Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:67 50:66 51:65 52:64 53:63 175:214 176:213 177:212
	    178:211 179:210 231:262 232:261 233:260 234:259 235:258 280:317
	    281:316 282:315 283:314 284:312 285:311 286:310
	Energy of Broken Structure: -69.0
	Energy of Pseudo-Helices:   -39.6
	Pseudoknot Energy Penalty:  31.9
	Total Free Energy:          -76.7
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-377
		Stack = -1.5  for stack of 2-376
		Stack = -2.1  for stack of 3-375
		Stack = -3.4  for stack of 4-374
		Stack = -2.1  for stack of 5-373
		Stack = -2.1  for stack of 6-372
	Helix total = -14.5
	Multiloop = 5.2  for closure of 7-371
		Stack = -3.4  for stack of 354-370
		Stack = -2.4  for stack of 355-369
		Stack = -3.3  for stack of 356-368
		Stack = -3.3  for stack of 357-367
	Helix total = -12.4
	Hairpin = 4.4  for closure of 358-366
		Stack = -2.1  for stack of 21-350
		Stack = -2.1  for stack of 22-349
		Stack = -1.5  for stack of 23-348
		Stack = -1.3  for stack of 24-347
		Stack = -1.1  for stack of 25-346
		Stack = -0.9  for stack of 26-345
	Helix total = -9.0
	Internal/bulge = 3.0  for closure of 27-344	Size = 11
		Stack = -2.5  for stack of 34-338
		Stack = -3.3  for stack of 35-337
	Helix total = -5.8
	Internal/bulge = 1.2  for closure of 36-336	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 38-334	Size = 2
		Stack = -3.3  for stack of 40-332
	Helix total = -3.3
	Internal/bulge = 1.0  for closure of 41-331	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.7  for closure of 43-329	Size = 3
		Stack = -2.1  for stack of 44-325
		Stack = -1.1  for stack of 45-324
		Stack = -2.1  for stack of 46-323
		Stack = -3.4  for stack of 47-322
	Helix total = -8.7
	Multiloop = 3.7  for closure of 48-321
		Stack = -2.5  for stack of 265-300
		Stack = -0.5  for stack of 266-299
	Helix total = -3.0
	Internal/bulge = 1.2  for closure of 267-298	Size = 2
		Stack = -2.2  for stack of 269-296
		Stack = -0.9  for stack of 270-295
		Stack = -1.3  for stack of 271-294
		Stack = -2.1  for stack of 272-293
		Stack = -2.5  for stack of 273-292
	Helix total = -9.0
	Internal/bulge = 2.2  for closure of 274-291	Size = 2
		Stack = -3.4  for stack of 276-289
		Stack = -2.4  for stack of 277-288
	Helix total = -5.8
	Hairpin = 3.9  for closure of 278-287
		Stack = -2.4  for stack of 219-246
		Stack = -2.5  for stack of 220-245
	Helix total = -4.9
	Internal/bulge = 2.1  for closure of 221-244	Size = 8
		Stack = -2.5  for stack of 226-239
		Stack = -3.3  for stack of 227-238
		Stack = -3.3  for stack of 228-237
	Helix total = -9.1
	Hairpin = 4.4  for closure of 229-236
		Stack = -3.3  for stack of 156-199
		Stack = -2.1  for stack of 157-198
		Stack = -2.4  for stack of 158-197
		Stack = -2.1  for stack of 159-196
		Stack = -2.4  for stack of 160-195
		Stack = -2.1  for stack of 161-194
	Helix total = -14.4
	Internal/bulge = 4.1  for closure of 162-193	Size = 4
		Stack = -3.3  for stack of 163-188
		Stack = -3.3  for stack of 164-187
		Stack = -2.1  for stack of 165-186
	Helix total = -8.7
	Internal/bulge = 0.7  for closure of 166-185	Size = 4
		Stack = -3.3  for stack of 169-182
		Stack = -2.1  for stack of 170-181
	Helix total = -5.4
	Hairpin = 5.5  for closure of 171-180
		Stack = -2.5  for stack of 109-153
	Helix total = -2.5
	Internal/bulge = 1.9  for closure of 110-152	Size = 6
		Stack = 0.3  for stack of 114-148
	Helix total = 0.3
	Internal/bulge = 1.9  for closure of 115-147	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.8  for closure of 117-145	Size = 6
		Stack = -0.9  for stack of 121-141
		Stack = -1.3  for stack of 122-140
	Helix total = -2.2
	Internal/bulge = 1.3  for closure of 123-139	Size = 1 BP stack across bulge = -2.1
		Stack = -3.4  for stack of 124-137
	Helix total = -3.4
	Internal/bulge = 0.9  for closure of 125-136	Size = 2
	Helix total = 0.0
	Hairpin = 4.9  for closure of 127-134
		Stack = -3.4  for stack of 55-78
		Stack = -2.4  for stack of 56-77
		Stack = -3.3  for stack of 57-76
		Stack = -2.5  for stack of 58-75
		Stack = -0.6  for stack of 59-74
	Helix total = -12.2
	Hairpin = 6.5  for closure of 60-73


	Total energy = -69.0



