Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    56:81 57:80 59:78 60:77 61:76 152:184 153:183 154:182
	    155:181 156:180 157:179 159:177 200:234 202:232 203:231 204:230
	    205:229 206:228 207:227 253:290 254:289 255:288 256:286 257:285
	    258:284
	Energy of Broken Structure: -65.4
	Energy of Pseudo-Helices:   -42.4
	Pseudoknot Energy Penalty:  31.8
	Total Free Energy:          -76.0
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 = -3.3  for stack of 4-348
		Stack = -2.2  for stack of 5-347
		Stack = -2.1  for stack of 6-346
	Helix total = -14.5
	Multiloop = 5.1  for closure of 7-345
		Stack = -3.3  for stack of 328-344
		Stack = -3.4  for stack of 329-343
		Stack = -2.4  for stack of 330-342
		Stack = -3.3  for stack of 331-341
	Helix total = -12.4
	Hairpin = 4.4  for closure of 332-340
		Stack = -2.4  for stack of 20-324
		Stack = -1.5  for stack of 21-323
		Stack = -0.5  for stack of 22-322
		Stack = -0.5  for stack of 23-321
		Stack = -2.1  for stack of 24-320
		Stack = -2.2  for stack of 25-319
	Helix total = -9.2
	Internal/bulge = 3.6  for closure of 26-318	Size = 11
		Stack = -1.1  for stack of 33-312
		Stack = -2.4  for stack of 34-311
	Helix total = -3.5
	Internal/bulge = 0.5  for closure of 35-310	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.3  for closure of 37-308	Size = 1 BP stack across bulge = -2.1
		Stack = -1.4  for stack of 39-307
		Stack = -3.3  for stack of 40-306
		Stack = -2.5  for stack of 41-305
	Helix total = -7.2
	Internal/bulge = 4.5  for closure of 42-304	Size = 5
		Stack = -2.1  for stack of 44-299
		Stack = -1.1  for stack of 45-298
		Stack = -2.1  for stack of 46-297
		Stack = -3.4  for stack of 47-296
	Helix total = -8.7
	Multiloop = 1.8  for closure of 48-295
		Stack = -2.2  for stack of 235-273
		Stack = -1.3  for stack of 236-272
	Helix total = -3.5
	Internal/bulge = 1.2  for closure of 237-271	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.1  for closure of 239-269	Size = 3
		Stack = -3.3  for stack of 242-267
	Helix total = -3.3
	Internal/bulge = 2.3  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
		Stack = -2.5  for stack of 188-218
		Stack = -2.1  for stack of 189-217
		Stack = 0.3  for stack of 190-216
		Stack = -1.3  for stack of 191-215
		Stack = -2.1  for stack of 192-214
	Helix total = -7.7
	Internal/bulge = 2.3  for closure of 193-213	Size = 3
		Stack = -2.2  for stack of 196-211
		Stack = -2.1  for stack of 197-210
		Stack = -3.3  for stack of 198-209
	Helix total = -7.6
	Hairpin = 4.8  for closure of 199-208
		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 = 4.2  for closure of 140-167	Size = 3
		Stack = -1.4  for stack of 144-166
	Helix total = -1.4
	Internal/bulge = 1.3  for closure of 145-165	Size = 1 BP stack across bulge = -2.5
		Stack = -0.6  for stack of 147-164
		Stack = -2.1  for stack of 148-163
		Stack = -2.5  for stack of 149-162
		Stack = -1.4  for stack of 150-161
	Helix total = -6.6
	Hairpin = 3.9  for closure of 151-160
		Stack = -3.4  for stack of 112-135
		Stack = -2.1  for stack of 113-134
	Helix total = -5.5
	Internal/bulge = 1.5  for closure of 114-133	Size = 4
		Stack = -2.1  for stack of 117-130
		Stack = -3.4  for stack of 118-129
		Stack = -3.3  for stack of 119-128
	Helix total = -8.8
	Hairpin = 3.1  for closure of 120-127
		Stack = -2.4  for stack of 49-68
		Stack = -2.4  for stack of 50-67
		Stack = -2.1  for stack of 51-66
		Stack = -3.3  for stack of 52-65
	Helix total = -10.2
	Hairpin = 5.0  for closure of 53-64


	Total energy = -65.4



