Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    108:184 109:183 110:182 111:181 112:180 113:179 114:177 115:176
	    116:175
	Energy of Broken Structure: -128.5
	Energy of Pseudo-Helices:   -14.0
	Pseudoknot Energy Penalty:  8.9
	Total Free Energy:          -133.6
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -3.2
		Stack = -2.4  for stack of 378-439
		Stack = -2.1  for stack of 379-438
		Stack = -3.4  for stack of 380-437
		Stack = -3.3  for stack of 381-436
	Helix total = -11.2
	Internal/bulge = 1.5  for closure of 382-435	Size = 3
		Stack = -2.2  for stack of 384-432
		Stack = -2.4  for stack of 385-431
	Helix total = -4.6
	Internal/bulge = 0.3  for closure of 386-430	Size = 2
	Helix total = 0.0
	Internal/bulge = 5.4  for closure of 388-428	Size = 9
		Stack = -3.3  for stack of 397-426
		Stack = -3.3  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 = -13.9
	Internal/bulge = 1.2  for closure of 402-421	Size = 2
		Stack = -2.4  for stack of 404-419
		Stack = -2.1  for stack of 405-418
		Stack = -1.5  for stack of 406-417
	Helix total = -6.0
	Hairpin = 3.4  for closure of 407-416
		Stack = -3.3  for stack of 210-367
		Stack = -2.1  for stack of 211-366
		Stack = -2.1  for stack of 212-365
		Stack = -3.4  for stack of 213-364
		Stack = -2.4  for stack of 214-363
		Stack = -3.3  for stack of 215-362
	Helix total = -16.6
	Internal/bulge = 6.2  for closure of 216-361	Size = 19
	Helix total = 0.0
	Internal/bulge = 0.5  for closure of 223-347	Size = 2
	Helix total = 0.0
	Internal/bulge = 0.5  for closure of 225-345	Size = 1 BP stack across bulge = -3.3
	Helix total = 0.0
	Internal/bulge = 0.8  for closure of 226-343	Size = 4
		Stack = -2.1  for stack of 229-340
		Stack = -1.4  for stack of 230-339
	Helix total = -3.5
	Internal/bulge = 2.8  for closure of 231-338	Size = 2
		Stack = -3.4  for stack of 232-335
		Stack = -3.3  for stack of 233-334
		Stack = -3.3  for stack of 234-333
		Stack = -3.3  for stack of 235-332
		Stack = -3.3  for stack of 236-331
		Stack = -2.4  for stack of 237-330
	Helix total = -19.0
	Internal/bulge = 2.7  for closure of 238-329	Size = 8
		Stack = -3.3  for stack of 242-323
		Stack = -3.3  for stack of 243-322
		Stack = -2.4  for stack of 244-321
		Stack = -3.4  for stack of 245-320
	Helix total = -12.4
	Multiloop = 5.7  for closure of 246-319
		Stack = -2.1  for stack of 299-311
		Stack = -2.4  for stack of 300-310
		Stack = -2.1  for stack of 301-309
	Helix total = -6.6
	Hairpin = 4.1  for closure of 302-308
	Helix total = 0.0
	Internal/bulge = -0.4  for closure of 254-297	Size = 2
		Stack = -2.4  for stack of 256-295
		Stack = -3.3  for stack of 257-294
	Helix total = -5.7
	Internal/bulge = 1.3  for closure of 258-293	Size = 1 BP stack across bulge = -2.5
		Stack = -1.4  for stack of 260-292
		Stack = -3.3  for stack of 261-291
		Stack = -3.4  for stack of 262-290
	Helix total = -8.1
	Internal/bulge = 0.2  for closure of 263-289	Size = 6
		Stack = -3.3  for stack of 267-285
	Helix total = -3.3
	Hairpin = 4.7  for closure of 268-284
		Stack = -3.3  for stack of 18-207
	Helix total = -3.3
	Internal/bulge = 0.8  for closure of 19-206	Size = 1 BP stack across bulge = -2.4
		Stack = -3.3  for stack of 20-204
		Stack = -3.3  for stack of 21-203
		Stack = -2.4  for stack of 22-202
		Stack = -2.1  for stack of 23-201
		Stack = -3.3  for stack of 24-200
		Stack = -3.3  for stack of 25-199
		Stack = -3.3  for stack of 26-198
	Helix total = -21.0
	Internal/bulge = -0.1  for closure of 27-197	Size = 2
		Stack = -3.3  for stack of 29-195
	Helix total = -3.3
	Internal/bulge = 2.3  for closure of 30-194	Size = 4
		Stack = -3.3  for stack of 32-190
	Helix total = -3.3
	Internal/bulge = -2.3  for closure of 33-189	Size = 2
		Stack = -2.1  for stack of 35-187
	Helix total = -2.1
	Internal/bulge = 7.2  for closure of 36-186	Size = 67
		Stack = -2.4  for stack of 65-146
		Stack = -2.2  for stack of 66-145
		Stack = -2.4  for stack of 67-144
	Helix total = -7.0
	Internal/bulge = 0.0  for closure of 68-143	Size = 1 BP stack across bulge = -2.5
		Stack = -1.0  for stack of 69-141
		Stack = -2.1  for stack of 70-140
		Stack = -3.3  for stack of 71-139
		Stack = -3.4  for stack of 72-138
	Helix total = -9.8
	Internal/bulge = 2.0  for closure of 73-137	Size = 9
		Stack = -3.4  for stack of 79-132
		Stack = -2.1  for stack of 80-131
		Stack = -0.9  for stack of 81-130
		Stack = -0.9  for stack of 82-129
	Helix total = -7.3
	Internal/bulge = 6.1  for closure of 83-128	Size = 9
		Stack = -2.4  for stack of 91-125
		Stack = -3.4  for stack of 92-124
		Stack = -1.4  for stack of 93-123
		Stack = -2.5  for stack of 94-122
		Stack = -2.4  for stack of 95-121
		Stack = -3.4  for stack of 96-120
		Stack = -2.1  for stack of 97-119
		Stack = -2.1  for stack of 98-118
	Helix total = -19.7
	Hairpin = 5.5  for closure of 99-117


	Total energy = -128.5



