Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    47:65 48:64 49:63 50:62 51:61 148:183 149:182 150:181
	    151:180 152:179 153:178 154:177 198:227 199:226 200:225 201:224
	    202:223 247:286 248:285 249:284 250:283 251:282 252:281 253:280
	Energy of Broken Structure: -84.2
	Energy of Pseudo-Helices:   -46.7
	Pseudoknot Energy Penalty:  36.6
	Total Free Energy:          -94.3
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-346
		Stack = -1.5  for stack of 2-345
		Stack = -2.1  for stack of 3-344
		Stack = -3.3  for stack of 4-343
		Stack = -3.4  for stack of 5-342
		Stack = -2.4  for stack of 6-341
	Helix total = -16.0
	Multiloop = 5.0  for closure of 7-340
		Stack = -3.4  for stack of 323-339
		Stack = -2.4  for stack of 324-338
		Stack = -3.3  for stack of 325-337
		Stack = -3.3  for stack of 326-336
	Helix total = -12.4
	Hairpin = 4.4  for closure of 327-335
		Stack = -2.4  for stack of 19-319
		Stack = -1.5  for stack of 20-318
		Stack = -1.3  for stack of 21-317
		Stack = -2.1  for stack of 22-316
		Stack = -3.3  for stack of 23-315
		Stack = -2.2  for stack of 24-314
	Helix total = -12.8
	Internal/bulge = 3.7  for closure of 25-313	Size = 3
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 28-311	Size = 2
	Helix total = 0.0
	Internal/bulge = 0.9  for closure of 30-309	Size = 6
		Stack = -2.1  for stack of 34-305
		Stack = -1.3  for stack of 35-304
		Stack = -0.9  for stack of 36-303
		Stack = -2.1  for stack of 37-302
		Stack = -3.4  for stack of 38-301
	Helix total = -9.8
	Internal/bulge = 3.3  for closure of 39-300	Size = 7
		Stack = -2.1  for stack of 42-294
		Stack = -1.1  for stack of 43-293
		Stack = -2.1  for stack of 44-292
		Stack = -3.4  for stack of 45-291
	Helix total = -8.7
	Multiloop = 4.7  for closure of 46-290
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 229-270	Size = 2
		Stack = -3.3  for stack of 231-268
		Stack = -2.4  for stack of 232-267
		Stack = -0.6  for stack of 233-266
	Helix total = -6.3
	Internal/bulge = 1.9  for closure of 234-265	Size = 2
		Stack = -0.9  for stack of 236-263
		Stack = -1.3  for stack of 237-262
		Stack = -2.1  for stack of 238-261
	Helix total = -4.3
	Internal/bulge = 0.2  for closure of 239-260	Size = 6
		Stack = -3.4  for stack of 243-256
		Stack = -3.3  for stack of 244-255
	Helix total = -6.7
	Hairpin = 4.5  for closure of 245-254
		Stack = -1.5  for stack of 186-214
		Stack = -3.3  for stack of 187-213
		Stack = -2.1  for stack of 188-212
		Stack = -1.3  for stack of 189-211
		Stack = -0.9  for stack of 190-210
		Stack = -2.1  for stack of 191-209
		Stack = -3.3  for stack of 192-208
		Stack = -3.4  for stack of 193-207
		Stack = -2.1  for stack of 194-206
	Helix total = -20.0
	Hairpin = 6.3  for closure of 195-205
		Stack = -2.4  for stack of 132-169
		Stack = -2.5  for stack of 133-168
		Stack = -1.5  for stack of 134-167
		Stack = -2.1  for stack of 135-166
		Stack = -0.9  for stack of 136-165
	Helix total = -9.4
	Internal/bulge = 1.2  for closure of 137-164	Size = 2
		Stack = -3.3  for stack of 139-162
	Helix total = -3.3
	Internal/bulge = 1.2  for closure of 140-161	Size = 2
		Stack = -0.6  for stack of 142-159
	Helix total = -0.6
	Internal/bulge = 1.9  for closure of 143-158	Size = 2
		Stack = -1.5  for stack of 145-156
	Helix total = -1.5
	Hairpin = 4.5  for closure of 146-155
		Stack = -3.4  for stack of 112-131
		Stack = -2.1  for stack of 113-130
		Stack = -2.1  for stack of 114-129
		Stack = -3.4  for stack of 115-128
		Stack = -2.1  for stack of 116-127
		Stack = -0.9  for stack of 117-126
	Helix total = -14.0
	Hairpin = 4.9  for closure of 118-125
		Stack = -1.5  for stack of 53-79
		Stack = -3.3  for stack of 54-78
		Stack = -2.1  for stack of 55-77
		Stack = -1.0  for stack of 56-76
		Stack = -2.5  for stack of 57-75
		Stack = -3.3  for stack of 58-74
	Helix total = -13.7
	Hairpin = 5.3  for closure of 59-73


	Total energy = -84.2



