Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:64 49:63 50:62 51:61 147:181 148:180 149:179 150:178
	    151:177 152:176 196:228 197:227 199:225 200:224 246:287 247:286
	    248:285 249:284 250:283 251:281 252:280 253:279
	Energy of Broken Structure: -96.7
	Energy of Pseudo-Helices:   -38.7
	Pseudoknot Energy Penalty:  33.5
	Total Free Energy:          -101.9
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 = 5.1  for closure of 7-342
		Stack = -3.4  for stack of 325-341
		Stack = -2.4  for stack of 326-340
		Stack = -3.3  for stack of 327-339
		Stack = -3.3  for stack of 328-338
	Helix total = -12.4
	Hairpin = 4.4  for closure of 329-337
		Stack = -2.4  for stack of 20-321
		Stack = -1.5  for stack of 21-320
		Stack = -0.5  for stack of 22-319
		Stack = -1.3  for stack of 23-318
		Stack = -1.1  for stack of 24-317
		Stack = -0.9  for stack of 25-316
	Helix total = -7.7
	Internal/bulge = 4.0  for closure of 26-315	Size = 5
		Stack = -2.1  for stack of 30-312
	Helix total = -2.1
	Internal/bulge = 0.4  for closure of 31-311	Size = 1 BP stack across bulge = -3.4
		Stack = -1.4  for stack of 32-309
		Stack = -2.1  for stack of 33-308
	Helix total = -3.5
	Internal/bulge = 1.2  for closure of 34-307	Size = 2
		Stack = -0.9  for stack of 36-305
		Stack = -0.9  for stack of 37-304
		Stack = -2.1  for stack of 38-303
		Stack = -2.4  for stack of 39-302
		Stack = -2.1  for stack of 40-301
		Stack = -1.5  for stack of 41-300
	Helix total = -9.9
	Internal/bulge = 3.7  for closure of 42-299	Size = 3
		Stack = -2.1  for stack of 43-295
		Stack = -1.1  for stack of 44-294
		Stack = -2.1  for stack of 45-293
		Stack = -3.4  for stack of 46-292
	Helix total = -8.7
	Multiloop = 2.2  for closure of 47-291
		Stack = -3.4  for stack of 230-267
		Stack = -2.1  for stack of 231-266
		Stack = -1.4  for stack of 232-265
		Stack = -0.6  for stack of 233-264
		Stack = -2.4  for stack of 234-263
		Stack = -2.1  for stack of 235-262
		Stack = -2.1  for stack of 236-261
		Stack = -3.4  for stack of 237-260
		Stack = -2.4  for stack of 238-259
	Helix total = -19.9
	Internal/bulge = 3.2  for closure of 239-258	Size = 3
		Stack = -2.1  for stack of 243-257
		Stack = -0.9  for stack of 244-256
	Helix total = -3.0
	Hairpin = 6.1  for closure of 245-255
		Stack = -1.4  for stack of 184-214
		Stack = -1.3  for stack of 185-213
		Stack = -1.5  for stack of 186-212
		Stack = -3.3  for stack of 187-211
		Stack = -2.1  for stack of 188-210
	Helix total = -9.6
	Internal/bulge = 1.2  for closure of 189-209	Size = 2
		Stack = -2.4  for stack of 191-207
		Stack = -3.3  for stack of 192-206
		Stack = -3.4  for stack of 193-205
		Stack = -2.1  for stack of 194-204
	Helix total = -11.2
	Hairpin = 4.9  for closure of 195-203
		Stack = -2.4  for stack of 131-168
		Stack = -2.2  for stack of 132-167
		Stack = -2.4  for stack of 133-166
		Stack = -3.3  for stack of 134-165
	Helix total = -10.3
	Internal/bulge = 2.3  for closure of 135-164	Size = 3
		Stack = -2.1  for stack of 137-161
	Helix total = -2.1
	Internal/bulge = -0.3  for closure of 138-160	Size = 4
		Stack = -3.3  for stack of 141-157
		Stack = -3.4  for stack of 142-156
		Stack = -2.1  for stack of 143-155
		Stack = -0.5  for stack of 144-154
	Helix total = -9.3
	Hairpin = 6.0  for closure of 145-153
		Stack = -3.4  for stack of 109-130
		Stack = -2.1  for stack of 110-129
		Stack = -0.6  for stack of 111-128
		Stack = -2.5  for stack of 112-127
		Stack = -2.1  for stack of 113-126
		Stack = -0.9  for stack of 114-125
		Stack = -1.3  for stack of 115-124
	Helix total = -12.9
	Hairpin = 5.1  for closure of 116-123
		Stack = -2.5  for stack of 54-75
		Stack = -1.4  for stack of 55-74
		Stack = -1.5  for stack of 56-73
		Stack = -2.1  for stack of 57-72
		Stack = -3.4  for stack of 58-71
	Helix total = -10.9
	Hairpin = 5.0  for closure of 59-70


	Total energy = -96.7



