Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    55:78 56:77 57:76 58:75 59:74 149:238 150:237 151:236
	    152:235 153:234 154:233 254:285 256:283 257:282 258:281 259:280
	    302:342 303:341 304:340 305:339 306:338 307:337 308:336
	Energy of Broken Structure: -103.9
	Energy of Pseudo-Helices:   -37.3
	Pseudoknot Energy Penalty:  31.1
	Total Free Energy:          -110.1
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-402
		Stack = -1.5  for stack of 2-401
		Stack = -2.1  for stack of 3-400
		Stack = -3.4  for stack of 4-399
		Stack = -3.3  for stack of 5-398
		Stack = -2.4  for stack of 6-397
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-396
		Stack = -3.3  for stack of 379-395
		Stack = -3.3  for stack of 380-394
		Stack = -3.3  for stack of 381-393
		Stack = -3.3  for stack of 382-392
	Helix total = -13.2
	Hairpin = 4.4  for closure of 383-391
		Stack = -2.4  for stack of 20-375
		Stack = -2.5  for stack of 21-374
		Stack = 0.3  for stack of 22-373
		Stack = -0.5  for stack of 23-372
		Stack = -2.1  for stack of 24-371
		Stack = -2.5  for stack of 25-370
		Stack = -1.5  for stack of 26-369
	Helix total = -11.2
	Internal/bulge = 1.2  for closure of 27-368	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.4  for closure of 29-366	Size = 7
		Stack = -2.1  for stack of 34-362
		Stack = -2.1  for stack of 35-361
	Helix total = -4.2
	Internal/bulge = 1.2  for closure of 36-360	Size = 1 BP stack across bulge = -2.2
		Stack = -2.4  for stack of 38-359
		Stack = -2.1  for stack of 39-358
		Stack = -2.1  for stack of 40-357
	Helix total = -6.6
	Internal/bulge = 2.9  for closure of 41-356	Size = 7
		Stack = -2.1  for stack of 44-350
		Stack = -1.1  for stack of 45-349
		Stack = -2.1  for stack of 46-348
		Stack = -2.5  for stack of 47-347
	Helix total = -7.8
	Multiloop = 3.8  for closure of 48-346
		Stack = -2.1  for stack of 288-322
		Stack = -0.5  for stack of 289-321
		Stack = -1.5  for stack of 290-320
		Stack = -2.4  for stack of 291-319
		Stack = -3.3  for stack of 292-318
	Helix total = -9.8
	Internal/bulge = -0.6  for closure of 293-317	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.0  for closure of 295-315	Size = 3
		Stack = -2.1  for stack of 297-312
		Stack = -3.4  for stack of 298-311
		Stack = -3.3  for stack of 299-310
	Helix total = -8.8
	Hairpin = 4.4  for closure of 300-309
		Stack = -2.5  for stack of 243-270
		Stack = -1.5  for stack of 244-269
		Stack = -2.1  for stack of 245-268
		Stack = -2.1  for stack of 246-267
	Helix total = -8.2
	Internal/bulge = 1.2  for closure of 247-266	Size = 2
		Stack = -2.5  for stack of 249-264
		Stack = -2.1  for stack of 250-263
		Stack = -1.4  for stack of 251-262
	Helix total = -6.0
	Hairpin = 3.0  for closure of 252-261
		Stack = -1.4  for stack of 134-225
		Stack = -2.5  for stack of 135-224
		Stack = -2.1  for stack of 136-223
		Stack = -2.1  for stack of 137-222
		Stack = -3.4  for stack of 138-221
	Helix total = -11.5
	Multiloop = 3.1  for closure of 139-220
		Stack = -3.4  for stack of 161-218
		Stack = -2.4  for stack of 162-217
		Stack = -3.3  for stack of 163-216
	Helix total = -9.1
	Multiloop = 8.1  for closure of 164-215
		Stack = -0.5  for stack of 200-211
		Stack = -2.1  for stack of 201-210
		Stack = -3.3  for stack of 202-209
	Helix total = -5.9
	Hairpin = 4.9  for closure of 203-208
		Stack = -2.1  for stack of 174-187
		Stack = -2.4  for stack of 175-186
		Stack = -3.3  for stack of 176-185
		Stack = -3.3  for stack of 177-184
	Helix total = -11.1
	Hairpin = 3.3  for closure of 178-183
		Stack = -2.1  for stack of 141-160
		Stack = -2.1  for stack of 142-159
		Stack = -2.4  for stack of 143-158
		Stack = -1.4  for stack of 144-157
		Stack = -1.5  for stack of 145-156
	Helix total = -9.5
	Hairpin = 4.5  for closure of 146-155
		Stack = -2.1  for stack of 113-132
		Stack = -2.4  for stack of 114-131
		Stack = -1.4  for stack of 115-130
		Stack = -2.5  for stack of 116-129
		Stack = -3.3  for stack of 117-128
		Stack = -2.4  for stack of 118-127
		Stack = -3.4  for stack of 119-126
	Helix total = -17.5
	Hairpin = 4.6  for closure of 120-125
		Stack = -2.4  for stack of 49-66
		Stack = -2.4  for stack of 50-65
		Stack = -2.1  for stack of 51-64
		Stack = -3.4  for stack of 52-63
	Helix total = -10.3
	Hairpin = 4.0  for closure of 53-62


	Total energy = -103.9



