Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    52:69 53:68 54:67 55:66 149:184 150:183 151:182 152:181
	    153:180 154:179 200:229 201:228 202:227 203:226 204:225 249:284
	    250:283 251:282 252:281 253:280 254:279 255:278
	Energy of Broken Structure: -52.9
	Energy of Pseudo-Helices:   -37.6
	Pseudoknot Energy Penalty:  31.5
	Total Free Energy:          -59.0
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 = -0.6  for stack of 5-342
		Stack = -2.1  for stack of 6-341
	Helix total = -12.1
	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 = -2.2  for stack of 25-314
		Stack = -2.1  for stack of 26-313
	Helix total = -12.1
	Internal/bulge = 2.7  for closure of 27-312	Size = 8
		Stack = -0.5  for stack of 32-307
		Stack = -2.5  for stack of 33-306
		Stack = -2.1  for stack of 34-305
		Stack = -1.1  for stack of 35-304
		Stack = -1.0  for stack of 36-303
		Stack = -1.4  for stack of 37-302
		Stack = -0.9  for stack of 38-301
		Stack = -0.9  for stack of 39-300
	Helix total = -10.4
	Internal/bulge = 4.6  for closure of 40-299	Size = 7
		Stack = -2.1  for stack of 43-293
		Stack = -0.9  for stack of 44-292
		Stack = -2.2  for stack of 45-291
		Stack = -2.1  for stack of 46-290
	Helix total = -7.3
	Multiloop = 7.6  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
		Stack = -0.9  for stack of 235-265
	Helix total = -6.8
	Internal/bulge = 4.0  for closure of 236-264	Size = 5
	Helix total = 0.0
	Internal/bulge = 2.2  for closure of 240-261	Size = 3
		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 = -2.2  for stack of 189-214
		Stack = -2.1  for stack of 190-213
		Stack = -1.3  for stack of 191-212
		Stack = -0.9  for stack of 192-211
	Helix total = -6.5
	Internal/bulge = 1.2  for closure of 193-210	Size = 2
		Stack = -3.4  for stack of 195-208
	Helix total = -3.4
	Hairpin = 5.5  for closure of 196-207
		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 = -0.9  for stack of 137-166
		Stack = -2.4  for stack of 138-165
	Helix total = -10.0
	Internal/bulge = 2.2  for closure of 139-164	Size = 3
		Stack = -2.4  for stack of 141-161
		Stack = -2.1  for stack of 142-160
	Helix total = -4.5
	Internal/bulge = 1.2  for closure of 143-159	Size = 2
		Stack = -2.4  for stack of 145-157
		Stack = -1.4  for stack of 146-156
	Helix total = -3.8
	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 = -0.6  for stack of 108-130
		Stack = -1.3  for stack of 109-129
		Stack = -2.1  for stack of 110-128
		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 = -11.6
	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 = -52.9



