Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    47:64 48:63 49:62 50:61 51:60 158:190 159:189 160:188
	    161:187 162:186 163:185 207:238 208:237 209:236 210:235 211:234
	    256:294 257:293 258:292 259:291 260:290 261:289 263:287
	Energy of Broken Structure: -75.4
	Energy of Pseudo-Helices:   -48.0
	Pseudoknot Energy Penalty:  36.2
	Total Free Energy:          -87.2
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-355
		Stack = -1.5  for stack of 2-354
		Stack = -2.1  for stack of 3-353
		Stack = -3.3  for stack of 4-352
		Stack = -3.4  for stack of 5-351
		Stack = -2.4  for stack of 6-350
	Helix total = -16.0
	Multiloop = 5.0  for closure of 7-349
		Stack = -3.4  for stack of 332-348
		Stack = -2.4  for stack of 333-347
		Stack = -3.3  for stack of 334-346
		Stack = -3.3  for stack of 335-345
	Helix total = -12.4
	Hairpin = 4.4  for closure of 336-344
		Stack = -2.4  for stack of 19-328
		Stack = -3.3  for stack of 20-327
		Stack = -1.5  for stack of 21-326
		Stack = -0.5  for stack of 22-325
		Stack = -1.3  for stack of 23-324
		Stack = -1.4  for stack of 24-323
		Stack = 0.3  for stack of 25-322
	Helix total = -10.1
	Internal/bulge = 2.7  for closure of 26-321	Size = 9
		Stack = -3.4  for stack of 32-316
	Helix total = -3.4
	Internal/bulge = 1.3  for closure of 33-315	Size = 1 BP stack across bulge = -2.1
		Stack = -0.9  for stack of 34-313
		Stack = -2.1  for stack of 35-312
		Stack = -1.5  for stack of 36-311
		Stack = -1.3  for stack of 37-310
		Stack = -2.2  for stack of 38-309
	Helix total = -8.0
	Internal/bulge = 0.5  for closure of 39-308	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.2  for closure of 41-306	Size = 3
		Stack = -2.1  for stack of 42-302
		Stack = -1.1  for stack of 43-301
		Stack = -2.1  for stack of 44-300
		Stack = -3.4  for stack of 45-299
	Helix total = -8.7
	Multiloop = 5.0  for closure of 46-298
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 239-279	Size = 2
		Stack = -2.5  for stack of 241-277
		Stack = -2.1  for stack of 242-276
		Stack = 0.3  for stack of 243-275
		Stack = -1.3  for stack of 244-274
		Stack = -1.4  for stack of 245-273
		Stack = -1.4  for stack of 246-272
		Stack = -2.4  for stack of 247-271
		Stack = -2.2  for stack of 248-270
		Stack = -2.4  for stack of 249-269
		Stack = -3.3  for stack of 250-268
		Stack = -3.3  for stack of 251-267
	Helix total = -22.0
	Hairpin = 5.2  for closure of 252-266
		Stack = -2.5  for stack of 194-223
		Stack = -3.3  for stack of 195-222
	Helix total = -5.8
	Internal/bulge = 0.6  for closure of 196-221	Size = 4
		Stack = -2.1  for stack of 199-218
		Stack = -3.3  for stack of 200-217
		Stack = -2.4  for stack of 201-216
		Stack = -0.9  for stack of 202-215
		Stack = -2.2  for stack of 203-214
	Helix total = -10.9
	Hairpin = 4.1  for closure of 204-213
		Stack = -2.4  for stack of 140-177
		Stack = -3.4  for stack of 141-176
		Stack = -2.1  for stack of 142-175
	Helix total = -7.9
	Internal/bulge = 3.7  for closure of 143-174	Size = 3
		Stack = -2.4  for stack of 146-172
		Stack = -2.4  for stack of 147-171
		Stack = -3.3  for stack of 148-170
	Helix total = -8.1
	Internal/bulge = 2.2  for closure of 149-169	Size = 3
		Stack = -0.5  for stack of 152-167
		Stack = -0.5  for stack of 153-166
		Stack = -1.4  for stack of 154-165
	Helix total = -2.4
	Hairpin = 4.8  for closure of 155-164
	Helix total = 0.0
	Internal/bulge = 3.4  for closure of 109-139	Size = 6
		Stack = 0.3  for stack of 113-135
		Stack = -2.5  for stack of 114-134
		Stack = -2.1  for stack of 115-133
		Stack = -0.9  for stack of 116-132
		Stack = -1.3  for stack of 117-131
		Stack = -0.9  for stack of 118-130
		Stack = -1.1  for stack of 119-129
	Helix total = -8.5
	Hairpin = 5.8  for closure of 120-128
		Stack = -3.3  for stack of 53-77
		Stack = -3.3  for stack of 54-76
		Stack = -2.1  for stack of 55-75
		Stack = -0.6  for stack of 56-74
		Stack = -0.5  for stack of 57-73
	Helix total = -9.8
	Hairpin = 6.5  for closure of 58-72


	Total energy = -75.4



