Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    50:68 51:67 52:66 53:65 54:64 161:200 162:199 164:197
	    166:195 216:250 217:249 218:248 219:247 220:246 221:245 222:244
	    252:288 254:286 255:285 261:279 263:274 264:273
	Energy of Broken Structure: -45.5
	Energy of Pseudo-Helices:   -27.6
	Pseudoknot Energy Penalty:  32.1
	Total Free Energy:          -41.0
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 = 5.2  for closure of 7-359
		Stack = -3.4  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 = -12.4
	Hairpin = 4.4  for closure of 346-354
		Stack = -2.1  for stack of 21-338
		Stack = -0.9  for stack of 22-337
		Stack = -0.9  for stack of 23-336
		Stack = -0.9  for stack of 24-335
		Stack = -1.1  for stack of 25-334
		Stack = -0.9  for stack of 26-333
	Helix total = -6.8
	Internal/bulge = 1.9  for closure of 27-332	Size = 2
	Helix total = 0.0
	Internal/bulge = 4.4  for closure of 29-330	Size = 9
		Stack = -0.9  for stack of 35-325
	Helix total = -0.9
	Internal/bulge = 2.9  for closure of 36-324	Size = 5
		Stack = -0.9  for stack of 40-321
		Stack = -2.1  for stack of 41-320
		Stack = -2.5  for stack of 42-319
	Helix total = -5.5
	Internal/bulge = 4.5  for closure of 43-318	Size = 5
		Stack = -2.1  for stack of 45-313
		Stack = -1.1  for stack of 46-312
		Stack = -2.1  for stack of 47-311
		Stack = -3.4  for stack of 48-310
	Helix total = -8.7
	Multiloop = 3.1  for closure of 49-309
		Stack = -2.2  for stack of 266-305
		Stack = -0.9  for stack of 267-304
		Stack = -0.9  for stack of 268-303
	Helix total = -4.0
	Internal/bulge = 1.8  for closure of 269-302	Size = 1 BP stack across bulge = -0.9
		Stack = -0.9  for stack of 270-300
		Stack = -2.4  for stack of 271-299
	Helix total = -3.3
	Hairpin = 6.5  for closure of 272-298
		Stack = -2.4  for stack of 205-232
		Stack = -2.2  for stack of 206-231
		Stack = -2.1  for stack of 207-230
	Helix total = -6.7
	Internal/bulge = 1.9  for closure of 208-229	Size = 3
		Stack = -1.3  for stack of 211-227
		Stack = -1.1  for stack of 212-226
		Stack = -2.4  for stack of 213-225
	Helix total = -4.8
	Hairpin = 4.9  for closure of 214-224
		Stack = -3.3  for stack of 143-187
		Stack = -2.1  for stack of 144-186
		Stack = -0.9  for stack of 145-185
		Stack = -2.4  for stack of 146-184
		Stack = -3.3  for stack of 147-183
		Stack = -2.1  for stack of 148-182
	Helix total = -14.1
	Internal/bulge = 4.6  for closure of 149-181	Size = 4
		Stack = -2.4  for stack of 150-176
		Stack = -2.1  for stack of 151-175
		Stack = -1.3  for stack of 152-174
		Stack = -1.0  for stack of 153-173
	Helix total = -6.8
	Internal/bulge = 3.0  for closure of 154-172	Size = 3
	Helix total = 0.0
	Hairpin = 5.7  for closure of 156-169
		Stack = -3.4  for stack of 113-142
		Stack = -2.1  for stack of 114-141
		Stack = -0.9  for stack of 115-140
		Stack = -0.9  for stack of 116-139
		Stack = -1.3  for stack of 117-138
	Helix total = -8.6
	Internal/bulge = 1.9  for closure of 118-137	Size = 3
		Stack = -2.1  for stack of 120-134
		Stack = -2.1  for stack of 121-133
	Helix total = -4.2
	Hairpin = 5.3  for closure of 122-132
		Stack = -2.2  for stack of 56-79
		Stack = -2.4  for stack of 57-78
		Stack = -3.3  for stack of 58-77
		Stack = -2.5  for stack of 59-76
		Stack = -0.6  for stack of 60-75
	Helix total = -11.0
	Hairpin = 6.5  for closure of 61-74


	Total energy = -45.5



