 121-138	Size = 2
		Stack = -2.5  for stack of 123-136
		Stack = -3.3  for stack of 124-135
		Stack = -2.1  for stack of 125-134
	Helix total = -7.9
	Hairpin = 5.1  for closure of 126-133
		Stack = -1.1  for stack of 58-83
		Stack = -2.4  for stack of 59-82
		Stack = -2.1  for stack of 60-81
		Stack = -2.1  for stack of 61-80
		Stack = -2.5  for stack of 62-79
		Stack = -0.6  for stack of 63-78
	Helix total = -10.8
	Hairpin = 5.2  for closure of 64-77


	Total energy = -59.6



