Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    56:82 57:81 58:80 59:79 163:195 164:194 165:193 166:192
	    167:191 211:247 212:246 213:245 214:244 215:243 216:242 217:241
	    266:305 267:304 268:303 269:302 270:301 271:300
	Energy of Broken Structure: -88.6
	Energy of Pseudo-Helices:   -41.8
	Pseudoknot Energy Penalty:  35.8
	Total Free Energy:          -94.6
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-365
		Stack = -1.5  for stack of 2-364
		Stack = -2.1  for stack of 3-363
		Stack = -3.4  for stack of 4-362
		Stack = -2.1  for stack of 5-361
		Stack = -2.1  for stack of 6-360
	Helix total = -14.5
	Multiloop = 4.9  for closure of 7-359
		Stack = -3.3  for stack of 342-358
		Stack = -2.4  for stack of 343-357
		Stack = -3.3  for stack of 344-356
		Stack = -3.3  for stack of 345-355
	Helix total = -12.3
	Hairpin = 4.4  for closure of 346-354
		Stack = -2.1  for stack of 19-338
	Helix total = -2.1
	Internal/bulge = 1.2  for closure of 20-337	Size = 2
		Stack = -2.4  for stack of 22-335
	Helix total = -2.4
	Internal/bulge = 0.5  for closure of 23-334	Size = 1 BP stack across bulge = -3.3
		Stack = -3.4  for stack of 25-333
		Stack = -2.1  for stack of 26-332
		Stack = -1.1  for stack of 27-331
	Helix total = -6.6
	Internal/bulge = 2.7  for closure of 28-330	Size = 8
		Stack = -2.4  for stack of 33-325
	Helix total = -2.4
	Internal/bulge = 1.2  for closure of 34-324	Size = 2
		Stack = -2.1  for stack of 36-322
		Stack = -3.3  for stack of 37-321
	Helix total = -5.4
	Internal/bulge = 1.7  for closure of 38-320	Size = 10
		Stack = -2.4  for stack of 43-313
		Stack = -2.2  for stack of 44-312
		Stack = -2.1  for stack of 45-311
		Stack = -3.4  for stack of 46-310
	Helix total = -10.1
	Multiloop = 3.1  for closure of 47-309
		Stack = -3.3  for stack of 248-286
		Stack = -2.4  for stack of 249-285
		Stack = -1.1  for stack of 250-284
		Stack = -2.4  for stack of 251-283
	Helix total = -9.2
	Internal/bulge = 4.1  for closure of 252-282	Size = 4
		Stack = -2.4  for stack of 257-281
		Stack = -2.1  for stack of 258-280
		Stack = -1.5  for stack of 259-279
		Stack = -2.4  for stack of 260-278
		Stack = -3.3  for stack of 261-277
	Helix total = -11.7
	Hairpin = 5.7  for closure of 262-276
		Stack = -3.3  for stack of 201-229
		Stack = -3.3  for stack of 202-228
		Stack = -2.1  for stack of 203-227
		Stack = -2.2  for stack of 204-226
		Stack = -1.4  for stack of 205-225
		Stack = -2.1  for stack of 206-224
		Stack = -3.3  for stack of 207-223
		Stack = -2.2  for stack of 208-222
		Stack = -1.3  for stack of 209-221
	Helix total = -21.2
	Hairpin = 6.2  for closure of 210-220
		Stack = -2.1  for stack of 147-183
		Stack = -2.5  for stack of 148-182
		Stack = -1.5  for stack of 149-181
		Stack = -2.1  for stack of 150-180
		Stack = -2.1  for stack of 151-179
	Helix total = -10.3
	Internal/bulge = 2.3  for closure of 152-178	Size = 4
		Stack = -3.3  for stack of 154-174
		Stack = -2.4  for stack of 155-173
		Stack = -3.3  for stack of 156-172
		Stack = -3.3  for stack of 157-171
	Helix total = -12.3
	Hairpin = 5.3  for closure of 158-170
	Helix total = 0.0
	Internal/bulge = 3.0  for closure of 116-144	Size = 4
		Stack = -3.4  for stack of 119-141
		Stack = -3.3  for stack of 120-140
	Helix total = -6.7
	Internal/bulge = 1.2  for closure of 121-139	Size = 2
		Stack = -2.4  for stack of 123-137
		Stack = -2.4  for stack of 124-136
		Stack = -3.4  for stack of 125-135
	Helix total = -8.2
	Hairpin = 5.0  for closure of 126-134
		Stack = -2.4  for stack of 48-69
		Stack = -3.3  for stack of 49-68
		Stack = -2.2  for stack of 50-67
		Stack = -2.1  for stack of 51-66
	Helix total = -10.0
	Hairpin = 6.0  for closure of 52-65


	Total energy = -88.6



