Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    53:76 54:75 56:73 57:72 58:71 161:196 162:195 163:194
	    164:193 165:192 214:243 215:242 216:241 217:240 218:239 262:302
	    264:300 266:298 267:297 268:296
	Energy of Broken Structure: -64.1
	Energy of Pseudo-Helices:   -29.7
	Pseudoknot Energy Penalty:  32.5
	Total Free Energy:          -61.3
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-363
		Stack = -1.5  for stack of 2-362
		Stack = -2.1  for stack of 3-361
		Stack = -1.5  for stack of 4-360
		Stack = -2.5  for stack of 5-359
		Stack = -2.4  for stack of 6-358
	Helix total = -13.3
	Multiloop = 5.1  for closure of 7-357
		Stack = -3.4  for stack of 340-356
		Stack = -2.4  for stack of 341-355
		Stack = -3.3  for stack of 342-354
		Stack = -3.3  for stack of 343-353
	Helix total = -12.4
	Hairpin = 4.4  for closure of 344-352
		Stack = -2.1  for stack of 20-336
		Stack = -0.6  for stack of 21-335
		Stack = -0.5  for stack of 22-334
		Stack = -2.5  for stack of 23-333
		Stack = -2.1  for stack of 24-332
		Stack = -1.1  for stack of 25-331
		Stack = -1.3  for stack of 26-330
	Helix total = -10.2
	Internal/bulge = 1.9  for closure of 27-329	Size = 10
		Stack = -2.5  for stack of 33-323
		Stack = -2.1  for stack of 34-322
		Stack = -0.9  for stack of 35-321
		Stack = -1.0  for stack of 36-320
		Stack = -1.3  for stack of 37-319
		Stack = -0.9  for stack of 38-318
		Stack = -1.1  for stack of 39-317
		Stack = -1.3  for stack of 40-316
	Helix total = -11.1
	Internal/bulge = 4.5  for closure of 41-315	Size = 5
		Stack = -2.4  for stack of 43-310
		Stack = -2.2  for stack of 44-309
		Stack = -0.9  for stack of 45-308
		Stack = -1.3  for stack of 46-307
	Helix total = -6.8
	Multiloop = 4.1  for closure of 47-306
		Stack = -3.4  for stack of 246-283
	Helix total = -3.4
	Internal/bulge = 2.0  for closure of 247-282	Size = 4
	Helix total = 0.0
	Internal/bulge = 2.9  for closure of 250-279	Size = 5
	Helix total = 0.0
	Internal/bulge = 4.0  for closure of 254-276	Size = 5
		Stack = -2.1  for stack of 257-272
		Stack = -3.4  for stack of 258-271
		Stack = -3.3  for stack of 259-270
	Helix total = -8.8
	Hairpin = 4.1  for closure of 260-269
		Stack = -2.1  for stack of 202-228
		Stack = -1.3  for stack of 203-227
		Stack = -0.9  for stack of 204-226
		Stack = -0.9  for stack of 205-225
		Stack = -1.1  for stack of 206-224
		Stack = -0.9  for stack of 207-223
		Stack = -0.9  for stack of 208-222
		Stack = -0.9  for stack of 209-221
	Helix total = -9.0
	Hairpin = 5.5  for closure of 210-220
		Stack = -2.4  for stack of 145-182
		Stack = -1.4  for stack of 146-181
		Stack = -1.5  for stack of 147-180
		Stack = -3.3  for stack of 148-179
		Stack = -2.1  for stack of 149-178
	Helix total = -10.7
	Internal/bulge = 3.3  for closure of 150-177	Size = 2
		Stack = -3.3  for stack of 151-174
		Stack = -3.3  for stack of 152-173
		Stack = -2.4  for stack of 153-172
	Helix total = -9.0
	Internal/bulge = 0.5  for closure of 154-171	Size = 1 BP stack across bulge = -3.3
		Stack = -3.4  for stack of 155-169
		Stack = -2.1  for stack of 156-168
		Stack = -1.4  for stack of 157-167
	Helix total = -6.9
	Hairpin = 6.0  for closure of 158-166
	Helix total = 0.0
	Internal/bulge = 1.0  for closure of 116-142	Size = 2
		Stack = -0.6  for stack of 118-140
		Stack = -1.3  for stack of 119-139
		Stack = -2.1  for stack of 120-138
		Stack = -3.4  for stack of 121-137
		Stack = -2.1  for stack of 122-136
		Stack = -2.1  for stack of 123-135
	Helix total = -11.6
	Hairpin = 5.7  for closure of 124-134
		Stack = -2.4  for stack of 48-64
		Stack = -2.2  for stack of 49-63
		Stack = -1.3  for stack of 50-62
		Stack = -2.1  for stack of 51-61
	Helix total = -8.0
	Hairpin = 3.8  for closure of 52-60


	Total energy = -64.1



