Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:61 50:60 51:59 52:58 141:176 142:175 143:174 144:173
	    145:172 146:171 147:170 192:225 193:224 194:223 195:222 196:221
	    197:220 198:219 242:279 243:278 244:277 245:276 246:275 247:274
	    248:273
	Energy of Broken Structure: -133.2
	Energy of Pseudo-Helices:   -59.1
	Pseudoknot Energy Penalty:  50.0
	Total Free Energy:          -142.3
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-343
		Stack = -1.5  for stack of 2-342
		Stack = -2.1  for stack of 3-341
		Stack = -3.3  for stack of 4-340
		Stack = -3.4  for stack of 5-339
		Stack = -2.4  for stack of 6-338
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-337
		Stack = -3.4  for stack of 320-336
		Stack = -2.4  for stack of 321-335
		Stack = -3.3  for stack of 322-334
		Stack = -3.3  for stack of 323-333
	Helix total = -12.4
	Hairpin = 4.4  for closure of 324-332
		Stack = -2.4  for stack of 20-316
		Stack = -1.5  for stack of 21-315
		Stack = -2.1  for stack of 22-314
		Stack = -3.3  for stack of 23-313
		Stack = -2.4  for stack of 24-312
		Stack = -2.2  for stack of 25-311
	Helix total = -13.9
	Internal/bulge = 1.4  for closure of 26-310	Size = 1 BP stack across bulge = -2.4
		Stack = -3.3  for stack of 28-309
		Stack = -3.4  for stack of 29-308
		Stack = -2.4  for stack of 30-307
		Stack = -3.3  for stack of 31-306
		Stack = -2.5  for stack of 32-305
		Stack = -1.5  for stack of 33-304
	Helix total = -16.4
	Internal/bulge = 0.5  for closure of 34-303	Size = 1 BP stack across bulge = -3.3
	Helix total = 0.0
	Internal/bulge = 2.8  for closure of 35-301	Size = 2
		Stack = -3.3  for stack of 36-298
		Stack = -2.4  for stack of 37-297
		Stack = -2.4  for stack of 38-296
		Stack = -2.1  for stack of 39-295
		Stack = -3.3  for stack of 40-294
	Helix total = -13.5
	Internal/bulge = 3.1  for closure of 41-293	Size = 7
		Stack = -2.1  for stack of 44-287
		Stack = -2.1  for stack of 45-286
		Stack = -3.3  for stack of 46-285
		Stack = -3.4  for stack of 47-284
	Helix total = -10.9
	Multiloop = 4.3  for closure of 48-283
		Stack = -3.3  for stack of 228-262
		Stack = -3.3  for stack of 229-261
		Stack = -2.1  for stack of 230-260
	Helix total = -8.7
	Internal/bulge = 0.5  for closure of 231-259	Size = 4
		Stack = -3.3  for stack of 234-256
		Stack = -3.3  for stack of 235-255
	Helix total = -6.6
	Internal/bulge = 1.2  for closure of 236-254	Size = 3
		Stack = -3.4  for stack of 238-251
		Stack = -2.1  for stack of 239-250
	Helix total = -5.5
	Hairpin = 5.3  for closure of 240-249
		Stack = -2.1  for stack of 180-209
		Stack = -3.4  for stack of 181-208
		Stack = -2.1  for stack of 182-207
		Stack = -1.3  for stack of 183-206
		Stack = -2.2  for stack of 184-205
		Stack = -2.1  for stack of 185-204
		Stack = -2.4  for stack of 186-203
		Stack = -1.4  for stack of 187-202
		Stack = -2.1  for stack of 188-201
		Stack = -2.5  for stack of 189-200
	Helix total = -21.6
	Hairpin = 5.3  for closure of 190-199
		Stack = -2.4  for stack of 125-162
		Stack = -2.5  for stack of 126-161
		Stack = -1.5  for stack of 127-160
		Stack = -3.3  for stack of 128-159
	Helix total = -9.7
	Internal/bulge = 0.5  for closure of 129-158	Size = 1 BP stack across bulge = -3.3
		Stack = -3.3  for stack of 130-156
		Stack = -2.4  for stack of 131-155
		Stack = -3.3  for stack of 132-154
		Stack = -2.2  for stack of 133-153
		Stack = -1.3  for stack of 134-152
		Stack = -2.1  for stack of 135-151
		Stack = -3.3  for stack of 136-150
		Stack = -2.5  for stack of 137-149
	Helix total = -20.4
	Hairpin = 6.2  for closure of 138-148
		Stack = -2.4  for stack of 102-124
		Stack = -3.4  for stack of 103-123
		Stack = -2.1  for stack of 104-122
		Stack = -2.1  for stack of 105-121
		Stack = -3.4  for stack of 106-120
		Stack = -3.3  for stack of 107-119
	Helix total = -16.7
	Hairpin = 5.0  for closure of 108-118
		Stack = -1.4  for stack of 53-70
		Stack = -3.3  for stack of 54-69
		Stack = -3.4  for stack of 55-68
		Stack = -2.1  for stack of 56-67
	Helix total = -10.2
	Hairpin = 5.4  for closure of 57-66


	Total energy = -133.2



