Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    52:69 53:68 54:67 55:66 149:183 150:182 151:181 152:180
	    153:179 154:178 199:228 200:227 201:226 202:225 203:224 204:223
	    248:283 249:282 250:281 251:280 252:279 253:278 254:277
	Energy of Broken Structure: -53.2
	Energy of Pseudo-Helices:   -37.3
	Pseudoknot Energy Penalty:  32.1
	Total Free Energy:          -58.4
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-345
		Stack = -1.5  for stack of 2-344
		Stack = -2.1  for stack of 3-343
		Stack = -2.5  for stack of 4-342
		Stack = -0.6  for stack of 5-341
		Stack = -2.1  for stack of 6-340
	Helix total = -12.1
	Multiloop = 5.1  for closure of 7-339
		Stack = -2.2  for stack of 322-338
		Stack = -2.1  for stack of 323-337
		Stack = -3.3  for stack of 324-336
		Stack = -3.3  for stack of 325-335
	Helix total = -10.9
	Hairpin = 4.4  for closure of 326-334
		Stack = -2.1  for stack of 20-318
		Stack = -0.6  for stack of 21-317
		Stack = -0.5  for stack of 22-316
		Stack = -2.5  for stack of 23-315
		Stack = -2.1  for stack of 24-314
		Stack = -1.4  for stack of 25-313
		Stack = -0.5  for stack of 26-312
	Helix total = -9.7
	Internal/bulge = 3.7  for closure of 27-311	Size = 8
		Stack = -0.5  for stack of 32-306
		Stack = -2.5  for stack of 33-305
		Stack = -3.3  for stack of 34-304
		Stack = -2.1  for stack of 35-303
		Stack = -1.3  for stack of 36-302
		Stack = -1.1  for stack of 37-301
		Stack = -0.9  for stack of 38-300
		Stack = -0.9  for stack of 39-299
	Helix total = -12.6
	Internal/bulge = 4.6  for closure of 40-298	Size = 7
		Stack = -2.1  for stack of 43-292
		Stack = -0.9  for stack of 44-291
		Stack = -2.2  for stack of 45-290
		Stack = -2.1  for stack of 46-289
	Helix total = -7.3
	Multiloop = 7.9  for closure of 47-288
		Stack = -2.5  for stack of 231-267
		Stack = -2.1  for stack of 232-266
		Stack = -2.1  for stack of 233-265
		Stack = -1.5  for stack of 234-264
	Helix total = -8.2
	Internal/bulge = 5.1  for closure of 235-263	Size = 1 BP stack across bulge = 1.3
	Helix total = 0.0
	Internal/bulge = 1.1  for closure of 237-262	Size = 6
		Stack = -3.3  for stack of 241-258
	Helix total = -3.3
	Internal/bulge = 1.2  for closure of 242-257	Size = 2
	Helix total = 0.0
	Hairpin = 5.6  for closure of 244-255
		Stack = -0.9  for stack of 188-213
		Stack = -0.9  for stack of 189-212
		Stack = -1.3  for stack of 190-211
		Stack = -2.1  for stack of 191-210
		Stack = -3.3  for stack of 192-209
		Stack = -2.2  for stack of 193-208
		Stack = -2.1  for stack of 194-207
		Stack = -2.4  for stack of 195-206
	Helix total = -15.2
	Hairpin = 5.4  for closure of 196-205
		Stack = -2.4  for stack of 134-169
		Stack = -2.2  for stack of 135-168
		Stack = -2.1  for stack of 136-167
		Stack = -0.6  for stack of 137-166
		Stack = -2.4  for stack of 138-165
	Helix total = -9.7
	Internal/bulge = 2.2  for closure of 139-164	Size = 3
		Stack = -1.1  for stack of 141-161
		Stack = -1.3  for stack of 142-160
		Stack = -0.6  for stack of 143-159
		Stack = -2.1  for stack of 144-158
		Stack = -2.4  for stack of 145-157
		Stack = -1.4  for stack of 146-156
	Helix total = -8.9
	Hairpin = 5.1  for closure of 147-155
		Stack = -2.5  for stack of 105-133
	Helix total = -2.5
	Internal/bulge = 1.0  for closure of 106-132	Size = 2
		Stack = -0.5  for stack of 108-130
	Helix total = -0.5
	Internal/bulge = 1.2  for closure of 109-129	Size = 2
		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 = -53.2



