Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:67 49:66 50:65 51:64 52:63 197:231 198:230 199:229
	    200:228 201:227 247:278 248:277 249:276 250:275 251:274 252:273
	    295:333 296:332 297:331 299:328 300:327 301:326
	Energy of Broken Structure: -82.5
	Energy of Pseudo-Helices:   -36.4
	Pseudoknot Energy Penalty:  32.7
	Total Free Energy:          -86.2
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-393
		Stack = -1.5  for stack of 2-392
		Stack = -2.1  for stack of 3-391
		Stack = -3.4  for stack of 4-390
		Stack = -3.3  for stack of 5-389
		Stack = -2.4  for stack of 6-388
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-387
		Stack = -3.3  for stack of 370-386
		Stack = -3.3  for stack of 371-385
		Stack = -3.3  for stack of 372-384
		Stack = -3.3  for stack of 373-383
	Helix total = -13.2
	Hairpin = 4.4  for closure of 374-382
		Stack = -2.4  for stack of 20-366
		Stack = -3.4  for stack of 21-365
		Stack = -3.3  for stack of 22-364
		Stack = -1.4  for stack of 23-363
		Stack = -2.1  for stack of 24-362
		Stack = -2.2  for stack of 25-361
	Helix total = -14.8
	Internal/bulge = 5.5  for closure of 26-360	Size = 14
		Stack = -0.6  for stack of 35-353
	Helix total = -0.6
	Internal/bulge = 2.2  for closure of 36-352	Size = 5
		Stack = -3.3  for stack of 39-348
		Stack = -2.2  for stack of 40-347
		Stack = -1.0  for stack of 41-346
	Helix total = -6.5
	Internal/bulge = 3.7  for closure of 42-345	Size = 3
		Stack = -2.1  for stack of 43-341
		Stack = -1.1  for stack of 44-340
		Stack = -2.1  for stack of 45-339
		Stack = -3.4  for stack of 46-338
	Helix total = -8.7
	Multiloop = 1.9  for closure of 47-337
		Stack = -2.5  for stack of 281-315
		Stack = -3.3  for stack of 282-314
		Stack = -3.3  for stack of 283-313
	Helix total = -9.1
	Internal/bulge = 2.2  for closure of 284-312	Size = 5
	Helix total = 0.0
	Internal/bulge = 3.4  for closure of 288-309	Size = 7
		Stack = -3.3  for stack of 292-304
		Stack = -2.1  for stack of 293-303
	Helix total = -5.4
	Hairpin = 5.7  for closure of 294-302
		Stack = -3.4  for stack of 235-263
		Stack = -3.3  for stack of 236-262
		Stack = -2.4  for stack of 237-261
		Stack = -2.5  for stack of 238-260
	Helix total = -11.6
	Internal/bulge = 0.7  for closure of 239-259	Size = 6
		Stack = -2.2  for stack of 243-255
	Helix total = -2.2
	Hairpin = 5.9  for closure of 244-254
		Stack = -2.1  for stack of 181-217
		Stack = -0.9  for stack of 182-216
		Stack = -1.1  for stack of 183-215
		Stack = -2.4  for stack of 184-214
		Stack = -2.1  for stack of 185-213
		Stack = -2.2  for stack of 186-212
	Helix total = -10.8
	Internal/bulge = 2.6  for closure of 187-211	Size = 5
		Stack = -3.3  for stack of 190-207
		Stack = -3.3  for stack of 191-206
	Helix total = -6.6
	Internal/bulge = 0.1  for closure of 192-205	Size = 4
	Helix total = 0.0
	Hairpin = 5.1  for closure of 195-202
		Stack = -2.1  for stack of 162-180
		Stack = -2.1  for stack of 163-179
		Stack = -3.3  for stack of 164-178
	Helix total = -7.5
	Internal/bulge = 1.4  for closure of 165-177	Size = 1 BP stack across bulge = -2.4
		Stack = -2.2  for stack of 167-176
		Stack = -3.3  for stack of 168-175
	Helix total = -5.5
	Hairpin = 3.7  for closure of 169-174
		Stack = -2.1  for stack of 119-160
	Helix total = -2.1
	Internal/bulge = 1.7  for closure of 120-159	Size = 12
		Stack = -3.4  for stack of 127-152
		Stack = -2.1  for stack of 128-151
	Helix total = -5.5
	Internal/bulge = 2.7  for closure of 129-150	Size = 6
		Stack = -3.4  for stack of 133-146
		Stack = -2.1  for stack of 134-145
		Stack = -2.1  for stack of 135-144
		Stack = -3.4  for stack of 136-143
	Helix total = -11.0
	Hairpin = 3.3  for closure of 137-142
		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 = -82.5



