Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    55:75 56:74 57:73 148:185 149:184 150:183 151:182 152:181
	    153:180 202:232 203:231 204:230 205:229 206:228 250:290 251:289
	    252:288 253:287 254:286 255:285 256:284
	Energy of Broken Structure: -60.2
	Energy of Pseudo-Helices:   -35.8
	Pseudoknot Energy Penalty:  32.2
	Total Free Energy:          -63.8
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-351
		Stack = -1.5  for stack of 2-350
		Stack = -2.1  for stack of 3-349
		Stack = -2.4  for stack of 4-348
		Stack = -2.2  for stack of 5-347
		Stack = -2.4  for stack of 6-346
	Helix total = -13.9
	Multiloop = 5.1  for closure of 7-345
		Stack = -2.2  for stack of 328-344
		Stack = -2.1  for stack of 329-343
		Stack = -3.3  for stack of 330-342
		Stack = -3.3  for stack of 331-341
	Helix total = -10.9
	Hairpin = 4.4  for closure of 332-340
		Stack = -2.1  for stack of 20-324
		Stack = -0.6  for stack of 21-323
		Stack = -0.5  for stack of 22-322
		Stack = -0.5  for stack of 23-321
		Stack = -1.3  for stack of 24-320
		Stack = -1.1  for stack of 25-319
		Stack = -1.3  for stack of 26-318
	Helix total = -7.4
	Internal/bulge = 1.9  for closure of 27-317	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.0  for closure of 29-315	Size = 3
	Helix total = 0.0
	Internal/bulge = 1.0  for closure of 32-313	Size = 2
		Stack = -2.5  for stack of 34-311
		Stack = -2.1  for stack of 35-310
		Stack = -0.9  for stack of 36-309
		Stack = -1.3  for stack of 37-308
		Stack = -0.6  for stack of 38-307
		Stack = -2.1  for stack of 39-306
		Stack = -2.5  for stack of 40-305
		Stack = -0.6  for stack of 41-304
	Helix total = -12.6
	Internal/bulge = 4.5  for closure of 42-303	Size = 5
		Stack = -2.4  for stack of 44-298
		Stack = -2.4  for stack of 45-297
		Stack = -2.1  for stack of 46-296
		Stack = -2.2  for stack of 47-295
	Helix total = -9.1
	Multiloop = 3.8  for closure of 48-294
		Stack = -3.4  for stack of 235-271
	Helix total = -3.4
	Internal/bulge = 1.1  for closure of 236-270	Size = 1 BP stack across bulge = -2.1
		Stack = -0.9  for stack of 237-268
	Helix total = -0.9
	Internal/bulge = 2.4  for closure of 238-267	Size = 1 BP stack across bulge = -1.4
		Stack = -0.6  for stack of 240-266
	Helix total = -0.6
	Internal/bulge = 2.1  for closure of 241-265	Size = 7
		Stack = -2.1  for stack of 245-260
		Stack = -3.4  for stack of 246-259
		Stack = -3.3  for stack of 247-258
	Helix total = -8.8
	Hairpin = 4.5  for closure of 248-257
		Stack = -3.3  for stack of 190-216
	Helix total = -3.3
	Internal/bulge = 1.0  for closure of 191-215	Size = 6
		Stack = -2.2  for stack of 195-211
		Stack = -1.3  for stack of 196-210
		Stack = -1.5  for stack of 197-209
	Helix total = -5.0
	Hairpin = 4.1  for closure of 198-208
		Stack = -2.2  for stack of 133-170
		Stack = -1.3  for stack of 134-169
		Stack = -1.5  for stack of 135-168
		Stack = -3.3  for stack of 136-167
		Stack = -2.1  for stack of 137-166
	Helix total = -10.4
	Internal/bulge = 3.3  for closure of 138-165	Size = 2
		Stack = -3.3  for stack of 139-162
		Stack = -3.3  for stack of 140-161
		Stack = -2.1  for stack of 141-160
	Helix total = -8.7
	Internal/bulge = 1.4  for closure of 142-159	Size = 1 BP stack across bulge = -2.4
		Stack = -3.3  for stack of 143-157
		Stack = -2.1  for stack of 144-156
		Stack = -1.4  for stack of 145-155
	Helix total = -6.8
	Hairpin = 6.0  for closure of 146-154
		Stack = -0.6  for stack of 109-132
		Stack = -0.9  for stack of 110-131
	Helix total = -1.5
	Internal/bulge = 1.9  for closure of 111-130	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 113-128	Size = 2
		Stack = -2.1  for stack of 115-126
		Stack = -3.4  for stack of 116-125
	Helix total = -5.5
	Hairpin = 3.3  for closure of 117-124
		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 = -3.3  for stack of 52-62
	Helix total = -10.2
	Hairpin = 3.8  for closure of 53-61


	Total energy = -60.2



