Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:65 49:64 50:63 51:62 52:61 157:186 158:185 159:184
	    160:183 201:233 202:232 203:231 204:230 205:229 206:228 251:290
	    252:289 253:288 254:287 255:286 256:285 257:284
	Energy of Broken Structure: -28.2
	Energy of Pseudo-Helices:   -28.5
	Pseudoknot Energy Penalty:  31.5
	Total Free Energy:          -25.2
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-351
		Stack = -1.5  for stack of 2-350
		Stack = -2.1  for stack of 3-349
		Stack = -3.3  for stack of 4-348
		Stack = -3.4  for stack of 5-347
		Stack = -2.4  for stack of 6-346
	Helix total = -16.0
	Multiloop = 5.0  for closure of 7-345
		Stack = -3.3  for stack of 328-344
		Stack = -3.3  for stack of 329-343
		Stack = -2.4  for stack of 330-342
		Stack = -2.1  for stack of 331-341
	Helix total = -11.1
	Hairpin = 4.4  for closure of 332-340
		Stack = -2.4  for stack of 19-324
		Stack = -1.5  for stack of 20-323
		Stack = -2.1  for stack of 21-322
		Stack = -1.5  for stack of 22-321
		Stack = -1.4  for stack of 23-320
		Stack = -1.3  for stack of 24-319
	Helix total = -10.2
	Internal/bulge = 1.9  for closure of 25-318	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.1  for closure of 27-316	Size = 7
		Stack = -1.0  for stack of 32-312
		Stack = -1.3  for stack of 33-311
		Stack = -1.4  for stack of 34-310
		Stack = -1.0  for stack of 35-309
		Stack = -0.9  for stack of 36-308
		Stack = -0.6  for stack of 37-307
		Stack = -1.3  for stack of 38-306
		Stack = -1.4  for stack of 39-305
	Helix total = -8.9
	Internal/bulge = 4.6  for closure of 40-304	Size = 7
		Stack = -2.1  for stack of 43-298
		Stack = -1.1  for stack of 44-297
		Stack = -1.0  for stack of 45-296
		Stack = -2.5  for stack of 46-295
	Helix total = -6.7
	Multiloop = 4.5  for closure of 47-294
		Stack = -1.4  for stack of 236-272
		Stack = -0.9  for stack of 237-271
		Stack = -2.1  for stack of 238-270
		Stack = -2.4  for stack of 239-269
	Helix total = -6.8
	Internal/bulge = 3.9  for closure of 240-268	Size = 11
		Stack = -3.3  for stack of 246-261
		Stack = -1.5  for stack of 247-260
		Stack = 1.3  for stack of 248-259
	Helix total = -3.5
	Hairpin = 4.6  for closure of 249-258
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 187-219	Size = 2
		Stack = -1.4  for stack of 189-217
		Stack = -2.4  for stack of 190-216
		Stack = -3.3  for stack of 191-215
		Stack = -3.3  for stack of 192-214
		Stack = -2.1  for stack of 193-213
	Helix total = -12.5
	Internal/bulge = 3.7  for closure of 194-212	Size = 4
		Stack = -1.3  for stack of 198-210
		Stack = -0.6  for stack of 199-209
	Helix total = -1.9
	Hairpin = 5.7  for closure of 200-208
	Helix total = 0.0
	Internal/bulge = 2.1  for closure of 139-173	Size = 4
		Stack = -0.6  for stack of 142-170
	Helix total = -0.6
	Internal/bulge = 4.2  for closure of 143-169	Size = 3
		Stack = -0.6  for stack of 147-168
		Stack = -0.9  for stack of 148-167
		Stack = -1.0  for stack of 149-166
	Helix total = -2.5
	Hairpin = 6.6  for closure of 150-165
	Helix total = 0.0
	Internal/bulge = 2.5  for closure of 110-137	Size = 10
		Stack = -3.4  for stack of 116-131
	Helix total = -3.4
	Internal/bulge = 0.9  for closure of 117-130	Size = 4
	Helix total = 0.0
	Hairpin = 4.9  for closure of 120-127
		Stack = -0.9  for stack of 53-79
		Stack = -2.4  for stack of 54-78
		Stack = -2.4  for stack of 55-77
		Stack = -3.3  for stack of 56-76
		Stack = -3.3  for stack of 57-75
	Helix total = -12.3
	Hairpin = 5.4  for closure of 58-74


	Total energy = -28.2



