Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:68 49:67 50:66 51:65 52:64 198:237 199:236 200:235
	    201:234 202:233 203:232 252:278 253:277 254:276 255:275 298:335
	    299:334 302:331 303:330 304:329
	Energy of Broken Structure: -55.4
	Energy of Pseudo-Helices:   -34.4
	Pseudoknot Energy Penalty:  32.8
	Total Free Energy:          -57.0
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-396
		Stack = -1.5  for stack of 2-395
		Stack = -2.5  for stack of 3-394
		Stack = -2.1  for stack of 4-393
		Stack = -0.6  for stack of 5-392
		Stack = -2.1  for stack of 6-391
	Helix total = -12.1
	Multiloop = 4.9  for closure of 7-390
		Stack = -2.4  for stack of 373-389
		Stack = -3.3  for stack of 374-388
		Stack = -2.4  for stack of 375-387
		Stack = -2.1  for stack of 376-386
	Helix total = -10.2
	Hairpin = 4.4  for closure of 377-385
		Stack = -2.4  for stack of 19-369
	Helix total = -2.4
	Internal/bulge = 2.3  for closure of 20-368	Size = 1 BP stack across bulge = -1.5
		Stack = -2.5  for stack of 21-366
		Stack = -2.1  for stack of 22-365
		Stack = -0.9  for stack of 23-364
		Stack = -2.1  for stack of 24-363
	Helix total = -7.6
	Internal/bulge = 2.8  for closure of 25-362	Size = 2
		Stack = -2.4  for stack of 28-361
		Stack = -0.9  for stack of 29-360
		Stack = -0.9  for stack of 30-359
		Stack = -1.4  for stack of 31-358
	Helix total = -5.6
	Internal/bulge = -0.7  for closure of 32-357	Size = 2
		Stack = -1.4  for stack of 34-355
		Stack = -1.3  for stack of 35-354
		Stack = -1.4  for stack of 36-353
		Stack = -1.4  for stack of 37-352
		Stack = -2.5  for stack of 38-351
	Helix total = -8.0
	Internal/bulge = 4.9  for closure of 39-350	Size = 9
		Stack = -2.1  for stack of 43-343
		Stack = -1.1  for stack of 44-342
		Stack = -2.1  for stack of 45-341
		Stack = -3.4  for stack of 46-340
	Helix total = -8.7
	Multiloop = 4.1  for closure of 47-339
	Helix total = 0.0
	Internal/bulge = 2.0  for closure of 285-318	Size = 8
		Stack = -1.4  for stack of 290-313
		Stack = -0.9  for stack of 291-312
		Stack = -2.1  for stack of 292-311
		Stack = -3.3  for stack of 293-310
		Stack = -2.5  for stack of 294-309
	Helix total = -10.2
	Hairpin = 6.4  for closure of 295-308
		Stack = -1.4  for stack of 241-266
		Stack = -0.9  for stack of 242-265
		Stack = -0.9  for stack of 243-264
		Stack = -2.1  for stack of 244-263
		Stack = -3.3  for stack of 245-262
		Stack = -3.3  for stack of 246-261
		Stack = -2.5  for stack of 247-260
		Stack = -1.0  for stack of 248-259
	Helix total = -15.4
	Hairpin = 5.2  for closure of 249-258
		Stack = -2.1  for stack of 179-222
		Stack = -2.2  for stack of 180-221
		Stack = -2.1  for stack of 181-220
		Stack = -1.4  for stack of 182-219
		Stack = -3.4  for stack of 183-218
	Helix total = -11.2
	Internal/bulge = 4.1  for closure of 184-217	Size = 4
		Stack = -1.5  for stack of 185-212
		Stack = -3.3  for stack of 186-211
	Helix total = -4.8
	Internal/bulge = 1.0  for closure of 187-210	Size = 6
		Stack = -2.4  for stack of 191-206
		Stack = -1.1  for stack of 192-205
	Helix total = -3.5
	Hairpin = 5.0  for closure of 193-204
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 113-173	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 115-171	Size = 2
		Stack = -2.5  for stack of 117-169
		Stack = -2.1  for stack of 118-168
		Stack = -1.0  for stack of 119-167
	Helix total = -5.6
	Internal/bulge = 5.4  for closure of 120-166	Size = 15
		Stack = -2.4  for stack of 127-156
		Stack = -2.4  for stack of 128-155
		Stack = -0.9  for stack of 129-154
	Helix total = -5.7
	Internal/bulge = 0.7  for closure of 130-153	Size = 4
	Helix total = 0.0
	Internal/bulge = 2.4  for closure of 133-150	Size = 6
		Stack = -1.0  for stack of 137-146
		Stack = -2.1  for stack of 138-145
	Helix total = -3.1
	Hairpin = 4.5  for closure of 139-144
		Stack = -1.5  for stack of 56-83
		Stack = -1.4  for stack of 57-82
		Stack = -1.3  for stack of 58-81
		Stack = -0.6  for stack of 59-80
		Stack = -2.5  for stack of 60-79
		Stack = -2.1  for stack of 61-78
	Helix total = -9.4
	Hairpin = 6.6  for closure of 62-77


	Total energy = -55.4



