Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:67 49:66 50:65 51:64 52:63 199:233 200:232 201:231
	    202:230 203:229 249:280 250:279 251:278 252:277 253:276 254:275
	    297:335 298:334 299:333 301:330 302:329 303:328
	Energy of Broken Structure: -73.2
	Energy of Pseudo-Helices:   -39.6
	Pseudoknot Energy Penalty:  32.3
	Total Free Energy:          -80.5
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-395
		Stack = -1.5  for stack of 2-394
		Stack = -2.1  for stack of 3-393
		Stack = -3.4  for stack of 4-392
		Stack = -3.3  for stack of 5-391
		Stack = -2.4  for stack of 6-390
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-389
		Stack = -3.3  for stack of 372-388
		Stack = -3.3  for stack of 373-387
		Stack = -3.3  for stack of 374-386
		Stack = -3.3  for stack of 375-385
	Helix total = -13.2
	Hairpin = 4.4  for closure of 376-384
		Stack = -2.4  for stack of 20-368
		Stack = -3.4  for stack of 21-367
		Stack = -3.3  for stack of 22-366
		Stack = -1.4  for stack of 23-365
		Stack = -2.1  for stack of 24-364
		Stack = -2.2  for stack of 25-363
		Stack = -1.3  for stack of 26-362
	Helix total = -16.1
	Internal/bulge = 4.3  for closure of 27-361	Size = 12
	Helix total = 0.0
	Internal/bulge = 2.4  for closure of 35-355	Size = 7
		Stack = -3.3  for stack of 39-350
		Stack = -2.2  for stack of 40-349
		Stack = -1.0  for stack of 41-348
	Helix total = -6.5
	Internal/bulge = 3.7  for closure of 42-347	Size = 3
		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 = 2.2  for closure of 47-339
		Stack = -1.1  for stack of 283-317
		Stack = -2.4  for stack of 284-316
		Stack = -3.3  for stack of 285-315
	Helix total = -6.8
	Internal/bulge = 2.2  for closure of 286-314	Size = 5
	Helix total = 0.0
	Internal/bulge = 3.4  for closure of 290-311	Size = 7
		Stack = -3.3  for stack of 294-306
		Stack = -2.1  for stack of 295-305
	Helix total = -5.4
	Hairpin = 5.7  for closure of 296-304
		Stack = -2.2  for stack of 237-265
		Stack = -2.4  for stack of 238-264
		Stack = -1.4  for stack of 239-263
		Stack = -2.5  for stack of 240-262
	Helix total = -8.5
	Internal/bulge = 1.2  for closure of 241-261	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 243-259	Size = 2
		Stack = -3.4  for stack of 245-257
	Helix total = -3.4
	Hairpin = 5.0  for closure of 246-256
		Stack = -2.1  for stack of 183-219
		Stack = -0.9  for stack of 184-218
		Stack = -1.1  for stack of 185-217
		Stack = -2.4  for stack of 186-216
		Stack = -2.1  for stack of 187-215
	Helix total = -8.6
	Internal/bulge = 2.4  for closure of 188-214	Size = 7
		Stack = -3.3  for stack of 192-209
		Stack = -3.3  for stack of 193-208
	Helix total = -6.6
	Internal/bulge = 0.1  for closure of 194-207	Size = 4
	Helix total = 0.0
	Hairpin = 5.1  for closure of 197-204
		Stack = -2.1  for stack of 164-182
		Stack = -2.1  for stack of 165-181
		Stack = -3.3  for stack of 166-180
	Helix total = -7.5
	Internal/bulge = 1.4  for closure of 167-179	Size = 1 BP stack across bulge = -2.4
		Stack = -2.1  for stack of 169-178
		Stack = -3.4  for stack of 170-177
	Helix total = -5.5
	Hairpin = 3.7  for closure of 171-176
		Stack = -0.5  for stack of 114-163
	Helix total = -0.5
	Internal/bulge = 3.4  for closure of 115-162	Size = 6
	Helix total = 0.0
	Internal/bulge = 0.9  for closure of 119-158	Size = 4
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 122-155	Size = 4
		Stack = -2.1  for stack of 125-152
		Stack = -0.9  for stack of 126-151
		Stack = -2.1  for stack of 127-150
	Helix total = -5.1
	Internal/bulge = 1.2  for closure of 128-149	Size = 4
		Stack = -1.5  for stack of 131-146
		Stack = -2.5  for stack of 132-145
		Stack = -2.1  for stack of 133-144
		Stack = -2.1  for stack of 134-143
		Stack = -3.4  for stack of 135-142
	Helix total = -11.6
	Hairpin = 3.3  for closure of 136-141
		Stack = -2.5  for stack of 55-82
		Stack = -1.0  for stack of 56-81
		Stack = -0.9  for stack of 57-80
		Stack = -2.2  for stack of 58-79
		Stack = -2.1  for stack of 59-78
		Stack = -2.1  for stack of 60-77
	Helix total = -10.8
	Hairpin = 5.8  for closure of 61-76


	Total energy = -73.2



