Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:66 49:65 50:64 51:63 147:181 148:180 149:179 150:178
	    151:177 152:176 197:225 198:224 199:223 200:222 201:221 202:220
	    203:219 229:264 230:263 233:260 238:256 241:251
	Energy of Broken Structure: -75.3
	Energy of Pseudo-Helices:   -32.1
	Pseudoknot Energy Penalty:  36.3
	Total Free Energy:          -71.1
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 = -1.5  for stack of 4-343
		Stack = -2.5  for stack of 5-342
		Stack = -2.4  for stack of 6-341
	Helix total = -13.3
	Multiloop = 6.5  for closure of 7-340
		Stack = -2.1  for stack of 323-339
		Stack = -3.3  for stack of 324-338
		Stack = -3.3  for stack of 325-337
		Stack = -3.3  for stack of 326-336
	Helix total = -12.0
	Hairpin = 4.4  for closure of 327-335
		Stack = -2.4  for stack of 20-319
		Stack = -2.5  for stack of 21-318
		Stack = 0.3  for stack of 22-317
		Stack = -0.5  for stack of 23-316
		Stack = -0.5  for stack of 24-315
		Stack = -1.4  for stack of 25-314
		Stack = -1.3  for stack of 26-313
		Stack = -0.6  for stack of 27-312
	Helix total = -8.9
	Internal/bulge = 1.0  for closure of 28-311	Size = 8
		Stack = -2.1  for stack of 33-306
		Stack = -0.9  for stack of 34-305
		Stack = -2.1  for stack of 35-304
	Helix total = -5.1
	Internal/bulge = -0.7  for closure of 36-303	Size = 4
		Stack = -3.4  for stack of 39-300
	Helix total = -3.4
	Internal/bulge = 3.3  for closure of 40-299	Size = 7
		Stack = -2.1  for stack of 43-293
		Stack = -1.1  for stack of 44-292
		Stack = -2.1  for stack of 45-291
		Stack = -2.5  for stack of 46-290
	Helix total = -7.8
	Multiloop = 4.7  for closure of 47-289
		Stack = -3.4  for stack of 244-285
		Stack = -3.3  for stack of 245-284
		Stack = -2.1  for stack of 246-283
	Helix total = -8.8
	Internal/bulge = 1.2  for closure of 247-282	Size = 1 BP stack across bulge = -2.2
		Stack = -2.1  for stack of 248-280
		Stack = -0.9  for stack of 249-279
	Helix total = -3.0
	Hairpin = 6.0  for closure of 250-278
		Stack = -2.1  for stack of 184-213
		Stack = -1.3  for stack of 185-212
		Stack = -2.2  for stack of 186-211
		Stack = -2.1  for stack of 187-210
		Stack = -0.9  for stack of 188-209
		Stack = -1.3  for stack of 189-208
		Stack = -1.0  for stack of 190-207
		Stack = -0.6  for stack of 191-206
		Stack = -2.1  for stack of 192-205
	Helix total = -13.6
	Hairpin = 4.0  for closure of 193-204
		Stack = -2.4  for stack of 132-168
		Stack = -2.2  for stack of 133-167
		Stack = -2.4  for stack of 134-166
		Stack = -3.3  for stack of 135-165
	Helix total = -10.3
	Internal/bulge = 3.0  for closure of 136-164	Size = 3
		Stack = -2.4  for stack of 138-161
		Stack = -2.1  for stack of 139-160
		Stack = -0.9  for stack of 140-159
		Stack = -1.3  for stack of 141-158
		Stack = -2.1  for stack of 142-157
		Stack = -2.2  for stack of 143-156
		Stack = -2.4  for stack of 144-155
	Helix total = -13.4
	Hairpin = 4.4  for closure of 145-154
		Stack = -2.1  for stack of 114-131
		Stack = -3.4  for stack of 115-130
		Stack = -2.1  for stack of 116-129
		Stack = -2.1  for stack of 117-128
		Stack = -3.4  for stack of 118-127
	Helix total = -13.1
	Hairpin = 4.6  for closure of 119-126
		Stack = -2.1  for stack of 55-78
		Stack = -1.5  for stack of 56-77
		Stack = -2.1  for stack of 57-76
		Stack = 0.3  for stack of 58-75
		Stack = -2.1  for stack of 59-74
	Helix total = -7.5
	Hairpin = 4.2  for closure of 60-73


	Total energy = -75.3



