Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    54:70 55:69 56:68 164:199 165:198 166:197 167:196 168:195
	    169:194 214:244 215:243 216:242 217:241 218:240 268:316 269:315
	    270:314 271:313 272:312 273:311 274:310 275:309 276:308
	Energy of Broken Structure: -41.3
	Energy of Pseudo-Helices:   -35.1
	Pseudoknot Energy Penalty:  38.7
	Total Free Energy:          -37.7
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-382
		Stack = -1.5  for stack of 2-381
		Stack = -2.1  for stack of 3-380
		Stack = -3.4  for stack of 4-379
		Stack = -2.1  for stack of 5-378
		Stack = -2.1  for stack of 6-377
	Helix total = -14.5
	Multiloop = 6.8  for closure of 7-376
		Stack = -2.1  for stack of 359-375
		Stack = -3.3  for stack of 360-374
		Stack = -3.3  for stack of 361-373
		Stack = -3.3  for stack of 362-372
	Helix total = -12.0
	Hairpin = 4.4  for closure of 363-371
		Stack = -2.1  for stack of 21-355
		Stack = -0.6  for stack of 22-354
		Stack = -1.3  for stack of 23-353
	Helix total = -4.0
	Internal/bulge = 0.6  for closure of 24-352	Size = 4
		Stack = -2.4  for stack of 27-349
		Stack = -2.1  for stack of 28-348
		Stack = -0.9  for stack of 29-347
		Stack = -2.1  for stack of 30-346
		Stack = -2.2  for stack of 31-345
		Stack = -2.4  for stack of 32-344
	Helix total = -12.1
	Internal/bulge = 3.3  for closure of 33-343	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 34-340	Size = 2
		Stack = -2.2  for stack of 36-338
	Helix total = -2.2
	Internal/bulge = 3.3  for closure of 37-337	Size = 2
		Stack = -0.6  for stack of 38-334
		Stack = -1.3  for stack of 39-333
		Stack = -1.4  for stack of 40-332
	Helix total = -3.3
	Internal/bulge = 6.3  for closure of 41-331	Size = 10
		Stack = -1.1  for stack of 45-323
		Stack = -2.1  for stack of 46-322
		Stack = -3.4  for stack of 47-321
	Helix total = -6.6
	Multiloop = 4.8  for closure of 48-320
		Stack = -0.9  for stack of 246-293
		Stack = -1.0  for stack of 247-292
		Stack = -1.3  for stack of 248-291
		Stack = -0.9  for stack of 249-290
	Helix total = -4.1
	Internal/bulge = 3.7  for closure of 250-289	Size = 3
	Helix total = 0.0
	Internal/bulge = 3.4  for closure of 253-287	Size = 6
	Helix total = 0.0
	Internal/bulge = 2.7  for closure of 257-283	Size = 6
		Stack = -3.3  for stack of 261-279
		Stack = -2.2  for stack of 262-278
	Helix total = -5.5
	Hairpin = 6.6  for closure of 263-277
		Stack = -0.9  for stack of 204-228
		Stack = -0.9  for stack of 205-227
		Stack = -1.3  for stack of 206-226
		Stack = -0.9  for stack of 207-225
		Stack = -0.9  for stack of 208-224
		Stack = -0.9  for stack of 209-223
		Stack = -2.1  for stack of 210-222
		Stack = -3.3  for stack of 211-221
		Stack = -2.5  for stack of 212-220
	Helix total = -13.7
	Hairpin = 5.4  for closure of 213-219
		Stack = -2.1  for stack of 148-184
		Stack = -3.3  for stack of 149-183
		Stack = -2.4  for stack of 150-182
	Helix total = -7.8
	Internal/bulge = 1.9  for closure of 151-181	Size = 2
		Stack = -1.4  for stack of 153-179
		Stack = -2.4  for stack of 154-178
		Stack = -1.1  for stack of 155-177
		Stack = -0.9  for stack of 156-176
		Stack = -1.3  for stack of 157-175
		Stack = -0.6  for stack of 158-174
		Stack = -1.3  for stack of 159-173
		Stack = -0.9  for stack of 160-172
		Stack = -1.4  for stack of 161-171
	Helix total = -11.3
	Hairpin = 5.9  for closure of 162-170
		Stack = -3.4  for stack of 108-147
		Stack = -2.1  for stack of 109-146
		Stack = -1.3  for stack of 110-145
	Helix total = -6.8
	Internal/bulge = 3.9  for closure of 111-144	Size = 7
		Stack = -0.9  for stack of 117-141
		Stack = -0.9  for stack of 118-140
		Stack = -2.1  for stack of 119-139
	Helix total = -3.9
	Hairpin = 6.4  for closure of 120-138
		Stack = -2.1  for stack of 49-61
		Stack = -0.9  for stack of 50-60
		Stack = -2.1  for stack of 51-59
		Stack = -3.4  for stack of 52-58
	Helix total = -8.5
	Hairpin = 5.4  for closure of 53-57


	Total energy = -41.3



