Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    52:72 53:71 54:70 55:69 56:68 161:194 162:193 163:192
	    164:191 165:190 209:246 210:245 211:244 212:243 217:238 263:303
	    264:302 265:301 266:300 267:299 268:298 269:297
	Energy of Broken Structure: -84.7
	Energy of Pseudo-Helices:   -38.9
	Pseudoknot Energy Penalty:  32.6
	Total Free Energy:          -91.0
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-364
		Stack = -1.5  for stack of 2-363
		Stack = -2.1  for stack of 3-362
		Stack = -3.3  for stack of 4-361
		Stack = -3.4  for stack of 5-360
		Stack = -2.4  for stack of 6-359
	Helix total = -16.0
	Multiloop = 5.3  for closure of 7-358
		Stack = -3.3  for stack of 341-357
		Stack = -3.3  for stack of 342-356
		Stack = -3.3  for stack of 343-355
		Stack = -3.3  for stack of 344-354
	Helix total = -13.2
	Hairpin = 4.4  for closure of 345-353
		Stack = -2.4  for stack of 23-337
		Stack = -1.5  for stack of 24-336
		Stack = -0.5  for stack of 25-335
		Stack = -2.1  for stack of 26-334
		Stack = -3.3  for stack of 27-333
		Stack = -3.4  for stack of 28-332
		Stack = -2.1  for stack of 29-331
	Helix total = -15.3
	Internal/bulge = 1.9  for closure of 30-330	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.4  for closure of 32-328	Size = 1 BP stack across bulge = -1.4
		Stack = -1.5  for stack of 34-327
		Stack = -1.3  for stack of 35-326
		Stack = -1.4  for stack of 36-325
		Stack = -0.6  for stack of 37-324
		Stack = -2.4  for stack of 38-323
		Stack = -3.3  for stack of 39-322
		Stack = -2.1  for stack of 40-321
		Stack = -0.9  for stack of 41-320
		Stack = -0.9  for stack of 42-319
		Stack = -1.4  for stack of 43-318
	Helix total = -15.8
	Internal/bulge = 3.6  for closure of 44-317	Size = 7
		Stack = -2.4  for stack of 47-311
		Stack = -3.3  for stack of 48-310
		Stack = -3.3  for stack of 49-309
		Stack = -2.2  for stack of 50-308
	Helix total = -11.2
	Multiloop = 5.9  for closure of 51-307
		Stack = -3.3  for stack of 248-283
		Stack = -3.3  for stack of 249-282
		Stack = -2.4  for stack of 250-281
		Stack = -0.9  for stack of 251-280
	Helix total = -9.9
	Internal/bulge = 3.7  for closure of 252-279	Size = 3
		Stack = -0.9  for stack of 255-277
		Stack = -0.9  for stack of 256-276
	Helix total = -1.8
	Internal/bulge = 2.9  for closure of 257-275	Size = 6
	Helix total = 0.0
	Hairpin = 5.4  for closure of 260-270
		Stack = -2.2  for stack of 198-233
		Stack = -3.3  for stack of 199-232
	Helix total = -5.5
	Internal/bulge = -1.4  for closure of 200-231	Size = 2
		Stack = -0.9  for stack of 202-229
		Stack = -0.9  for stack of 203-228
		Stack = -0.6  for stack of 204-227
	Helix total = -2.4
	Hairpin = 6.9  for closure of 205-226
		Stack = -2.4  for stack of 145-181
		Stack = -2.5  for stack of 146-180
		Stack = -1.5  for stack of 147-179
		Stack = -3.3  for stack of 148-178
		Stack = -2.4  for stack of 149-177
	Helix total = -12.1
	Internal/bulge = 2.3  for closure of 150-176	Size = 4
		Stack = -2.4  for stack of 152-172
		Stack = -3.3  for stack of 153-171
		Stack = -2.4  for stack of 154-170
		Stack = -2.1  for stack of 155-169
		Stack = -3.3  for stack of 156-168
	Helix total = -13.5
	Hairpin = 5.3  for closure of 157-167
		Stack = -0.9  for stack of 120-144
		Stack = -1.3  for stack of 121-143
		Stack = -2.1  for stack of 122-142
		Stack = -3.4  for stack of 123-141
		Stack = -2.1  for stack of 124-140
		Stack = -2.1  for stack of 125-139
	Helix total = -11.9
	Hairpin = 5.5  for closure of 126-138
		Stack = -2.4  for stack of 60-86
		Stack = -2.1  for stack of 61-85
		Stack = -2.4  for stack of 62-84
		Stack = -2.4  for stack of 63-83
		Stack = -3.3  for stack of 64-82
		Stack = -2.2  for stack of 65-81
	Helix total = -14.8
	Hairpin = 6.3  for closure of 66-80


	Total energy = -84.7



