Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    56:82 57:81 58:80 163:195 164:194 165:193 166:192 167:191
	    211:246 212:245 213:244 214:243 215:242 216:241 217:240 265:304
	    266:303 267:302 268:301 269:300 270:299
	Energy of Broken Structure: -93.0
	Energy of Pseudo-Helices:   -41.3
	Pseudoknot Energy Penalty:  35.5
	Total Free Energy:          -98.8
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-364
		Stack = -1.5  for stack of 2-363
		Stack = -2.1  for stack of 3-362
		Stack = -3.4  for stack of 4-361
		Stack = -2.1  for stack of 5-360
		Stack = -2.1  for stack of 6-359
	Helix total = -14.5
	Multiloop = 4.9  for closure of 7-358
		Stack = -3.3  for stack of 341-357
		Stack = -2.4  for stack of 342-356
		Stack = -3.3  for stack of 343-355
		Stack = -3.3  for stack of 344-354
	Helix total = -12.3
	Hairpin = 4.4  for closure of 345-353
		Stack = -2.1  for stack of 19-337
	Helix total = -2.1
	Internal/bulge = 1.2  for closure of 20-336	Size = 2
		Stack = -2.4  for stack of 22-334
	Helix total = -2.4
	Internal/bulge = 0.5  for closure of 23-333	Size = 1 BP stack across bulge = -3.3
		Stack = -3.4  for stack of 25-332
		Stack = -2.1  for stack of 26-331
		Stack = -1.1  for stack of 27-330
	Helix total = -6.6
	Internal/bulge = 2.7  for closure of 28-329	Size = 8
		Stack = -2.4  for stack of 33-324
		Stack = -2.1  for stack of 34-323
		Stack = -0.9  for stack of 35-322
		Stack = -2.1  for stack of 36-321
		Stack = -3.3  for stack of 37-320
	Helix total = -10.8
	Internal/bulge = 1.7  for closure of 38-319	Size = 10
		Stack = -2.4  for stack of 43-312
		Stack = -2.2  for stack of 44-311
		Stack = -2.1  for stack of 45-310
		Stack = -3.4  for stack of 46-309
	Helix total = -10.1
	Multiloop = 3.1  for closure of 47-308
		Stack = -3.3  for stack of 247-285
		Stack = -2.4  for stack of 248-284
		Stack = -1.1  for stack of 249-283
		Stack = -2.4  for stack of 250-282
	Helix total = -9.2
	Internal/bulge = 4.1  for closure of 251-281	Size = 4
		Stack = -2.4  for stack of 256-280
		Stack = -3.3  for stack of 257-279
		Stack = -2.1  for stack of 258-278
		Stack = -2.1  for stack of 259-277
		Stack = -3.3  for stack of 260-276
	Helix total = -13.2
	Hairpin = 5.7  for closure of 261-275
		Stack = -3.3  for stack of 201-229
		Stack = -2.4  for stack of 202-228
		Stack = -2.4  for stack of 203-227
		Stack = -1.1  for stack of 204-226
		Stack = -2.1  for stack of 205-225
		Stack = -2.4  for stack of 206-224
		Stack = -2.1  for stack of 207-223
		Stack = -2.5  for stack of 208-222
		Stack = -0.5  for stack of 209-221
	Helix total = -18.8
	Hairpin = 6.2  for closure of 210-220
		Stack = -2.1  for stack of 147-183
		Stack = -2.5  for stack of 148-182
		Stack = -1.5  for stack of 149-181
		Stack = -2.4  for stack of 150-180
		Stack = -3.3  for stack of 151-179
	Helix total = -11.8
	Internal/bulge = 2.3  for closure of 152-178	Size = 4
		Stack = -3.3  for stack of 154-174
		Stack = -2.4  for stack of 155-173
		Stack = -3.3  for stack of 156-172
		Stack = -3.3  for stack of 157-171
	Helix total = -12.3
	Hairpin = 5.1  for closure of 158-170
	Helix total = 0.0
	Internal/bulge = 1.7  for closure of 116-144	Size = 4
		Stack = -3.4  for stack of 119-141
		Stack = -2.1  for stack of 120-140
	Helix total = -5.5
	Internal/bulge = 1.9  for closure of 121-139	Size = 2
		Stack = -2.4  for stack of 123-137
		Stack = -2.4  for stack of 124-136
		Stack = -3.4  for stack of 125-135
	Helix total = -8.2
	Hairpin = 5.0  for closure of 126-134
		Stack = -2.4  for stack of 48-69
		Stack = -3.3  for stack of 49-68
		Stack = -2.2  for stack of 50-67
		Stack = -2.1  for stack of 51-66
	Helix total = -10.0
	Hairpin = 6.0  for closure of 52-65


	Total energy = -93.0



