Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    54:77 56:75 57:74 58:73 147:183 148:182 149:181 150:180
	    151:179 152:178 200:230 201:229 202:228 203:227 204:226 248:287
	    249:286 250:285 251:284 252:283 253:282 254:281
	Energy of Broken Structure: -95.6
	Energy of Pseudo-Helices:   -45.1
	Pseudoknot Energy Penalty:  31.1
	Total Free Energy:          -109.6
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-348
		Stack = -1.5  for stack of 2-347
		Stack = -2.1  for stack of 3-346
		Stack = -2.4  for stack of 4-345
		Stack = -2.2  for stack of 5-344
		Stack = -2.4  for stack of 6-343
	Helix total = -13.9
	Multiloop = 5.1  for closure of 7-342
		Stack = -2.2  for stack of 325-341
		Stack = -2.1  for stack of 326-340
		Stack = -3.3  for stack of 327-339
		Stack = -3.3  for stack of 328-338
	Helix total = -10.9
	Hairpin = 4.4  for closure of 329-337
		Stack = -2.1  for stack of 20-321
		Stack = -2.1  for stack of 21-320
		Stack = -1.5  for stack of 22-319
		Stack = -2.1  for stack of 23-318
		Stack = -3.3  for stack of 24-317
		Stack = -2.5  for stack of 25-316
		Stack = -1.0  for stack of 26-315
	Helix total = -14.6
	Internal/bulge = 1.7  for closure of 27-314	Size = 6
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 31-310	Size = 3
		Stack = -2.5  for stack of 34-308
		Stack = -2.1  for stack of 35-307
		Stack = -0.9  for stack of 36-306
		Stack = -1.3  for stack of 37-305
		Stack = -0.9  for stack of 38-304
		Stack = -2.1  for stack of 39-303
		Stack = -3.4  for stack of 40-302
		Stack = -1.4  for stack of 41-301
	Helix total = -14.6
	Internal/bulge = 4.5  for closure of 42-300	Size = 5
		Stack = -2.4  for stack of 44-295
		Stack = -2.4  for stack of 45-294
		Stack = -2.1  for stack of 46-293
		Stack = -3.4  for stack of 47-292
	Helix total = -10.3
	Multiloop = 2.4  for closure of 48-291
		Stack = -3.4  for stack of 233-269
		Stack = -3.3  for stack of 234-268
		Stack = -2.4  for stack of 235-267
	Helix total = -9.1
	Internal/bulge = 0.5  for closure of 236-266	Size = 2
	Helix total = 0.0
	Internal/bulge = -1.4  for closure of 238-264	Size = 2
	Helix total = 0.0
	Internal/bulge = 0.7  for closure of 240-262	Size = 7
		Stack = -3.4  for stack of 244-257
		Stack = -3.3  for stack of 245-256
	Helix total = -6.7
	Hairpin = 4.5  for closure of 246-255
		Stack = -3.3  for stack of 188-214
		Stack = -3.3  for stack of 189-213
	Helix total = -6.6
	Internal/bulge = 0.9  for closure of 190-212	Size = 4
		Stack = -1.1  for stack of 193-209
		Stack = -2.4  for stack of 194-208
		Stack = -3.3  for stack of 195-207
	Helix total = -6.8
	Hairpin = 4.1  for closure of 196-206
		Stack = -3.4  for stack of 132-168
		Stack = -2.1  for stack of 133-167
		Stack = -1.5  for stack of 134-166
		Stack = -3.3  for stack of 135-165
		Stack = -2.1  for stack of 136-164
	Helix total = -12.4
	Internal/bulge = 3.9  for closure of 137-163	Size = 6
		Stack = -2.4  for stack of 140-158
		Stack = -3.4  for stack of 141-157
		Stack = -3.3  for stack of 142-156
		Stack = -2.1  for stack of 143-155
		Stack = -1.4  for stack of 144-154
	Helix total = -12.6
	Hairpin = 5.9  for closure of 145-153
		Stack = -1.3  for stack of 109-131
		Stack = -2.1  for stack of 110-130
		Stack = -3.4  for stack of 111-129
		Stack = -2.1  for stack of 112-128
		Stack = -2.1  for stack of 113-127
		Stack = -3.4  for stack of 114-126
	Helix total = -14.4
	Hairpin = 5.6  for closure of 115-125
		Stack = -2.4  for stack of 49-65
		Stack = -2.4  for stack of 50-64
		Stack = -2.1  for stack of 51-63
		Stack = -3.3  for stack of 52-62
	Helix total = -10.2
	Hairpin = 4.5  for closure of 53-61


	Total energy = -95.6



