Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:67 50:66 51:65 52:64 151:181 152:180 153:179 154:178
	    155:176 156:175 197:226 198:225 200:223 201:222 242:280 244:278
	    245:277 246:276 247:275 248:274
	Energy of Broken Structure: -13.0
	Energy of Pseudo-Helices:   -24.3
	Pseudoknot Energy Penalty:  31.8
	Total Free Energy:          -5.5
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-341
		Stack = -1.5  for stack of 2-340
		Stack = -2.1  for stack of 3-339
		Stack = -3.3  for stack of 4-338
		Stack = -3.4  for stack of 5-337
		Stack = -2.4  for stack of 6-336
	Helix total = -16.0
	Multiloop = 5.2  for closure of 7-335
		Stack = -2.5  for stack of 318-334
		Stack = -1.4  for stack of 319-333
		Stack = -3.3  for stack of 320-332
		Stack = -3.3  for stack of 321-331
	Helix total = -10.5
	Hairpin = 4.4  for closure of 322-330
		Stack = -2.4  for stack of 21-314
		Stack = -2.2  for stack of 22-313
		Stack = -2.4  for stack of 23-312
	Helix total = -7.0
	Internal/bulge = 1.4  for closure of 24-311	Size = 4
	Helix total = 0.0
	Internal/bulge = 2.4  for closure of 27-308	Size = 13
		Stack = -3.3  for stack of 35-301
		Stack = -3.3  for stack of 36-300
	Helix total = -6.6
	Internal/bulge = 1.2  for closure of 37-299	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.5  for closure of 39-297	Size = 4
	Helix total = 0.0
	Internal/bulge = 4.5  for closure of 42-294	Size = 5
		Stack = -2.1  for stack of 44-289
		Stack = -1.1  for stack of 45-288
		Stack = -1.3  for stack of 46-287
		Stack = -2.2  for stack of 47-286
	Helix total = -6.7
	Multiloop = 5.1  for closure of 48-285
		Stack = -2.5  for stack of 228-263
		Stack = -2.1  for stack of 229-262
		Stack = -0.9  for stack of 230-261
	Helix total = -5.5
	Internal/bulge = 1.2  for closure of 231-260	Size = 2
	Helix total = 0.0
	Internal/bulge = 4.4  for closure of 233-258	Size = 10
		Stack = -1.5  for stack of 238-251
		Stack = -2.1  for stack of 239-250
	Helix total = -3.6
	Hairpin = 5.4  for closure of 240-249
	Helix total = 0.0
	Internal/bulge = 2.7  for closure of 186-209	Size = 4
	Helix total = 0.0
	Internal/bulge = 5.8  for closure of 189-206	Size = 6
		Stack = -2.1  for stack of 195-204
	Helix total = -2.1
	Hairpin = 4.3  for closure of 196-203
		Stack = -2.1  for stack of 134-169
		Stack = -1.4  for stack of 135-168
		Stack = -2.2  for stack of 136-167
		Stack = -0.9  for stack of 137-166
		Stack = -1.3  for stack of 138-165
		Stack = -1.1  for stack of 139-164
	Helix total = -9.0
	Internal/bulge = 3.8  for closure of 140-163	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.0  for closure of 143-162	Size = 3
	Helix total = 0.0
	Hairpin = 5.8  for closure of 146-160
		Stack = -2.2  for stack of 113-133
		Stack = -0.9  for stack of 114-132
	Helix total = -3.1
	Internal/bulge = 1.1  for closure of 115-131	Size = 1 BP stack across bulge = -2.1
		Stack = -3.3  for stack of 117-130
		Stack = -3.4  for stack of 118-129
		Stack = -2.1  for stack of 119-128
	Helix total = -8.8
	Hairpin = 4.2  for closure of 120-127
		Stack = -1.3  for stack of 56-80
		Stack = -0.9  for stack of 57-79
		Stack = -2.2  for stack of 58-78
		Stack = -2.1  for stack of 59-77
	Helix total = -6.5
	Hairpin = 5.7  for closure of 60-76


	Total energy = -13.0



