Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    106:183 107:182 108:181 109:180 110:179 111:178 112:176 113:175
	    114:174
	Energy of Broken Structure: -141.3
	Energy of Pseudo-Helices:   -14.0
	Pseudoknot Energy Penalty:  8.7
	Total Free Energy:          -146.6
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -3.9
		Stack = -2.4  for stack of 379-440
		Stack = -2.1  for stack of 380-439
		Stack = -3.4  for stack of 381-438
	Helix total = -7.9
	Internal/bulge = 3.3  for closure of 382-437	Size = 2
		Stack = -2.1  for stack of 383-434
		Stack = -2.5  for stack of 384-433
		Stack = -0.5  for stack of 385-432
		Stack = -1.5  for stack of 386-431
		Stack = -3.3  for stack of 387-430
	Helix total = -9.9
	Internal/bulge = 5.5  for closure of 388-429	Size = 10
		Stack = -2.5  for stack of 397-426
		Stack = -1.4  for stack of 398-425
		Stack = -3.4  for stack of 399-424
		Stack = -1.4  for stack of 400-423
		Stack = -2.5  for stack of 401-422
	Helix total = -11.2
	Internal/bulge = 0.8  for closure of 402-421	Size = 2
		Stack = -2.4  for stack of 404-419
		Stack = -3.3  for stack of 405-418
		Stack = -3.3  for stack of 406-417
	Helix total = -9.0
	Hairpin = 3.4  for closure of 407-416
		Stack = -3.3  for stack of 210-368
		Stack = -2.1  for stack of 211-367
		Stack = -2.1  for stack of 212-366
		Stack = -3.4  for stack of 213-365
	Helix total = -10.9
	Internal/bulge = 6.4  for closure of 214-364	Size = 23
		Stack = -3.4  for stack of 223-348
		Stack = -3.3  for stack of 224-347
	Helix total = -6.7
	Internal/bulge = 0.5  for closure of 225-346	Size = 1 BP stack across bulge = -3.3
		Stack = -2.4  for stack of 226-344
		Stack = -3.4  for stack of 227-343
		Stack = -3.3  for stack of 228-342
		Stack = -3.3  for stack of 229-341
	Helix total = -12.4
	Internal/bulge = 4.2  for closure of 230-340	Size = 9
		Stack = -3.3  for stack of 234-333
		Stack = -3.3  for stack of 235-332
		Stack = -2.4  for stack of 236-331
		Stack = -3.4  for stack of 237-330
	Helix total = -12.4
	Internal/bulge = 3.2  for closure of 238-329	Size = 6
		Stack = -3.3  for stack of 241-324
		Stack = -3.3  for stack of 242-323
		Stack = -2.4  for stack of 243-322
		Stack = -3.4  for stack of 244-321
	Helix total = -12.4
	Multiloop = 5.8  for closure of 245-320
		Stack = -2.1  for stack of 300-312
		Stack = -2.4  for stack of 301-311
		Stack = -2.1  for stack of 302-310
		Stack = -2.5  for stack of 303-309
	Helix total = -9.1
	Hairpin = 5.9  for closure of 304-308
		Stack = -2.4  for stack of 254-298
		Stack = -3.4  for stack of 255-297
		Stack = -2.4  for stack of 256-296
		Stack = -3.3  for stack of 257-295
	Helix total = -11.5
	Internal/bulge = 0.4  for closure of 258-294	Size = 1 BP stack across bulge = -3.4
		Stack = -2.4  for stack of 260-293
		Stack = -3.3  for stack of 261-292
		Stack = -3.4  for stack of 262-291
	Helix total = -9.1
	Internal/bulge = 2.6  for closure of 263-290	Size = 5
		Stack = -3.3  for stack of 266-286
		Stack = -3.3  for stack of 267-285
	Helix total = -6.6
	Hairpin = 5.4  for closure of 268-284
		Stack = -3.3  for stack of 18-207
		Stack = -3.3  for stack of 19-206
		Stack = -2.4  for stack of 20-205
		Stack = -3.3  for stack of 21-204
		Stack = -3.3  for stack of 22-203
		Stack = -2.4  for stack of 23-202
	Helix total = -18.0
	Internal/bulge = 0.0  for closure of 24-201	Size = 1 BP stack across bulge = -2.1
		Stack = -3.3  for stack of 25-199
		Stack = -3.3  for stack of 26-198
		Stack = -3.4  for stack of 27-197
		Stack = -2.4  for stack of 28-196
		Stack = -1.5  for stack of 29-195
	Helix total = -13.9
	Internal/bulge = 3.0  for closure of 30-194	Size = 3
		Stack = -3.3  for stack of 32-191
		Stack = -2.5  for stack of 33-190
		Stack = -1.5  for stack of 34-189
	Helix total = -7.3
	Internal/bulge = 6.5  for closure of 35-188	Size = 69
		Stack = -3.3  for stack of 63-145
		Stack = -3.4  for stack of 64-144
		Stack = -2.4  for stack of 65-143
	Helix total = -9.1
	Internal/bulge = 0.3  for closure of 66-142	Size = 1 BP stack across bulge = -2.2
		Stack = -1.3  for stack of 67-140
		Stack = -2.1  for stack of 68-139
		Stack = -1.5  for stack of 69-138
		Stack = -2.5  for stack of 70-137
	Helix total = -7.4
	Internal/bulge = 2.0  for closure of 71-136	Size = 9
		Stack = -3.4  for stack of 77-131
		Stack = -2.1  for stack of 78-130
		Stack = -0.9  for stack of 79-129
		Stack = -0.9  for stack of 80-128
	Helix total = -7.3
	Internal/bulge = 5.6  for closure of 81-127	Size = 10
		Stack = -2.4  for stack of 89-123
		Stack = -3.4  for stack of 90-122
	Helix total = -5.8
	Internal/bulge = -2.2  for closure of 91-121	Size = 2
		Stack = -2.4  for stack of 93-119
		Stack = -2.5  for stack of 94-118
		Stack = -0.6  for stack of 95-117
		Stack = -2.1  for stack of 96-116
	Helix total = -7.6
	Hairpin = 5.5  for closure of 97-115


	Total energy = -141.3



