Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:68 50:67 51:66 52:65 53:64 152:184 153:183 154:182
	    155:181 156:180 157:179 199:234 201:232 202:231 203:230 204:229
	    205:228 206:227 252:290 253:289 255:287 256:286 257:285 258:284
	Energy of Broken Structure: -71.3
	Energy of Pseudo-Helices:   -44.4
	Pseudoknot Energy Penalty:  31.4
	Total Free Energy:          -84.3
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-350
		Stack = -1.5  for stack of 2-349
		Stack = -2.1  for stack of 3-348
		Stack = -3.3  for stack of 4-347
		Stack = -2.2  for stack of 5-346
		Stack = -2.1  for stack of 6-345
	Helix total = -14.5
	Multiloop = 5.1  for closure of 7-344
		Stack = -3.3  for stack of 327-343
		Stack = -3.4  for stack of 328-342
		Stack = -2.4  for stack of 329-341
		Stack = -3.3  for stack of 330-340
	Helix total = -12.4
	Hairpin = 4.4  for closure of 331-339
		Stack = -2.4  for stack of 20-323
		Stack = -1.5  for stack of 21-322
		Stack = -0.5  for stack of 22-321
		Stack = -2.1  for stack of 23-320
		Stack = -3.3  for stack of 24-319
		Stack = -2.5  for stack of 25-318
	Helix total = -12.3
	Internal/bulge = 2.3  for closure of 26-317	Size = 4
	Helix total = 0.0
	Internal/bulge = 2.2  for closure of 29-314	Size = 5
		Stack = -1.4  for stack of 33-311
		Stack = -2.4  for stack of 34-310
	Helix total = -3.8
	Internal/bulge = -2.2  for closure of 35-309	Size = 2
	Helix total = 0.0
	Internal/bulge = 0.4  for closure of 37-307	Size = 1 BP stack across bulge = -2.1
		Stack = 0.3  for stack of 39-306
		Stack = -2.1  for stack of 40-305
		Stack = -3.4  for stack of 41-304
		Stack = -1.4  for stack of 42-303
	Helix total = -6.6
	Internal/bulge = 3.7  for closure of 43-302	Size = 3
		Stack = -2.1  for stack of 44-298
		Stack = -1.1  for stack of 45-297
		Stack = -2.1  for stack of 46-296
		Stack = -3.4  for stack of 47-295
	Helix total = -8.7
	Multiloop = 2.1  for closure of 48-294
		Stack = -2.2  for stack of 235-273
		Stack = -1.3  for stack of 236-272
		Stack = -1.5  for stack of 237-271
		Stack = -3.3  for stack of 238-270
	Helix total = -8.3
	Internal/bulge = 1.1  for closure of 239-269	Size = 3
		Stack = -2.4  for stack of 242-267
	Helix total = -2.4
	Internal/bulge = 3.0  for closure of 243-266	Size = 4
		Stack = -3.4  for stack of 245-262
		Stack = -1.4  for stack of 246-261
		Stack = -2.5  for stack of 247-260
	Helix total = -7.3
	Hairpin = 5.1  for closure of 248-259
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 186-219	Size = 2
	Helix total = 0.0
	Internal/bulge = -0.4  for closure of 188-217	Size = 2
		Stack = -3.4  for stack of 190-215
		Stack = -2.1  for stack of 191-214
		Stack = -1.4  for stack of 192-213
		Stack = -3.3  for stack of 193-212
		Stack = -1.5  for stack of 194-211
		Stack = 1.3  for stack of 195-210
	Helix total = -10.4
	Internal/bulge = 1.2  for closure of 196-209	Size = 2
	Helix total = 0.0
	Hairpin = 5.0  for closure of 198-207
		Stack = -2.1  for stack of 136-171
		Stack = -2.4  for stack of 137-170
	Helix total = -4.5
	Internal/bulge = 1.2  for closure of 138-169	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 140-167	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 142-165	Size = 2
		Stack = -2.4  for stack of 144-163
		Stack = -3.4  for stack of 145-162
	Helix total = -5.8
	Internal/bulge = 0.5  for closure of 146-161	Size = 4
	Helix total = 0.0
	Hairpin = 4.4  for closure of 149-158
		Stack = -3.4  for stack of 112-135
		Stack = -2.1  for stack of 113-134
	Helix total = -5.5
	Internal/bulge = 0.7  for closure of 114-133	Size = 4
		Stack = -3.3  for stack of 117-130
		Stack = -3.4  for stack of 118-129
		Stack = -3.3  for stack of 119-128
	Helix total = -10.0
	Hairpin = 3.1  for closure of 120-127
		Stack = -2.5  for stack of 56-81
		Stack = -1.0  for stack of 57-80
		Stack = -2.1  for stack of 58-79
		Stack = -3.4  for stack of 59-78
		Stack = -2.1  for stack of 60-77
	Helix total = -11.1
	Hairpin = 6.8  for closure of 61-76


	Total energy = -71.3



