Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    107:184 108:183 109:182 110:181 111:180 112:179 113:177 114:176
	    115:175
	Energy of Broken Structure: -165.8
	Energy of Pseudo-Helices:   -14.0
	Pseudoknot Energy Penalty:  8.9
	Total Free Energy:          -170.9
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -4.7
		Stack = -2.4  for stack of 381-443
		Stack = -2.1  for stack of 382-442
		Stack = -3.4  for stack of 383-441
	Helix total = -7.9
	Internal/bulge = 1.0  for closure of 384-440	Size = 1 BP stack across bulge = -2.4
		Stack = -1.5  for stack of 385-438
		Stack = -2.1  for stack of 386-437
		Stack = -2.2  for stack of 387-436
		Stack = -2.4  for stack of 388-435
		Stack = -3.3  for stack of 389-434
		Stack = -3.3  for stack of 390-433
	Helix total = -14.8
	Internal/bulge = 5.5  for closure of 391-432	Size = 10
		Stack = -2.2  for stack of 400-429
		Stack = -2.1  for stack of 401-428
		Stack = -3.4  for stack of 402-427
		Stack = -1.4  for stack of 403-426
	Helix total = -9.1
	Internal/bulge = 2.9  for closure of 404-425	Size = 4
		Stack = -2.4  for stack of 407-422
		Stack = -3.3  for stack of 408-421
		Stack = -3.3  for stack of 409-420
	Helix total = -9.0
	Hairpin = 3.4  for closure of 410-419
		Stack = -3.3  for stack of 212-370
		Stack = -2.1  for stack of 213-369
		Stack = -2.1  for stack of 214-368
		Stack = -3.4  for stack of 215-367
		Stack = -2.4  for stack of 216-366
		Stack = -3.3  for stack of 217-365
	Helix total = -16.6
	Internal/bulge = 6.2  for closure of 218-364	Size = 19
		Stack = -3.4  for stack of 225-350
		Stack = -3.3  for stack of 226-349
	Helix total = -6.7
	Internal/bulge = 0.5  for closure of 227-348	Size = 1 BP stack across bulge = -3.3
		Stack = -2.4  for stack of 228-346
		Stack = -3.4  for stack of 229-345
		Stack = -3.3  for stack of 230-344
		Stack = -3.3  for stack of 231-343
	Helix total = -12.4
	Internal/bulge = 2.8  for closure of 232-342	Size = 2
		Stack = -3.3  for stack of 233-339
		Stack = -3.4  for stack of 234-338
		Stack = -3.3  for stack of 235-337
		Stack = -3.3  for stack of 236-336
		Stack = -3.3  for stack of 237-335
		Stack = -3.3  for stack of 238-334
		Stack = -2.4  for stack of 239-333
	Helix total = -22.3
	Internal/bulge = 2.9  for closure of 240-332	Size = 8
		Stack = -3.3  for stack of 244-326
		Stack = -3.3  for stack of 245-325
		Stack = -2.4  for stack of 246-324
		Stack = -3.4  for stack of 247-323
	Helix total = -12.4
	Multiloop = 5.7  for closure of 248-322
		Stack = -2.1  for stack of 302-314
		Stack = -2.4  for stack of 303-313
		Stack = -2.1  for stack of 304-312
		Stack = -2.5  for stack of 305-311
	Helix total = -9.1
	Hairpin = 5.9  for closure of 306-310
		Stack = -2.4  for stack of 256-300
		Stack = -3.4  for stack of 257-299
		Stack = -2.4  for stack of 258-298
		Stack = -3.3  for stack of 259-297
	Helix total = -11.5
	Internal/bulge = 0.4  for closure of 260-296	Size = 1 BP stack across bulge = -3.4
		Stack = -2.4  for stack of 262-295
		Stack = -3.3  for stack of 263-294
		Stack = -3.4  for stack of 264-293
	Helix total = -9.1
	Internal/bulge = 2.6  for closure of 265-292	Size = 5
		Stack = -3.3  for stack of 268-288
		Stack = -3.3  for stack of 269-287
	Helix total = -6.6
	Hairpin = 4.7  for closure of 270-286
		Stack = -2.1  for stack of 18-209
		Stack = -1.5  for stack of 19-208
		Stack = -2.4  for stack of 20-207
		Stack = -3.3  for stack of 21-206
		Stack = -3.3  for stack of 22-205
		Stack = -2.4  for stack of 23-204
		Stack = -0.6  for stack of 24-203
		Stack = -2.1  for stack of 25-202
		Stack = -3.3  for stack of 26-201
		Stack = -3.3  for stack of 27-200
		Stack = -3.4  for stack of 28-199
	Helix total = -27.7
	Internal/bulge = 3.9  for closure of 29-198	Size = 7
		Stack = -3.3  for stack of 32-192
		Stack = -2.5  for stack of 33-191
		Stack = -1.5  for stack of 34-190
		Stack = -2.1  for stack of 35-189
	Helix total = -9.4
	Internal/bulge = 7.2  for closure of 36-188	Size = 67
		Stack = -3.3  for stack of 63-146
		Stack = -3.4  for stack of 64-145
		Stack = -2.4  for stack of 65-144
	Helix total = -9.1
	Internal/bulge = 0.3  for closure of 66-143	Size = 1 BP stack across bulge = -2.2
		Stack = -1.3  for stack of 67-141
		Stack = -2.1  for stack of 68-140
		Stack = -3.3  for stack of 69-139
		Stack = -3.4  for stack of 70-138
	Helix total = -10.1
	Internal/bulge = 2.0  for closure of 71-137	Size = 9
		Stack = -3.4  for stack of 77-132
		Stack = -2.1  for stack of 78-131
		Stack = -0.9  for stack of 79-130
		Stack = -0.9  for stack of 80-129
	Helix total = -7.3
	Internal/bulge = 6.3  for closure of 81-128	Size = 11
		Stack = -1.4  for stack of 90-124
		Stack = -2.5  for stack of 91-123
		Stack = -2.4  for stack of 92-122
		Stack = -3.4  for stack of 93-121
		Stack = -2.4  for stack of 94-120
		Stack = -3.4  for stack of 95-119
		Stack = -2.1  for stack of 96-118
		Stack = -2.1  for stack of 97-117
	Helix total = -19.7
	Hairpin = 5.5  for closure of 98-116


	Total energy = -165.8



