Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    54:72 55:71 56:70 57:69 167:200 168:199 169:198 170:197
	    171:196 172:195 214:238 215:237 216:236 218:234 261:298 262:297
	    263:296 264:295 265:294 266:293 267:292
	Energy of Broken Structure: -49.1
	Energy of Pseudo-Helices:   -31.0
	Pseudoknot Energy Penalty:  31.7
	Total Free Energy:          -48.4
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-362
		Stack = -1.5  for stack of 2-361
		Stack = -2.1  for stack of 3-360
		Stack = -3.4  for stack of 4-359
		Stack = -2.1  for stack of 5-358
		Stack = -2.1  for stack of 6-357
	Helix total = -14.5
	Multiloop = 6.8  for closure of 7-356
		Stack = -2.1  for stack of 339-355
		Stack = -3.3  for stack of 340-354
		Stack = -3.3  for stack of 341-353
		Stack = -3.3  for stack of 342-352
	Helix total = -12.0
	Hairpin = 5.0  for closure of 343-351
		Stack = -2.1  for stack of 21-335
		Stack = -0.6  for stack of 22-334
		Stack = -0.5  for stack of 23-333
		Stack = -1.3  for stack of 24-332
		Stack = -0.9  for stack of 25-331
		Stack = -1.1  for stack of 26-330
		Stack = -0.9  for stack of 27-329
		Stack = -1.0  for stack of 28-328
		Stack = -1.4  for stack of 29-327
		Stack = -1.3  for stack of 30-326
		Stack = -1.1  for stack of 31-325
		Stack = -2.4  for stack of 32-324
	Helix total = -14.6
	Internal/bulge = 2.4  for closure of 33-323	Size = 1 BP stack across bulge = -1.4
		Stack = -2.5  for stack of 34-321
	Helix total = -2.5
	Internal/bulge = -0.4  for closure of 35-320	Size = 4
		Stack = -3.3  for stack of 38-317
		Stack = -2.4  for stack of 39-316
		Stack = -1.1  for stack of 40-315
		Stack = -1.3  for stack of 41-314
	Helix total = -8.1
	Internal/bulge = 4.5  for closure of 42-313	Size = 5
		Stack = -2.1  for stack of 44-308
		Stack = -1.1  for stack of 45-307
		Stack = -2.1  for stack of 46-306
		Stack = -2.5  for stack of 47-305
	Helix total = -7.8
	Multiloop = 3.8  for closure of 48-304
		Stack = -0.9  for stack of 242-281
		Stack = -2.1  for stack of 243-280
		Stack = -3.4  for stack of 244-279
		Stack = -3.3  for stack of 245-278
	Helix total = -9.7
	Internal/bulge = 4.4  for closure of 246-277	Size = 10
		Stack = -2.1  for stack of 253-272
		Stack = -2.4  for stack of 254-271
		Stack = -1.1  for stack of 255-270
		Stack = -0.9  for stack of 256-269
	Helix total = -6.5
	Hairpin = 6.3  for closure of 257-268
		Stack = -3.4  for stack of 204-227
		Stack = -2.1  for stack of 205-226
		Stack = -0.9  for stack of 206-225
		Stack = -0.9  for stack of 207-224
		Stack = -0.9  for stack of 208-223
		Stack = -0.9  for stack of 209-222
		Stack = -0.9  for stack of 210-221
		Stack = -2.1  for stack of 211-220
	Helix total = -12.1
	Hairpin = 3.8  for closure of 212-219
		Stack = -2.4  for stack of 152-187
		Stack = -2.4  for stack of 153-186
		Stack = -1.4  for stack of 154-185
	Helix total = -6.2
	Internal/bulge = 3.3  for closure of 155-184	Size = 1 BP stack across bulge = -0.5
		Stack = -0.6  for stack of 157-183
		Stack = -0.9  for stack of 158-182
		Stack = -0.9  for stack of 159-181
		Stack = -0.9  for stack of 160-180
	Helix total = -3.3
	Internal/bulge = 3.3  for closure of 161-179	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 162-176	Size = 4
	Helix total = 0.0
	Hairpin = 5.7  for closure of 165-173
		Stack = -3.4  for stack of 111-151
		Stack = -2.1  for stack of 112-150
		Stack = -1.3  for stack of 113-149
	Helix total = -6.8
	Internal/bulge = 3.8  for closure of 114-148	Size = 6
		Stack = -0.9  for stack of 119-145
		Stack = -0.9  for stack of 120-144
	Helix total = -1.8
	Internal/bulge = 1.9  for closure of 121-143	Size = 2
	Helix total = 0.0
	Hairpin = 6.8  for closure of 123-141
		Stack = -2.4  for stack of 49-62
		Stack = -3.3  for stack of 50-61
		Stack = -2.2  for stack of 51-60
		Stack = -1.3  for stack of 52-59
	Helix total = -9.2
	Hairpin = 4.4  for closure of 53-58


	Total energy = -49.1



