Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    52:70 53:69 54:68 55:67 168:204 169:203 170:202 171:201
	    172:200 173:199 220:246 221:245 222:244 223:243 224:242 225:241
	    265:302 266:301 267:300 268:299 270:298 271:297 272:296 273:295
	Energy of Broken Structure: -48.2
	Energy of Pseudo-Helices:   -36.1
	Pseudoknot Energy Penalty:  31.4
	Total Free Energy:          -52.9
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 = 6.7  for closure of 7-359
		Stack = -2.1  for stack of 342-358
		Stack = -3.3  for stack of 343-357
		Stack = -3.3  for stack of 344-356
		Stack = -3.3  for stack of 345-355
	Helix total = -12.0
	Hairpin = 4.4  for closure of 346-354
		Stack = -2.1  for stack of 20-338
		Stack = -0.6  for stack of 21-337
		Stack = -0.5  for stack of 22-336
		Stack = -1.3  for stack of 23-335
		Stack = -2.1  for stack of 24-334
		Stack = -3.4  for stack of 25-333
	Helix total = -10.0
	Internal/bulge = 2.7  for closure of 26-332	Size = 6
	Helix total = 0.0
	Internal/bulge = 3.4  for closure of 30-328	Size = 7
		Stack = -2.1  for stack of 34-323
		Stack = -0.9  for stack of 35-322
		Stack = -1.3  for stack of 36-321
		Stack = -0.9  for stack of 37-320
		Stack = -2.1  for stack of 38-319
	Helix total = -7.3
	Internal/bulge = 0.7  for closure of 39-318	Size = 2
	Helix total = 0.0
	Internal/bulge = 4.1  for closure of 41-316	Size = 4
		Stack = -2.1  for stack of 42-311
		Stack = -1.1  for stack of 43-310
		Stack = -2.1  for stack of 44-309
		Stack = -2.2  for stack of 45-308
	Helix total = -7.5
	Multiloop = 6.7  for closure of 46-307
		Stack = -1.3  for stack of 250-285
		Stack = -1.4  for stack of 251-284
		Stack = -2.2  for stack of 252-283
		Stack = -2.1  for stack of 253-282
	Helix total = -7.0
	Internal/bulge = -0.1  for closure of 254-281	Size = 1 BP stack across bulge = -3.3
	Helix total = 0.0
	Internal/bulge = 3.0  for closure of 256-280	Size = 4
		Stack = -1.3  for stack of 260-278
		Stack = -1.1  for stack of 261-277
		Stack = -2.4  for stack of 262-276
	Helix total = -4.8
	Hairpin = 5.6  for closure of 263-275
		Stack = -2.4  for stack of 208-234
		Stack = -2.1  for stack of 209-233
		Stack = -0.9  for stack of 210-232
		Stack = -0.9  for stack of 211-231
		Stack = -0.9  for stack of 212-230
		Stack = -0.9  for stack of 213-229
		Stack = -2.1  for stack of 214-228
		Stack = -2.5  for stack of 215-227
	Helix total = -12.7
	Hairpin = 6.2  for closure of 216-226
		Stack = -1.4  for stack of 150-190
		Stack = -2.1  for stack of 151-189
		Stack = -3.4  for stack of 152-188
		Stack = -2.1  for stack of 153-187
		Stack = -0.9  for stack of 154-186
	Helix total = -9.9
	Internal/bulge = 1.9  for closure of 155-185	Size = 2
		Stack = -0.6  for stack of 157-183
		Stack = -1.3  for stack of 158-182
	Helix total = -1.9
	Internal/bulge = 2.4  for closure of 159-181	Size = 4
		Stack = -0.9  for stack of 162-178
		Stack = -2.4  for stack of 163-177
		Stack = -2.1  for stack of 164-176
		Stack = -1.3  for stack of 165-175
	Helix total = -6.7
	Hairpin = 5.5  for closure of 166-174
		Stack = -2.5  for stack of 109-149
		Stack = -2.1  for stack of 110-148
		Stack = -1.3  for stack of 111-147
	Helix total = -5.9
	Internal/bulge = 5.2  for closure of 112-146	Size = 5
		Stack = -0.9  for stack of 117-144
		Stack = -0.9  for stack of 118-143
		Stack = -0.9  for stack of 119-142
		Stack = -2.1  for stack of 120-141
	Helix total = -4.8
	Hairpin = 6.0  for closure of 121-140
		Stack = -2.4  for stack of 47-60
		Stack = -2.1  for stack of 48-59
		Stack = -3.4  for stack of 49-58
		Stack = -2.1  for stack of 50-57
	Helix total = -10.0
	Hairpin = 4.1  for closure of 51-56


	Total energy = -48.2



