Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    52:69 53:68 54:67 55:66 149:183 150:182 151:181 152:180
	    153:179 154:178 197:228 198:227 199:226 200:225 201:224 202:223
	    247:282 248:281 249:280 250:279 251:278 252:277 253:276
	Energy of Broken Structure: -51.4
	Energy of Pseudo-Helices:   -40.0
	Pseudoknot Energy Penalty:  31.7
	Total Free Energy:          -59.7
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 = -0.6  for stack of 5-340
		Stack = -2.1  for stack of 6-339
	Helix total = -12.1
	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 = -1.4  for stack of 25-312
		Stack = -0.5  for stack of 26-311
	Helix total = -9.7
	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 = -0.9  for stack of 35-302
		Stack = -1.0  for stack of 36-301
		Stack = -1.4  for stack of 37-300
		Stack = -0.9  for stack of 38-299
		Stack = -2.4  for stack of 39-298
	Helix total = -11.7
	Internal/bulge = 3.9  for closure of 40-297	Size = 7
		Stack = -2.1  for stack of 43-291
		Stack = -0.9  for stack of 44-290
		Stack = -2.2  for stack of 45-289
		Stack = -2.1  for stack of 46-288
	Helix total = -7.3
	Multiloop = 7.9  for closure of 47-287
		Stack = -2.5  for stack of 230-266
		Stack = -2.1  for stack of 231-265
		Stack = -0.9  for stack of 232-264
		Stack = -2.1  for stack of 233-263
	Helix total = -7.6
	Internal/bulge = 3.3  for closure of 234-262	Size = 5
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 238-259	Size = 3
		Stack = -1.5  for stack of 240-256
		Stack = -1.4  for stack of 241-255
	Helix total = -2.9
	Hairpin = 5.7  for closure of 242-254
		Stack = -0.9  for stack of 188-212
		Stack = -2.1  for stack of 189-211
		Stack = -3.3  for stack of 190-210
		Stack = -1.5  for stack of 191-209
		Stack = -1.3  for stack of 192-208
		Stack = -1.4  for stack of 193-207
		Stack = -0.6  for stack of 194-206
		Stack = -2.1  for stack of 195-205
	Helix total = -13.2
	Hairpin = 4.7  for closure of 196-204
		Stack = -2.4  for stack of 134-169
		Stack = -2.2  for stack of 135-168
		Stack = -3.3  for stack of 136-167
		Stack = -2.1  for stack of 137-166
		Stack = -0.6  for stack of 138-165
	Helix total = -10.6
	Internal/bulge = 3.3  for closure of 139-164	Size = 5
		Stack = -3.4  for stack of 142-160
		Stack = -1.4  for stack of 143-159
		Stack = -1.3  for stack of 144-158
		Stack = -0.9  for stack of 145-157
		Stack = -1.4  for stack of 146-156
	Helix total = -8.4
	Hairpin = 5.1  for closure of 147-155
		Stack = -2.5  for stack of 105-133
	Helix total = -2.5
	Internal/bulge = 0.5  for closure of 106-132	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 108-130	Size = 4
		Stack = -3.4  for stack of 111-127
		Stack = -2.1  for stack of 112-126
		Stack = -2.1  for stack of 113-125
	Helix total = -7.6
	Hairpin = 5.7  for closure of 114-124
		Stack = -2.1  for stack of 48-59
		Stack = -1.1  for stack of 49-58
		Stack = -2.4  for stack of 50-57
	Helix total = -5.6
	Hairpin = 3.3  for closure of 51-56


	Total energy = -51.4



