Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:67 50:66 51:65 52:64 53:63 152:185 153:184 154:183
	    155:182 156:181 157:180 202:230 203:229 204:228 205:227 206:226
	    249:288 250:287 251:286 252:285 253:283 254:282 255:281
	Energy of Broken Structure: -45.3
	Energy of Pseudo-Helices:   -41.7
	Pseudoknot Energy Penalty:  39.7
	Total Free Energy:          -47.3
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-348
		Stack = -1.5  for stack of 2-347
		Stack = -2.1  for stack of 3-346
		Stack = -3.3  for stack of 4-345
		Stack = -3.4  for stack of 5-344
		Stack = -2.4  for stack of 6-343
	Helix total = -16.0
	Multiloop = 5.2  for closure of 7-342
		Stack = -3.3  for stack of 325-341
		Stack = -3.3  for stack of 326-340
		Stack = -3.3  for stack of 327-339
		Stack = -3.3  for stack of 328-338
	Helix total = -13.2
	Hairpin = 4.4  for closure of 329-337
		Stack = -2.4  for stack of 21-321
	Helix total = -2.4
	Internal/bulge = -2.2  for closure of 22-320	Size = 2
		Stack = -1.5  for stack of 24-318
		Stack = -1.3  for stack of 25-317
		Stack = -1.1  for stack of 26-316
		Stack = -1.3  for stack of 27-315
	Helix total = -5.2
	Internal/bulge = 3.4  for closure of 28-314	Size = 9
		Stack = -2.5  for stack of 34-309
		Stack = -2.1  for stack of 35-308
	Helix total = -4.6
	Internal/bulge = 2.7  for closure of 36-307	Size = 6
		Stack = -3.3  for stack of 40-303
		Stack = -2.2  for stack of 41-302
		Stack = -1.0  for stack of 42-301
	Helix total = -6.5
	Internal/bulge = 3.7  for closure of 43-300	Size = 3
		Stack = -2.1  for stack of 44-296
		Stack = -1.1  for stack of 45-295
		Stack = -2.1  for stack of 46-294
		Stack = -2.2  for stack of 47-293
	Helix total = -7.5
	Multiloop = 8.2  for closure of 48-292
		Stack = -2.5  for stack of 234-269
		Stack = -2.1  for stack of 235-268
		Stack = -1.3  for stack of 236-267
		Stack = 0.3  for stack of 237-266
	Helix total = -5.6
	Internal/bulge = 3.7  for closure of 238-265	Size = 3
		Stack = -0.9  for stack of 241-263
		Stack = -0.9  for stack of 242-262
	Helix total = -1.8
	Internal/bulge = 2.2  for closure of 243-261	Size = 3
		Stack = -3.4  for stack of 245-258
		Stack = -3.3  for stack of 246-257
	Helix total = -6.7
	Hairpin = 3.4  for closure of 247-256
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 187-219	Size = 2
		Stack = -2.5  for stack of 189-217
		Stack = -2.1  for stack of 190-216
		Stack = -1.4  for stack of 191-215
		Stack = -1.5  for stack of 192-214
		Stack = -1.4  for stack of 193-213
		Stack = -0.9  for stack of 194-212
		Stack = -1.3  for stack of 195-211
		Stack = -0.9  for stack of 196-210
		Stack = -2.2  for stack of 197-209
		Stack = -1.4  for stack of 198-208
	Helix total = -15.6
	Hairpin = 5.8  for closure of 199-207
		Stack = -2.4  for stack of 136-172
		Stack = -3.4  for stack of 137-171
		Stack = -2.1  for stack of 138-170
		Stack = -0.9  for stack of 139-169
		Stack = -1.3  for stack of 140-168
		Stack = -2.2  for stack of 141-167
	Helix total = -12.3
	Internal/bulge = 3.0  for closure of 142-166	Size = 3
		Stack = -1.3  for stack of 144-163
		Stack = -0.6  for stack of 145-162
		Stack = -1.3  for stack of 146-161
		Stack = -1.4  for stack of 147-160
		Stack = -0.5  for stack of 148-159
	Helix total = -5.1
	Hairpin = 5.3  for closure of 149-158
	Helix total = 0.0
	Internal/bulge = 3.4  for closure of 111-135	Size = 6
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 115-131	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 117-129	Size = 2
		Stack = -0.5  for stack of 119-127
	Helix total = -0.5
	Hairpin = 5.6  for closure of 120-126
		Stack = -2.1  for stack of 55-80
		Stack = -2.4  for stack of 56-79
		Stack = -0.6  for stack of 57-78
		Stack = -1.3  for stack of 58-77
		Stack = -2.1  for stack of 59-76
	Helix total = -8.5
	Hairpin = 5.8  for closure of 60-75


	Total energy = -45.3



