Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:67 49:66 50:65 51:64 153:187 154:186 155:185 156:184
	    157:183 203:234 204:233 205:232 206:231 207:230 208:229 251:289
	    252:288 253:287 254:286 255:284 256:283 257:282
	Energy of Broken Structure: -79.6
	Energy of Pseudo-Helices:   -41.0
	Pseudoknot Energy Penalty:  32.6
	Total Free Energy:          -88.0
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-349
		Stack = -1.5  for stack of 2-348
		Stack = -2.1  for stack of 3-347
		Stack = -3.4  for stack of 4-346
		Stack = -3.3  for stack of 5-345
		Stack = -2.4  for stack of 6-344
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-343
		Stack = -3.3  for stack of 326-342
		Stack = -3.3  for stack of 327-341
		Stack = -3.3  for stack of 328-340
		Stack = -3.3  for stack of 329-339
	Helix total = -13.2
	Hairpin = 4.4  for closure of 330-338
		Stack = -2.4  for stack of 20-322
		Stack = -3.4  for stack of 21-321
		Stack = -3.3  for stack of 22-320
		Stack = -1.4  for stack of 23-319
		Stack = -2.1  for stack of 24-318
		Stack = -2.5  for stack of 25-317
	Helix total = -15.1
	Internal/bulge = 5.5  for closure of 26-316	Size = 14
		Stack = -0.6  for stack of 35-309
		Stack = -1.0  for stack of 36-308
	Helix total = -1.6
	Internal/bulge = 1.2  for closure of 37-307	Size = 3
		Stack = -3.3  for stack of 39-304
	Helix total = -3.3
	Internal/bulge = 2.9  for closure of 40-303	Size = 7
		Stack = -2.1  for stack of 43-297
		Stack = -1.1  for stack of 44-296
		Stack = -2.1  for stack of 45-295
		Stack = -3.4  for stack of 46-294
	Helix total = -8.7
	Multiloop = 2.6  for closure of 47-293
		Stack = -2.5  for stack of 237-271
		Stack = -2.1  for stack of 238-270
		Stack = -2.4  for stack of 239-269
		Stack = -3.3  for stack of 240-268
	Helix total = -10.3
	Internal/bulge = 2.7  for closure of 241-267	Size = 12
		Stack = -3.3  for stack of 248-260
		Stack = -2.1  for stack of 249-259
	Helix total = -5.4
	Hairpin = 5.7  for closure of 250-258
		Stack = -3.4  for stack of 191-219
		Stack = -3.3  for stack of 192-218
		Stack = -2.4  for stack of 193-217
	Helix total = -9.1
	Internal/bulge = 1.9  for closure of 194-216	Size = 4
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 197-213	Size = 2
		Stack = -2.2  for stack of 199-211
		Stack = -1.3  for stack of 200-210
	Helix total = -3.5
	Hairpin = 5.8  for closure of 201-209
		Stack = -2.1  for stack of 137-173
		Stack = -2.1  for stack of 138-172
		Stack = -2.2  for stack of 139-171
		Stack = -2.4  for stack of 140-170
		Stack = -2.4  for stack of 141-169
	Helix total = -11.2
	Internal/bulge = 1.7  for closure of 142-168	Size = 7
		Stack = -3.3  for stack of 146-163
		Stack = -3.3  for stack of 147-162
	Helix total = -6.6
	Internal/bulge = 0.1  for closure of 148-161	Size = 4
	Helix total = 0.0
	Hairpin = 5.1  for closure of 151-158
		Stack = -2.1  for stack of 116-136
		Stack = -1.3  for stack of 117-135
		Stack = -2.1  for stack of 118-134
		Stack = -3.4  for stack of 119-133
		Stack = -2.1  for stack of 120-132
		Stack = -1.4  for stack of 121-131
		Stack = -3.4  for stack of 122-130
	Helix total = -15.8
	Hairpin = 3.6  for closure of 123-129
		Stack = -2.5  for stack of 55-82
		Stack = -1.0  for stack of 56-81
		Stack = -2.1  for stack of 57-80
		Stack = -3.4  for stack of 58-79
		Stack = -2.1  for stack of 59-78
		Stack = -2.1  for stack of 60-77
	Helix total = -13.2
	Hairpin = 5.6  for closure of 61-76


	Total energy = -79.6



