Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:67 49:66 50:65 51:64 52:63 194:228 195:227 196:226
	    197:225 198:224 244:275 245:274 246:273 247:272 248:271 249:270
	    292:330 293:329 294:328 296:325 297:324 298:323
	Energy of Broken Structure: -88.7
	Energy of Pseudo-Helices:   -38.7
	Pseudoknot Energy Penalty:  32.7
	Total Free Energy:          -94.7
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-390
		Stack = -1.5  for stack of 2-389
		Stack = -2.1  for stack of 3-388
		Stack = -3.4  for stack of 4-387
		Stack = -3.3  for stack of 5-386
		Stack = -2.4  for stack of 6-385
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-384
		Stack = -3.3  for stack of 367-383
		Stack = -3.3  for stack of 368-382
		Stack = -3.3  for stack of 369-381
		Stack = -3.3  for stack of 370-380
	Helix total = -13.2
	Hairpin = 4.4  for closure of 371-379
		Stack = -2.4  for stack of 20-363
		Stack = -3.4  for stack of 21-362
		Stack = -3.3  for stack of 22-361
		Stack = -1.4  for stack of 23-360
		Stack = -2.1  for stack of 24-359
		Stack = -2.2  for stack of 25-358
	Helix total = -14.8
	Internal/bulge = 4.9  for closure of 26-357	Size = 14
		Stack = -0.6  for stack of 35-350
	Helix total = -0.6
	Internal/bulge = 2.2  for closure of 36-349	Size = 5
		Stack = -3.3  for stack of 39-345
		Stack = -2.2  for stack of 40-344
		Stack = -1.0  for stack of 41-343
	Helix total = -6.5
	Internal/bulge = 3.7  for closure of 42-342	Size = 3
		Stack = -2.1  for stack of 43-338
		Stack = -1.1  for stack of 44-337
		Stack = -2.1  for stack of 45-336
		Stack = -3.4  for stack of 46-335
	Helix total = -8.7
	Multiloop = 1.5  for closure of 47-334
		Stack = -2.5  for stack of 278-312
		Stack = -3.3  for stack of 279-311
		Stack = -3.3  for stack of 280-310
	Helix total = -9.1
	Internal/bulge = 2.2  for closure of 281-309	Size = 5
	Helix total = 0.0
	Internal/bulge = 3.4  for closure of 285-306	Size = 7
		Stack = -3.3  for stack of 289-301
		Stack = -2.1  for stack of 290-300
	Helix total = -5.4
	Hairpin = 5.7  for closure of 291-299
		Stack = -3.4  for stack of 232-260
		Stack = -3.3  for stack of 233-259
		Stack = -2.4  for stack of 234-258
		Stack = -2.5  for stack of 235-257
	Helix total = -11.6
	Internal/bulge = 0.7  for closure of 236-256	Size = 6
		Stack = -2.2  for stack of 240-252
	Helix total = -2.2
	Hairpin = 5.9  for closure of 241-251
		Stack = -2.1  for stack of 178-214
		Stack = -0.9  for stack of 179-213
		Stack = -1.1  for stack of 180-212
		Stack = -2.4  for stack of 181-211
		Stack = -2.1  for stack of 182-210
		Stack = -1.1  for stack of 183-209
	Helix total = -9.7
	Internal/bulge = 3.3  for closure of 184-208	Size = 5
		Stack = -3.3  for stack of 187-204
		Stack = -3.3  for stack of 188-203
	Helix total = -6.6
	Internal/bulge = 0.1  for closure of 189-202	Size = 4
	Helix total = 0.0
	Hairpin = 5.1  for closure of 192-199
		Stack = -2.1  for stack of 159-177
		Stack = -2.1  for stack of 160-176
		Stack = -3.3  for stack of 161-175
	Helix total = -7.5
	Internal/bulge = 1.4  for closure of 162-174	Size = 1 BP stack across bulge = -2.4
		Stack = -2.2  for stack of 164-173
		Stack = -3.3  for stack of 165-172
	Helix total = -5.5
	Hairpin = 3.7  for closure of 166-171
		Stack = -3.3  for stack of 115-158
		Stack = -3.3  for stack of 116-157
		Stack = -3.3  for stack of 117-156
	Helix total = -9.9
	Internal/bulge = 2.5  for closure of 118-155	Size = 10
		Stack = -3.4  for stack of 124-149
		Stack = -2.1  for stack of 125-148
	Helix total = -5.5
	Internal/bulge = 2.7  for closure of 126-147	Size = 6
		Stack = -3.4  for stack of 130-143
		Stack = -2.1  for stack of 131-142
		Stack = -2.1  for stack of 132-141
		Stack = -3.4  for stack of 133-140
	Helix total = -11.0
	Hairpin = 3.3  for closure of 134-139
		Stack = -2.5  for stack of 55-82
		Stack = -1.0  for stack of 56-81
		Stack = -0.9  for stack of 57-80
		Stack = -2.2  for stack of 58-79
		Stack = -2.1  for stack of 59-78
		Stack = -2.1  for stack of 60-77
	Helix total = -10.8
	Hairpin = 5.8  for closure of 61-76


	Total energy = -88.7



