Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    52:68 53:67 54:66 55:65 148:185 149:184 150:183 151:182
	    152:181 153:180 200:229 201:228 202:227 203:226 204:225 249:284
	    250:283 251:282 252:281 253:280 254:279 255:278
	Energy of Broken Structure: -49.0
	Energy of Pseudo-Helices:   -36.1
	Pseudoknot Energy Penalty:  32.0
	Total Free Energy:          -53.1
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-346
		Stack = -1.5  for stack of 2-345
		Stack = -2.1  for stack of 3-344
		Stack = -2.5  for stack of 4-343
		Stack = -1.5  for stack of 5-342
		Stack = -2.4  for stack of 6-341
	Helix total = -13.3
	Multiloop = 5.1  for closure of 7-340
		Stack = -2.2  for stack of 323-339
		Stack = -2.1  for stack of 324-338
		Stack = -3.3  for stack of 325-337
		Stack = -3.3  for stack of 326-336
	Helix total = -10.9
	Hairpin = 4.4  for closure of 327-335
		Stack = -2.1  for stack of 20-319
		Stack = -0.6  for stack of 21-318
		Stack = -0.5  for stack of 22-317
		Stack = -2.5  for stack of 23-316
		Stack = -2.1  for stack of 24-315
		Stack = -1.1  for stack of 25-314
		Stack = -1.3  for stack of 26-313
	Helix total = -10.2
	Internal/bulge = 3.7  for closure of 27-312	Size = 8
		Stack = -0.5  for stack of 32-307
		Stack = -1.4  for stack of 33-306
		Stack = -1.3  for stack of 34-305
		Stack = -1.1  for stack of 35-304
		Stack = -1.3  for stack of 36-303
		Stack = -1.1  for stack of 37-302
		Stack = -0.9  for stack of 38-301
		Stack = -0.9  for stack of 39-300
	Helix total = -8.5
	Internal/bulge = 4.6  for closure of 40-299	Size = 7
		Stack = -1.4  for stack of 43-293
		Stack = -1.3  for stack of 44-292
		Stack = -2.2  for stack of 45-291
		Stack = -2.1  for stack of 46-290
	Helix total = -7.0
	Multiloop = 7.0  for closure of 47-289
		Stack = -2.5  for stack of 232-268
		Stack = -2.1  for stack of 233-267
		Stack = -1.3  for stack of 234-266
	Helix total = -5.9
	Internal/bulge = 1.2  for closure of 235-265	Size = 2
		Stack = -2.2  for stack of 237-263
		Stack = -2.1  for stack of 238-262
		Stack = -2.4  for stack of 239-261
	Helix total = -6.7
	Internal/bulge = 1.2  for closure of 240-260	Size = 2
		Stack = -1.5  for stack of 242-258
		Stack = -2.5  for stack of 243-257
	Helix total = -4.0
	Hairpin = 4.5  for closure of 244-256
		Stack = -0.9  for stack of 190-214
		Stack = -0.9  for stack of 191-213
		Stack = -1.0  for stack of 192-212
		Stack = -0.5  for stack of 193-211
		Stack = -2.5  for stack of 194-210
		Stack = -2.1  for stack of 195-209
		Stack = -1.3  for stack of 196-208
	Helix total = -9.2
	Hairpin = 6.2  for closure of 197-207
		Stack = -2.4  for stack of 133-169
		Stack = -1.4  for stack of 134-168
		Stack = -1.5  for stack of 135-167
		Stack = -2.1  for stack of 136-166
		Stack = -0.9  for stack of 137-165
	Helix total = -8.3
	Internal/bulge = 3.9  for closure of 138-164	Size = 6
		Stack = -2.1  for stack of 141-159
		Stack = -0.9  for stack of 142-158
		Stack = -0.6  for stack of 143-157
		Stack = -1.3  for stack of 144-156
		Stack = -1.4  for stack of 145-155
	Helix total = -6.3
	Hairpin = 5.9  for closure of 146-154
		Stack = -2.5  for stack of 104-132
	Helix total = -2.5
	Internal/bulge = 0.5  for closure of 105-131	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 107-129	Size = 4
		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 = 5.3  for closure of 113-123
		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 = -49.0



