Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    54:78 55:77 56:76 57:75 58:74 149:218 150:217 151:216
	    152:215 153:214 154:213 155:212 232:265 233:264 234:263 235:262
	    237:260 238:259 239:258 268:303 271:300 272:299 279:292 280:291
	    281:290
	Energy of Broken Structure: -102.9
	Energy of Pseudo-Helices:   -40.6
	Pseudoknot Energy Penalty:  35.9
	Total Free Energy:          -107.6
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-383
		Stack = -1.5  for stack of 2-382
		Stack = -2.1  for stack of 3-381
		Stack = -3.4  for stack of 4-380
		Stack = -2.1  for stack of 5-379
		Stack = -2.1  for stack of 6-378
	Helix total = -14.5
	Multiloop = 5.1  for closure of 7-377
		Stack = -3.3  for stack of 360-376
		Stack = -3.3  for stack of 361-375
		Stack = -3.3  for stack of 362-374
		Stack = -3.3  for stack of 363-373
	Helix total = -13.2
	Hairpin = 4.4  for closure of 364-372
		Stack = -2.4  for stack of 20-356
		Stack = -3.4  for stack of 21-355
		Stack = -1.4  for stack of 22-354
		Stack = -0.5  for stack of 23-353
		Stack = -2.1  for stack of 24-352
		Stack = -2.5  for stack of 25-351
	Helix total = -12.3
	Internal/bulge = 2.5  for closure of 26-350	Size = 13
		Stack = -2.4  for stack of 34-343
		Stack = -3.4  for stack of 35-342
	Helix total = -5.8
	Internal/bulge = 1.4  for closure of 36-341	Size = 1 BP stack across bulge = -2.4
		Stack = -2.2  for stack of 38-340
		Stack = -1.0  for stack of 39-339
		Stack = -2.1  for stack of 40-338
	Helix total = -5.3
	Internal/bulge = 2.9  for closure of 41-337	Size = 7
		Stack = -2.1  for stack of 44-331
		Stack = -1.1  for stack of 45-330
		Stack = -2.1  for stack of 46-329
		Stack = -3.4  for stack of 47-328
	Helix total = -8.7
	Multiloop = 0.7  for closure of 48-327
		Stack = -3.4  for stack of 283-323
		Stack = -2.1  for stack of 284-322
		Stack = -1.4  for stack of 285-321
	Helix total = -6.9
	Internal/bulge = 0.4  for closure of 286-320	Size = 1 BP stack across bulge = -3.4
		Stack = -2.1  for stack of 287-318
		Stack = -2.1  for stack of 288-317
	Helix total = -4.2
	Hairpin = 7.0  for closure of 289-316
		Stack = -3.4  for stack of 221-249
		Stack = -3.3  for stack of 222-248
		Stack = -2.1  for stack of 223-247
		Stack = -2.1  for stack of 224-246
		Stack = -1.5  for stack of 225-245
		Stack = -1.4  for stack of 226-244
		Stack = -1.3  for stack of 227-243
		Stack = -2.2  for stack of 228-242
		Stack = -3.3  for stack of 229-241
	Helix total = -20.6
	Hairpin = 4.9  for closure of 230-240
		Stack = -3.3  for stack of 135-204
		Stack = -3.3  for stack of 136-203
		Stack = -2.1  for stack of 137-202
		Stack = -1.3  for stack of 138-201
		Stack = -2.2  for stack of 139-200
		Stack = -2.1  for stack of 140-199
	Helix total = -14.3
	Multiloop = 4.8  for closure of 141-198
		Stack = -3.4  for stack of 162-197
	Helix total = -3.4
	Internal/bulge = 0.2  for closure of 163-196	Size = 4
		Stack = -3.3  for stack of 166-193
		Stack = -1.5  for stack of 167-192
		Stack = -2.1  for stack of 168-191
		Stack = -2.5  for stack of 169-190
	Helix total = -9.4
	Internal/bulge = 1.9  for closure of 170-189	Size = 2
		Stack = -0.9  for stack of 172-187
		Stack = -1.3  for stack of 173-186
		Stack = -1.0  for stack of 174-185
		Stack = -0.6  for stack of 175-184
		Stack = -2.5  for stack of 176-183
	Helix total = -6.3
	Hairpin = 3.3  for closure of 177-182
		Stack = -2.1  for stack of 143-160
		Stack = -2.1  for stack of 144-159
		Stack = -3.4  for stack of 145-158
	Helix total = -7.6
	Hairpin = 5.1  for closure of 146-157
		Stack = -2.1  for stack of 112-134
		Stack = -2.4  for stack of 113-133
		Stack = -1.4  for stack of 114-132
		Stack = -2.5  for stack of 115-131
		Stack = -2.1  for stack of 116-130
		Stack = -2.1  for stack of 117-129
	Helix total = -12.6
	Hairpin = 5.7  for closure of 118-128
		Stack = -2.4  for stack of 49-65
		Stack = -2.4  for stack of 50-64
		Stack = -2.1  for stack of 51-63
		Stack = -3.4  for stack of 52-62
	Helix total = -10.3
	Hairpin = 3.9  for closure of 53-61


	Total energy = -102.9



