Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    56:86 57:85 58:84 59:83 166:200 167:199 168:198 169:197
	    170:196 171:195 216:250 217:249 218:248 219:247 220:246 221:245
	    222:244 268:308 269:307 270:306 271:305 272:304 273:303 275:301
	    276:300
	Energy of Broken Structure: -114.1
	Energy of Pseudo-Helices:   -48.6
	Pseudoknot Energy Penalty:  35.9
	Total Free Energy:          -126.8
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-368
		Stack = -1.5  for stack of 2-367
		Stack = -2.1  for stack of 3-366
		Stack = -3.3  for stack of 4-365
		Stack = -2.2  for stack of 5-364
		Stack = -2.1  for stack of 6-363
	Helix total = -14.5
	Multiloop = 5.0  for closure of 7-362
		Stack = -3.4  for stack of 345-361
		Stack = -2.4  for stack of 346-360
		Stack = -3.3  for stack of 347-359
		Stack = -3.3  for stack of 348-358
	Helix total = -12.4
	Hairpin = 4.4  for closure of 349-357
		Stack = -2.1  for stack of 19-341
		Stack = -0.9  for stack of 20-340
		Stack = -2.4  for stack of 21-339
		Stack = -2.4  for stack of 22-338
		Stack = -2.4  for stack of 23-337
		Stack = -1.1  for stack of 24-336
		Stack = -2.1  for stack of 25-335
	Helix total = -13.4
	Internal/bulge = -1.4  for closure of 26-334	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.3  for closure of 28-332	Size = 1 BP stack across bulge = -2.1
		Stack = -2.5  for stack of 30-331
	Helix total = -2.5
	Internal/bulge = 1.1  for closure of 31-330	Size = 2
		Stack = -2.5  for stack of 33-328
		Stack = -1.0  for stack of 34-327
		Stack = -2.1  for stack of 35-326
		Stack = -3.3  for stack of 36-325
		Stack = -3.3  for stack of 37-324
	Helix total = -12.2
	Internal/bulge = 1.7  for closure of 38-323	Size = 10
		Stack = -2.4  for stack of 43-316
		Stack = -3.3  for stack of 44-315
		Stack = -3.3  for stack of 45-314
		Stack = -3.4  for stack of 46-313
	Helix total = -12.4
	Multiloop = 2.2  for closure of 47-312
		Stack = -3.3  for stack of 252-288
		Stack = -3.4  for stack of 253-287
		Stack = -3.3  for stack of 254-286
		Stack = -2.1  for stack of 255-285
	Helix total = -12.1
	Internal/bulge = 3.3  for closure of 256-284	Size = 2
		Stack = -2.4  for stack of 259-283
		Stack = -3.3  for stack of 260-282
		Stack = -3.4  for stack of 261-281
		Stack = -2.4  for stack of 262-280
	Helix total = -11.5
	Hairpin = 5.6  for closure of 263-279
		Stack = -1.4  for stack of 205-233
		Stack = -2.1  for stack of 206-232
		Stack = -2.2  for stack of 207-231
		Stack = -2.4  for stack of 208-230
		Stack = -2.1  for stack of 209-229
		Stack = -2.1  for stack of 210-228
		Stack = -2.4  for stack of 211-227
		Stack = -1.1  for stack of 212-226
		Stack = -2.4  for stack of 213-225
	Helix total = -18.2
	Hairpin = 5.0  for closure of 214-224
		Stack = -2.1  for stack of 151-187
		Stack = -2.5  for stack of 152-186
		Stack = -1.5  for stack of 153-185
		Stack = -2.4  for stack of 154-184
		Stack = -3.3  for stack of 155-183
	Helix total = -11.8
	Internal/bulge = 2.3  for closure of 156-182	Size = 4
		Stack = -2.1  for stack of 158-178
		Stack = -2.1  for stack of 159-177
		Stack = -3.3  for stack of 160-176
		Stack = -3.3  for stack of 161-175
	Helix total = -10.8
	Hairpin = 5.5  for closure of 162-174
		Stack = -2.4  for stack of 117-150
		Stack = -2.1  for stack of 118-149
		Stack = -2.2  for stack of 119-148
		Stack = -1.3  for stack of 120-147
	Helix total = -8.0
	Internal/bulge = 4.1  for closure of 121-146	Size = 1 BP stack across bulge = 0.3
		Stack = -2.5  for stack of 123-145
		Stack = -2.1  for stack of 124-144
		Stack = -2.4  for stack of 125-143
		Stack = -2.1  for stack of 126-142
		Stack = -2.4  for stack of 127-141
		Stack = -2.4  for stack of 128-140
	Helix total = -13.9
	Hairpin = 5.9  for closure of 129-139
		Stack = -2.4  for stack of 48-70
		Stack = -2.4  for stack of 49-69
		Stack = -2.1  for stack of 50-68
		Stack = -3.3  for stack of 51-67
	Helix total = -10.2
	Hairpin = 5.5  for closure of 52-66


	Total energy = -114.1



