Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    53:67 54:66 55:65 149:182 150:181 151:180 152:179 153:178
	    198:227 199:226 200:225 201:224 202:223 247:282 248:281 249:280
	    250:279 251:278 252:277 253:276
	Energy of Broken Structure: -59.4
	Energy of Pseudo-Helices:   -32.2
	Pseudoknot Energy Penalty:  31.7
	Total Free Energy:          -59.9
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-344
		Stack = -1.5  for stack of 2-343
		Stack = -2.1  for stack of 3-342
		Stack = -2.5  for stack of 4-341
		Stack = -1.5  for stack of 5-340
		Stack = -2.4  for stack of 6-339
	Helix total = -13.3
	Multiloop = 5.1  for closure of 7-338
		Stack = -2.2  for stack of 321-337
		Stack = -2.1  for stack of 322-336
		Stack = -3.3  for stack of 323-335
		Stack = -3.3  for stack of 324-334
	Helix total = -10.9
	Hairpin = 4.4  for closure of 325-333
		Stack = -2.1  for stack of 20-317
		Stack = -0.6  for stack of 21-316
		Stack = -0.5  for stack of 22-315
		Stack = -2.5  for stack of 23-314
		Stack = -2.1  for stack of 24-313
		Stack = -1.1  for stack of 25-312
		Stack = -1.3  for stack of 26-311
	Helix total = -10.2
	Internal/bulge = 3.7  for closure of 27-310	Size = 8
		Stack = -0.5  for stack of 32-305
		Stack = -2.5  for stack of 33-304
		Stack = -2.1  for stack of 34-303
		Stack = -1.1  for stack of 35-302
		Stack = -1.3  for stack of 36-301
		Stack = -1.1  for stack of 37-300
		Stack = -0.9  for stack of 38-299
		Stack = -0.9  for stack of 39-298
	Helix total = -10.4
	Internal/bulge = 4.6  for closure of 40-297	Size = 7
		Stack = -1.4  for stack of 43-291
		Stack = -1.3  for stack of 44-290
		Stack = -2.2  for stack of 45-289
		Stack = -2.1  for stack of 46-288
	Helix total = -7.0
	Multiloop = 7.6  for closure of 47-287
		Stack = -2.5  for stack of 230-266
		Stack = -1.4  for stack of 231-265
		Stack = -2.1  for stack of 232-264
		Stack = -2.2  for stack of 233-263
		Stack = -1.3  for stack of 234-262
		Stack = -0.5  for stack of 235-261
		Stack = -1.5  for stack of 236-260
		Stack = -2.1  for stack of 237-259
	Helix total = -13.6
	Internal/bulge = 1.2  for closure of 238-258	Size = 2
		Stack = -1.5  for stack of 240-256
		Stack = -2.5  for stack of 241-255
	Helix total = -4.0
	Hairpin = 4.5  for closure of 242-254
		Stack = -1.1  for stack of 188-212
		Stack = -2.4  for stack of 189-211
		Stack = -2.1  for stack of 190-210
		Stack = -0.9  for stack of 191-209
		Stack = -2.1  for stack of 192-208
		Stack = -3.4  for stack of 193-207
		Stack = -3.3  for stack of 194-206
	Helix total = -15.3
	Hairpin = 5.0  for closure of 195-205
		Stack = -2.4  for stack of 133-168
		Stack = -2.2  for stack of 134-167
		Stack = -3.3  for stack of 135-166
	Helix total = -7.9
	Internal/bulge = 0.5  for closure of 136-165	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.3  for closure of 138-163	Size = 2
		Stack = -1.1  for stack of 139-160
		Stack = -0.9  for stack of 140-159
	Helix total = -2.0
	Internal/bulge = 1.1  for closure of 141-158	Size = 1 BP stack across bulge = -2.1
		Stack = -1.5  for stack of 143-157
		Stack = -1.3  for stack of 144-156
		Stack = -1.4  for stack of 145-155
	Helix total = -4.2
	Hairpin = 5.1  for closure of 146-154
		Stack = -2.5  for stack of 104-132
	Helix total = -2.5
	Internal/bulge = 0.0  for closure of 105-131	Size = 2
		Stack = -2.1  for stack of 107-129
	Helix total = -2.1
	Internal/bulge = 2.2  for closure of 108-128	Size = 2
		Stack = -3.4  for stack of 110-126
		Stack = -2.1  for stack of 111-125
		Stack = -2.1  for stack of 112-124
	Helix total = -7.6
	Hairpin = 5.7  for closure of 113-123
		Stack = -2.4  for stack of 48-59
		Stack = -2.2  for stack of 49-58
	Helix total = -4.6
	Hairpin = 3.9  for closure of 50-57


	Total energy = -59.4



