Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:67 50:66 51:65 52:64 53:63 159:198 160:197 161:196
	    162:195 163:194 216:248 217:247 218:246 219:245 220:244 266:302
	    267:301 268:300 269:299 270:297 271:296 272:295
	Energy of Broken Structure: -68.1
	Energy of Pseudo-Helices:   -36.7
	Pseudoknot Energy Penalty:  32.1
	Total Free Energy:          -72.7
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-362
		Stack = -1.5  for stack of 2-361
		Stack = -2.1  for stack of 3-360
		Stack = -3.4  for stack of 4-359
		Stack = -2.1  for stack of 5-358
		Stack = -2.1  for stack of 6-357
	Helix total = -14.5
	Multiloop = 5.2  for closure of 7-356
		Stack = -3.3  for stack of 339-355
		Stack = -3.3  for stack of 340-354
		Stack = -3.3  for stack of 341-353
		Stack = -3.3  for stack of 342-352
	Helix total = -13.2
	Hairpin = 4.4  for closure of 343-351
		Stack = -2.4  for stack of 21-335
		Stack = -1.5  for stack of 22-334
		Stack = -0.5  for stack of 23-333
		Stack = -1.3  for stack of 24-332
		Stack = -1.1  for stack of 25-331
		Stack = -0.9  for stack of 26-330
		Stack = -1.3  for stack of 27-329
	Helix total = -9.0
	Internal/bulge = 3.4  for closure of 28-328	Size = 9
		Stack = -2.5  for stack of 34-323
		Stack = -3.3  for stack of 35-322
	Helix total = -5.8
	Internal/bulge = 1.7  for closure of 36-321	Size = 6
		Stack = -2.1  for stack of 40-317
		Stack = -2.2  for stack of 41-316
		Stack = -1.0  for stack of 42-315
	Helix total = -5.3
	Internal/bulge = 3.7  for closure of 43-314	Size = 3
		Stack = -2.1  for stack of 44-310
		Stack = -2.2  for stack of 45-309
		Stack = -2.4  for stack of 46-308
		Stack = -2.2  for stack of 47-307
	Helix total = -8.9
	Multiloop = 6.1  for closure of 48-306
		Stack = -2.5  for stack of 251-285
		Stack = -2.1  for stack of 252-284
		Stack = -0.9  for stack of 253-283
		Stack = -1.3  for stack of 254-282
		Stack = -0.9  for stack of 255-281
		Stack = -2.1  for stack of 256-280
		Stack = -2.5  for stack of 257-279
	Helix total = -12.3
	Internal/bulge = 1.6  for closure of 258-278	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.7  for closure of 260-276	Size = 1 BP stack across bulge = -2.1
		Stack = -3.4  for stack of 262-275
		Stack = -2.4  for stack of 263-274
	Helix total = -5.8
	Hairpin = 4.5  for closure of 264-273
		Stack = -2.1  for stack of 203-232
		Stack = -2.5  for stack of 204-231
	Helix total = -4.6
	Internal/bulge = 3.1  for closure of 205-230	Size = 7
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 209-225	Size = 2
		Stack = -3.3  for stack of 211-223
	Helix total = -3.3
	Hairpin = 4.9  for closure of 212-222
		Stack = -2.1  for stack of 140-183
		Stack = -1.3  for stack of 141-182
		Stack = -1.5  for stack of 142-181
		Stack = -2.4  for stack of 143-180
		Stack = -3.4  for stack of 144-179
		Stack = -2.4  for stack of 145-178
	Helix total = -13.1
	Internal/bulge = 3.6  for closure of 146-177	Size = 4
		Stack = -2.1  for stack of 147-172
		Stack = -1.5  for stack of 148-171
		Stack = -3.3  for stack of 149-170
	Helix total = -6.9
	Internal/bulge = 0.3  for closure of 150-169	Size = 4
		Stack = -2.1  for stack of 153-166
		Stack = -0.9  for stack of 154-165
	Helix total = -3.0
	Hairpin = 5.5  for closure of 155-164
		Stack = -3.4  for stack of 110-139
		Stack = -2.1  for stack of 111-138
	Helix total = -5.5
	Internal/bulge = 1.1  for closure of 112-137	Size = 4
	Helix total = 0.0
	Internal/bulge = 1.7  for closure of 115-134	Size = 1 BP stack across bulge = -2.1
		Stack = -3.4  for stack of 116-132
		Stack = -2.1  for stack of 117-131
		Stack = -2.1  for stack of 118-130
	Helix total = -7.6
	Hairpin = 5.7  for closure of 119-129
		Stack = -2.1  for stack of 54-80
		Stack = -3.4  for stack of 55-79
		Stack = -2.4  for stack of 56-78
		Stack = -3.3  for stack of 57-77
		Stack = -2.2  for stack of 58-76
	Helix total = -13.4
	Hairpin = 6.4  for closure of 59-75


	Total energy = -68.1



