Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    47:65 48:64 49:63 50:62 51:61 150:185 151:184 152:183
	    153:182 154:181 155:180 156:179 202:236 203:235 204:234 205:233
	    206:232 207:231 208:230 255:292 256:291 257:290 258:289 259:288
	    260:287 261:286
	Energy of Broken Structure: -131.6
	Energy of Pseudo-Helices:   -58.0
	Pseudoknot Energy Penalty:  41.8
	Total Free Energy:          -147.8
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-353
		Stack = -1.5  for stack of 2-352
		Stack = -2.1  for stack of 3-351
		Stack = -3.3  for stack of 4-350
		Stack = -3.4  for stack of 5-349
		Stack = -2.4  for stack of 6-348
	Helix total = -16.0
	Multiloop = 5.0  for closure of 7-347
		Stack = -3.3  for stack of 330-346
		Stack = -3.3  for stack of 331-345
		Stack = -3.3  for stack of 332-344
		Stack = -3.3  for stack of 333-343
	Helix total = -13.2
	Hairpin = 4.4  for closure of 334-342
		Stack = -2.4  for stack of 19-326
		Stack = -1.5  for stack of 20-325
		Stack = -0.5  for stack of 21-324
		Stack = -2.1  for stack of 22-323
		Stack = -2.4  for stack of 23-322
		Stack = -1.1  for stack of 24-321
		Stack = -2.1  for stack of 25-320
		Stack = -3.3  for stack of 26-319
		Stack = -2.4  for stack of 27-318
		Stack = -2.1  for stack of 28-317
	Helix total = -19.9
	Internal/bulge = 0.5  for closure of 29-316	Size = 2
		Stack = -3.3  for stack of 31-314
		Stack = -3.3  for stack of 32-313
		Stack = -3.3  for stack of 33-312
		Stack = -2.1  for stack of 34-311
		Stack = -2.1  for stack of 35-310
		Stack = -3.3  for stack of 36-309
		Stack = -3.3  for stack of 37-308
	Helix total = -20.7
	Internal/bulge = 2.4  for closure of 38-307	Size = 9
		Stack = -2.4  for stack of 42-300
		Stack = -2.4  for stack of 43-299
		Stack = -2.1  for stack of 44-298
		Stack = -3.4  for stack of 45-297
	Helix total = -10.3
	Multiloop = 2.2  for closure of 46-296
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 237-277	Size = 2
		Stack = -1.4  for stack of 239-275
		Stack = -3.3  for stack of 240-274
		Stack = -3.3  for stack of 241-273
		Stack = -2.4  for stack of 242-272
		Stack = -0.9  for stack of 243-271
		Stack = -2.1  for stack of 244-270
	Helix total = -13.4
	Internal/bulge = 1.2  for closure of 245-269	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 247-267	Size = 2
	Helix total = 0.0
	Internal/bulge = 0.5  for closure of 249-265	Size = 2
	Helix total = 0.0
	Hairpin = 5.6  for closure of 251-263
		Stack = -3.3  for stack of 188-220
		Stack = -2.4  for stack of 189-219
		Stack = -2.4  for stack of 190-218
		Stack = -1.1  for stack of 191-217
		Stack = -2.4  for stack of 192-216
		Stack = -2.1  for stack of 193-215
		Stack = -1.4  for stack of 194-214
		Stack = -3.3  for stack of 195-213
		Stack = -3.3  for stack of 196-212
		Stack = -3.4  for stack of 197-211
		Stack = -2.1  for stack of 198-210
	Helix total = -27.2
	Hairpin = 6.3  for closure of 199-209
		Stack = -2.4  for stack of 134-171
		Stack = -2.5  for stack of 135-170
		Stack = -1.5  for stack of 136-169
		Stack = -3.3  for stack of 137-168
	Helix total = -9.7
	Internal/bulge = 1.7  for closure of 138-167	Size = 1 BP stack across bulge = -2.1
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 139-165	Size = 2
		Stack = -2.4  for stack of 141-163
		Stack = -3.3  for stack of 142-162
		Stack = -2.4  for stack of 143-161
		Stack = -3.3  for stack of 144-160
		Stack = -2.4  for stack of 145-159
		Stack = -2.1  for stack of 146-158
	Helix total = -15.9
	Hairpin = 5.3  for closure of 147-157
		Stack = -3.4  for stack of 113-133
		Stack = -3.3  for stack of 114-132
		Stack = -2.4  for stack of 115-131
		Stack = -3.4  for stack of 116-130
		Stack = -3.3  for stack of 117-129
		Stack = -2.1  for stack of 118-128
		Stack = -1.3  for stack of 119-127
	Helix total = -19.2
	Hairpin = 5.4  for closure of 120-126
		Stack = -3.3  for stack of 54-78
		Stack = -3.3  for stack of 55-77
		Stack = -2.1  for stack of 56-76
		Stack = -2.2  for stack of 57-75
		Stack = -3.3  for stack of 58-74
		Stack = -2.1  for stack of 59-73
	Helix total = -16.3
	Hairpin = 6.4  for closure of 60-72


	Total energy = -131.6



