Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:67 50:66 51:65 52:64 53:63 160:198 161:197 162:196
	    163:195 164:194 216:248 217:247 218:246 219:245 220:244 266:303
	    267:302 268:301 269:300 270:298 271:297 272:296
	Energy of Broken Structure: -62.5
	Energy of Pseudo-Helices:   -37.9
	Pseudoknot Energy Penalty:  33.9
	Total Free Energy:          -66.5
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 = -3.4  for stack of 4-360
		Stack = -2.1  for stack of 5-359
		Stack = -2.1  for stack of 6-358
	Helix total = -14.5
	Multiloop = 5.2  for closure of 7-357
		Stack = -3.3  for stack of 340-356
		Stack = -3.3  for stack of 341-355
		Stack = -3.3  for stack of 342-354
		Stack = -3.3  for stack of 343-353
	Helix total = -13.2
	Hairpin = 4.4  for closure of 344-352
		Stack = -2.4  for stack of 21-336
		Stack = -1.5  for stack of 22-335
		Stack = -0.5  for stack of 23-334
		Stack = -1.3  for stack of 24-333
		Stack = -1.1  for stack of 25-332
		Stack = -0.9  for stack of 26-331
	Helix total = -7.7
	Internal/bulge = 3.6  for closure of 27-330	Size = 11
		Stack = -2.5  for stack of 34-324
		Stack = -3.3  for stack of 35-323
	Helix total = -5.8
	Internal/bulge = 1.7  for closure of 36-322	Size = 6
		Stack = -2.1  for stack of 40-318
		Stack = -2.2  for stack of 41-317
		Stack = -1.0  for stack of 42-316
	Helix total = -5.3
	Internal/bulge = 3.7  for closure of 43-315	Size = 3
		Stack = -2.1  for stack of 44-311
		Stack = -1.1  for stack of 45-310
		Stack = -2.1  for stack of 46-309
		Stack = -2.2  for stack of 47-308
	Helix total = -7.5
	Multiloop = 4.6  for closure of 48-307
		Stack = -2.5  for stack of 251-286
		Stack = -0.6  for stack of 252-285
		Stack = -0.9  for stack of 253-284
		Stack = -1.3  for stack of 254-283
		Stack = -1.1  for stack of 255-282
		Stack = -0.9  for stack of 256-281
		Stack = -2.4  for stack of 257-280
		Stack = -2.1  for stack of 258-279
		Stack = -1.4  for stack of 259-278
	Helix total = -13.2
	Internal/bulge = 1.1  for closure of 260-277	Size = 2
		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 = -2.2  for stack of 204-231
	Helix total = -4.3
	Internal/bulge = 2.1  for closure of 205-230	Size = 11
		Stack = -3.3  for stack of 211-223
	Helix total = -3.3
	Hairpin = 4.1  for closure of 212-222
		Stack = -2.1  for stack of 141-184
		Stack = -0.9  for stack of 142-183
		Stack = -1.3  for stack of 143-182
		Stack = -1.1  for stack of 144-181
		Stack = -2.4  for stack of 145-180
		Stack = -2.1  for stack of 146-179
	Helix total = -9.9
	Internal/bulge = 4.1  for closure of 147-178	Size = 4
		Stack = -3.3  for stack of 148-173
		Stack = -2.1  for stack of 149-172
		Stack = -2.4  for stack of 150-171
	Helix total = -7.8
	Internal/bulge = 0.3  for closure of 151-170	Size = 4
		Stack = -2.1  for stack of 154-167
		Stack = -0.9  for stack of 155-166
	Helix total = -3.0
	Hairpin = 5.5  for closure of 156-165
		Stack = -3.4  for stack of 110-140
		Stack = -2.1  for stack of 111-139
		Stack = -0.9  for stack of 112-138
		Stack = -0.9  for stack of 113-137
		Stack = -1.3  for stack of 114-136
	Helix total = -8.6
	Internal/bulge = 2.6  for closure of 115-135	Size = 1 BP stack across bulge = -0.6
	Helix total = 0.0
	Internal/bulge = 2.3  for closure of 116-133	Size = 4
	Helix total = 0.0
	Hairpin = 6.3  for closure of 119-130
		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 = -62.5



