Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    56:78 58:76 59:75 161:197 162:196 163:195 164:194 165:193
	    166:192 215:245 216:244 217:243 218:242 219:241 220:240 264:302
	    265:301 266:300 267:299 268:298 269:297 270:296
	Energy of Broken Structure: -65.9
	Energy of Pseudo-Helices:   -41.6
	Pseudoknot Energy Penalty:  38.1
	Total Free Energy:          -69.4
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 = -3.3  for stack of 4-360
		Stack = -3.4  for stack of 5-359
		Stack = -2.4  for stack of 6-358
	Helix total = -16.0
	Multiloop = 6.6  for closure of 7-357
		Stack = -2.2  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 = -11.2
	Hairpin = 4.4  for closure of 344-352
		Stack = -1.4  for stack of 21-336
		Stack = -0.5  for stack of 22-335
		Stack = -0.5  for stack of 23-334
		Stack = -2.1  for stack of 24-333
		Stack = -2.4  for stack of 25-332
		Stack = -1.1  for stack of 26-331
		Stack = -1.3  for stack of 27-330
		Stack = -0.6  for stack of 28-329
		Stack = 1.3  for stack of 29-328
	Helix total = -8.6
	Internal/bulge = 3.1  for closure of 30-327	Size = 7
		Stack = -2.5  for stack of 35-323
		Stack = -2.1  for stack of 36-322
		Stack = -1.1  for stack of 37-321
		Stack = -1.0  for stack of 38-320
		Stack = -2.1  for stack of 39-319
		Stack = -3.3  for stack of 40-318
		Stack = -2.5  for stack of 41-317
	Helix total = -14.6
	Internal/bulge = 4.6  for closure of 42-316	Size = 7
		Stack = -2.4  for stack of 45-310
		Stack = -3.3  for stack of 46-309
		Stack = -3.3  for stack of 47-308
		Stack = -2.2  for stack of 48-307
	Helix total = -11.2
	Multiloop = 7.0  for closure of 49-306
		Stack = -2.2  for stack of 248-285
		Stack = -3.3  for stack of 249-284
		Stack = -2.1  for stack of 250-283
	Helix total = -7.6
	Internal/bulge = 3.5  for closure of 251-282	Size = 5
		Stack = -0.6  for stack of 255-279
	Helix total = -0.6
	Internal/bulge = 2.9  for closure of 256-278	Size = 6
		Stack = -3.3  for stack of 261-275
		Stack = -2.4  for stack of 262-274
	Helix total = -5.7
	Hairpin = 4.2  for closure of 263-273
	Helix total = 0.0
	Internal/bulge = 0.4  for closure of 202-229	Size = 2
		Stack = -2.5  for stack of 204-227
	Helix total = -2.5
	Internal/bulge = 3.2  for closure of 205-226	Size = 1 BP stack across bulge = -0.6
		Stack = -1.3  for stack of 207-225
		Stack = -2.1  for stack of 208-224
		Stack = -2.5  for stack of 209-223
		Stack = -1.5  for stack of 210-222
	Helix total = -7.4
	Hairpin = 5.4  for closure of 211-221
		Stack = -3.4  for stack of 145-182
		Stack = -2.1  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 = -12.4
	Internal/bulge = 2.4  for closure of 150-177	Size = 1 BP stack across bulge = -1.0
		Stack = -2.5  for stack of 151-175
		Stack = -2.1  for stack of 152-174
		Stack = -0.9  for stack of 153-173
	Helix total = -5.5
	Internal/bulge = 1.2  for closure of 154-172	Size = 2
		Stack = -3.4  for stack of 156-170
		Stack = -2.1  for stack of 157-169
		Stack = -1.4  for stack of 158-168
	Helix total = -6.9
	Hairpin = 6.0  for closure of 159-167
		Stack = -2.5  for stack of 116-144
	Helix total = -2.5
	Internal/bulge = 1.0  for closure of 117-143	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 119-141	Size = 2
		Stack = -2.1  for stack of 121-139
		Stack = -3.4  for stack of 122-138
		Stack = -2.1  for stack of 123-137
		Stack = -2.1  for stack of 124-136
	Helix total = -9.7
	Hairpin = 5.7  for closure of 125-135
		Stack = -2.1  for stack of 50-67
		Stack = -2.5  for stack of 51-66
		Stack = -1.4  for stack of 52-65
		Stack = -3.3  for stack of 53-64
	Helix total = -9.3
	Hairpin = 4.0  for closure of 54-63


	Total energy = -65.9



