Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:63 50:62 51:61 52:60 145:182 146:181 147:180 148:179
	    149:178 150:177 198:230 199:229 200:228 201:227 202:226 203:225
	    247:290 248:289 249:288 250:287 251:286 252:285 253:284
	Energy of Broken Structure: -99.0
	Energy of Pseudo-Helices:   -47.2
	Pseudoknot Energy Penalty:  35.9
	Total Free Energy:          -110.3
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-350
		Stack = -1.5  for stack of 2-349
		Stack = -2.1  for stack of 3-348
		Stack = -2.4  for stack of 4-347
		Stack = -1.1  for stack of 5-346
		Stack = -2.1  for stack of 6-345
	Helix total = -12.5
	Multiloop = 5.1  for closure of 7-344
		Stack = -3.3  for stack of 327-343
		Stack = -3.3  for stack of 328-342
		Stack = -3.3  for stack of 329-341
		Stack = -3.3  for stack of 330-340
	Helix total = -13.2
	Hairpin = 4.4  for closure of 331-339
		Stack = -2.1  for stack of 20-323
		Stack = -1.3  for stack of 21-322
		Stack = -0.6  for stack of 22-321
		Stack = -0.5  for stack of 23-320
		Stack = -2.1  for stack of 24-319
		Stack = -2.4  for stack of 25-318
	Helix total = -9.0
	Internal/bulge = 2.9  for closure of 26-317	Size = 6
		Stack = -1.5  for stack of 31-314
		Stack = -2.1  for stack of 32-313
		Stack = -2.2  for stack of 33-312
		Stack = -2.1  for stack of 34-311
		Stack = -2.5  for stack of 35-310
		Stack = -0.6  for stack of 36-309
		Stack = -2.1  for stack of 37-308
		Stack = -3.4  for stack of 38-307
		Stack = -2.4  for stack of 39-306
		Stack = -3.4  for stack of 40-305
	Helix total = -22.3
	Internal/bulge = 1.7  for closure of 41-304	Size = 1 BP stack across bulge = -2.1
	Helix total = 0.0
	Internal/bulge = 3.0  for closure of 42-302	Size = 4
		Stack = -2.1  for stack of 44-298
		Stack = -2.1  for stack of 45-297
		Stack = -3.3  for stack of 46-296
		Stack = -2.2  for stack of 47-295
	Helix total = -9.7
	Multiloop = 2.8  for closure of 48-294
	Helix total = 0.0
	Internal/bulge = 1.0  for closure of 231-271	Size = 4
		Stack = -2.4  for stack of 234-268
		Stack = -2.2  for stack of 235-267
		Stack = -2.1  for stack of 236-266
		Stack = -2.4  for stack of 237-265
		Stack = -2.1  for stack of 238-264
		Stack = -2.1  for stack of 239-263
	Helix total = -13.3
	Internal/bulge = 0.5  for closure of 240-262	Size = 4
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 243-259	Size = 2
	Helix total = 0.0
	Hairpin = 5.5  for closure of 245-257
		Stack = -2.1  for stack of 186-215
		Stack = -1.5  for stack of 187-214
		Stack = -2.1  for stack of 188-213
		Stack = -0.6  for stack of 189-212
		Stack = -1.3  for stack of 190-211
		Stack = -2.2  for stack of 191-210
		Stack = -2.4  for stack of 192-209
		Stack = -2.2  for stack of 193-208
		Stack = -1.3  for stack of 194-207
	Helix total = -15.7
	Hairpin = 5.4  for closure of 195-206
		Stack = -2.4  for stack of 127-168
		Stack = -3.3  for stack of 128-167
		Stack = -3.3  for stack of 129-166
		Stack = -3.4  for stack of 130-165
		Stack = -3.3  for stack of 131-164
	Helix total = -15.7
	Internal/bulge = 3.3  for closure of 132-163	Size = 2
		Stack = -1.0  for stack of 133-160
		Stack = -1.4  for stack of 134-159
		Stack = -2.1  for stack of 135-158
		Stack = -2.2  for stack of 136-157
		Stack = -0.9  for stack of 137-156
		Stack = -1.3  for stack of 138-155
		Stack = -1.4  for stack of 139-154
		Stack = -3.4  for stack of 140-153
	Helix total = -13.7
	Hairpin = 4.2  for closure of 141-152
		Stack = -2.4  for stack of 102-126
		Stack = -2.4  for stack of 103-125
	Helix total = -4.8
	Internal/bulge = 1.9  for closure of 104-124	Size = 2
		Stack = -1.3  for stack of 106-122
		Stack = -2.2  for stack of 107-121
		Stack = -2.4  for stack of 108-120
		Stack = -3.4  for stack of 109-119
		Stack = -2.4  for stack of 110-118
	Helix total = -11.7
	Hairpin = 5.0  for closure of 111-117
		Stack = -2.5  for stack of 54-72
		Stack = -1.5  for stack of 55-71
		Stack = -2.4  for stack of 56-70
		Stack = -2.4  for stack of 57-69
	Helix total = -8.8
	Hairpin = 5.2  for closure of 58-68


	Total energy = -99.0



