Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    56:83 57:82 58:81 59:80 183:217 184:216 185:215 186:214
	    187:213 188:212 222:248 224:246 225:245 229:241 230:240 284:322
	    285:321 286:320 287:319 288:318 289:317 291:315
	Energy of Broken Structure: -80.3
	Energy of Pseudo-Helices:   -38.3
	Pseudoknot Energy Penalty:  31.8
	Total Free Energy:          -86.8
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-382
		Stack = -1.5  for stack of 2-381
		Stack = -2.1  for stack of 3-380
		Stack = -2.4  for stack of 4-379
		Stack = -1.1  for stack of 5-378
		Stack = -2.1  for stack of 6-377
	Helix total = -12.5
	Multiloop = 5.0  for closure of 7-376
		Stack = -3.4  for stack of 359-375
		Stack = -2.4  for stack of 360-374
		Stack = -3.3  for stack of 361-373
		Stack = -3.3  for stack of 362-372
	Helix total = -12.4
	Hairpin = 4.4  for closure of 363-371
		Stack = -2.1  for stack of 19-355
		Stack = -0.6  for stack of 20-354
		Stack = -2.5  for stack of 21-353
		Stack = -2.4  for stack of 22-352
		Stack = -3.3  for stack of 23-351
	Helix total = -10.9
	Internal/bulge = 3.0  for closure of 24-350	Size = 9
		Stack = -2.4  for stack of 30-345
		Stack = -0.9  for stack of 31-344
		Stack = -2.1  for stack of 32-343
	Helix total = -5.4
	Internal/bulge = 1.2  for closure of 33-342	Size = 2
		Stack = -2.1  for stack of 35-340
		Stack = -3.3  for stack of 36-339
		Stack = -3.3  for stack of 37-338
	Helix total = -8.7
	Internal/bulge = 1.7  for closure of 38-337	Size = 10
		Stack = -2.4  for stack of 43-330
		Stack = -2.2  for stack of 44-329
		Stack = -2.1  for stack of 45-328
		Stack = -2.2  for stack of 46-327
	Helix total = -8.9
	Multiloop = 2.9  for closure of 47-326
		Stack = -3.4  for stack of 269-303
		Stack = -3.3  for stack of 270-302
		Stack = -3.3  for stack of 271-301
	Helix total = -10.0
	Internal/bulge = 2.8  for closure of 272-300	Size = 2
		Stack = -2.4  for stack of 275-299
		Stack = -3.3  for stack of 276-298
		Stack = -2.4  for stack of 277-297
		Stack = -2.1  for stack of 278-296
		Stack = -2.4  for stack of 279-295
	Helix total = -12.6
	Hairpin = 6.7  for closure of 280-294
		Stack = -1.4  for stack of 231-267
		Stack = -2.1  for stack of 232-266
		Stack = -2.2  for stack of 233-265
		Stack = -2.4  for stack of 234-264
		Stack = -2.1  for stack of 235-263
		Stack = -2.2  for stack of 236-262
	Helix total = -12.4
	Hairpin = 5.1  for closure of 237-261
		Stack = -2.1  for stack of 168-204
		Stack = -2.5  for stack of 169-203
		Stack = -1.5  for stack of 170-202
		Stack = -2.1  for stack of 171-201
		Stack = -2.1  for stack of 172-200
	Helix total = -10.3
	Internal/bulge = 2.3  for closure of 173-199	Size = 4
		Stack = -3.3  for stack of 175-195
		Stack = -2.4  for stack of 176-194
		Stack = -3.3  for stack of 177-193
		Stack = -3.3  for stack of 178-192
	Helix total = -12.3
	Hairpin = 4.1  for closure of 179-191
	Helix total = 0.0
	Internal/bulge = 5.6  for closure of 118-167	Size = 11
	Helix total = 0.0
	Internal/bulge = 0.9  for closure of 122-158	Size = 8
	Helix total = 0.0
	Internal/bulge = 0.5  for closure of 127-153	Size = 2
		Stack = -2.1  for stack of 129-151
	Helix total = -2.1
	Internal/bulge = 1.2  for closure of 130-150	Size = 2
		Stack = -3.4  for stack of 132-148
		Stack = -2.1  for stack of 133-147
		Stack = -2.1  for stack of 134-146
		Stack = -3.4  for stack of 135-145
	Helix total = -11.0
	Hairpin = 5.0  for closure of 136-144
		Stack = -2.4  for stack of 48-69
		Stack = -2.4  for stack of 49-68
		Stack = -2.1  for stack of 50-67
		Stack = -1.5  for stack of 51-66
	Helix total = -8.4
	Hairpin = 6.9  for closure of 52-65


	Total energy = -80.3



