Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:67 50:66 51:65 52:64 53:63 158:200 159:199 161:197
	    162:196 163:195 217:250 218:249 219:248 220:247 221:246 222:245
	    268:304 269:303 270:302 271:301 272:300 273:299 274:298
	Energy of Broken Structure: -69.8
	Energy of Pseudo-Helices:   -42.7
	Pseudoknot Energy Penalty:  32.2
	Total Free Energy:          -80.3
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 = 5.2  for closure of 7-358
		Stack = -3.4  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 = -12.4
	Hairpin = 4.4  for closure of 345-353
		Stack = -2.4  for stack of 21-337
		Stack = -1.5  for stack of 22-336
		Stack = -0.5  for stack of 23-335
		Stack = -1.3  for stack of 24-334
		Stack = -0.9  for stack of 25-333
		Stack = -1.4  for stack of 26-332
		Stack = -0.5  for stack of 27-331
	Helix total = -8.5
	Internal/bulge = 3.4  for closure of 28-330	Size = 9
		Stack = -1.4  for stack of 34-325
		Stack = -2.4  for stack of 35-324
	Helix total = -3.8
	Internal/bulge = 1.4  for closure of 36-323	Size = 6
		Stack = -3.3  for stack of 40-319
		Stack = -2.2  for stack of 41-318
		Stack = -1.0  for stack of 42-317
	Helix total = -6.5
	Internal/bulge = 3.7  for closure of 43-316	Size = 3
		Stack = -2.1  for stack of 44-312
		Stack = -1.1  for stack of 45-311
		Stack = -2.1  for stack of 46-310
		Stack = -3.4  for stack of 47-309
	Helix total = -8.7
	Multiloop = 3.9  for closure of 48-308
		Stack = -2.5  for stack of 253-288
		Stack = -1.5  for stack of 254-287
		Stack = -2.1  for stack of 255-286
		Stack = -1.4  for stack of 256-285
	Helix total = -7.5
	Internal/bulge = 1.9  for closure of 257-284	Size = 1 BP stack across bulge = -1.5
	Helix total = 0.0
	Internal/bulge = 1.3  for closure of 259-283	Size = 4
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 262-280	Size = 3
		Stack = -3.4  for stack of 264-277
		Stack = -2.4  for stack of 265-276
	Helix total = -5.8
	Hairpin = 3.9  for closure of 266-275
		Stack = -3.4  for stack of 203-234
		Stack = -3.3  for stack of 204-233
	Helix total = -6.7
	Internal/bulge = 2.6  for closure of 205-232	Size = 10
		Stack = -2.4  for stack of 211-226
		Stack = -2.1  for stack of 212-225
		Stack = -2.4  for stack of 213-224
	Helix total = -6.9
	Hairpin = 4.5  for closure of 214-223
		Stack = -2.4  for stack of 140-184
		Stack = -2.1  for stack of 141-183
		Stack = -1.5  for stack of 142-182
		Stack = -2.1  for stack of 143-181
		Stack = -2.4  for stack of 144-180
		Stack = -2.4  for stack of 145-179
	Helix total = -12.9
	Internal/bulge = 4.0  for closure of 146-178	Size = 5
		Stack = -3.3  for stack of 147-172
		Stack = -3.3  for stack of 148-171
		Stack = -2.1  for stack of 149-170
	Helix total = -8.7
	Internal/bulge = 0.7  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
	Helix total = -3.4
	Internal/bulge = 0.9  for closure of 111-138	Size = 2
		Stack = -2.1  for stack of 113-136
	Helix total = -2.1
	Internal/bulge = 3.0  for closure of 114-135	Size = 3
		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 = -69.8



