Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    55:78 56:77 57:76 58:75 59:74 149:194 150:193 151:192
	    152:191 153:190 154:189 209:238 210:237 211:236 213:234 258:296
	    259:295 260:294 261:293 262:291 263:290 264:289
	Energy of Broken Structure: -90.7
	Energy of Pseudo-Helices:   -28.6
	Pseudoknot Energy Penalty:  31.2
	Total Free Energy:          -88.1
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-356
		Stack = -1.5  for stack of 2-355
		Stack = -2.1  for stack of 3-354
		Stack = -3.4  for stack of 4-353
		Stack = -3.3  for stack of 5-352
		Stack = -2.4  for stack of 6-351
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-350
		Stack = -3.4  for stack of 333-349
		Stack = -2.4  for stack of 334-348
		Stack = -3.3  for stack of 335-347
		Stack = -3.3  for stack of 336-346
	Helix total = -12.4
	Hairpin = 4.4  for closure of 337-345
		Stack = -2.4  for stack of 20-329
		Stack = -2.5  for stack of 21-328
		Stack = 0.3  for stack of 22-327
		Stack = -0.5  for stack of 23-326
		Stack = -2.1  for stack of 24-325
		Stack = -2.5  for stack of 25-324
		Stack = -0.5  for stack of 26-323
	Helix total = -10.2
	Internal/bulge = 2.6  for closure of 27-322	Size = 9
		Stack = -2.5  for stack of 33-317
		Stack = -2.1  for stack of 34-316
		Stack = -2.1  for stack of 35-315
	Helix total = -6.7
	Internal/bulge = 2.3  for closure of 36-314	Size = 1 BP stack across bulge = -1.5
		Stack = -2.1  for stack of 38-313
		Stack = -2.4  for stack of 39-312
		Stack = -2.1  for stack of 40-311
	Helix total = -6.6
	Internal/bulge = 2.9  for closure of 41-310	Size = 7
		Stack = -2.1  for stack of 44-304
		Stack = -1.1  for stack of 45-303
		Stack = -1.3  for stack of 46-302
		Stack = -2.2  for stack of 47-301
	Helix total = -6.7
	Multiloop = 2.1  for closure of 48-300
		Stack = -3.3  for stack of 244-277
		Stack = -2.4  for stack of 245-276
	Helix total = -5.7
	Internal/bulge = 2.7  for closure of 246-275	Size = 9
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 252-270	Size = 3
		Stack = -3.4  for stack of 254-267
		Stack = -2.4  for stack of 255-266
	Helix total = -5.8
	Hairpin = 4.5  for closure of 256-265
		Stack = -2.1  for stack of 200-224
		Stack = -0.6  for stack of 201-223
		Stack = -2.4  for stack of 202-222
		Stack = -2.4  for stack of 203-221
		Stack = -3.3  for stack of 204-220
		Stack = -3.3  for stack of 205-219
	Helix total = -14.1
	Hairpin = 5.3  for closure of 206-218
		Stack = -3.3  for stack of 134-181
		Stack = -2.1  for stack of 135-180
		Stack = -2.4  for stack of 136-179
		Stack = -2.4  for stack of 137-178
		Stack = -3.4  for stack of 138-177
	Helix total = -13.6
	Multiloop = 3.1  for closure of 139-176
		Stack = -3.3  for stack of 161-174
		Stack = -2.2  for stack of 162-173
		Stack = -0.9  for stack of 163-172
		Stack = -2.4  for stack of 164-171
	Helix total = -8.8
	Hairpin = 3.3  for closure of 165-170
		Stack = -2.1  for stack of 141-160
		Stack = -1.0  for stack of 142-159
		Stack = -2.1  for stack of 143-158
		Stack = -3.4  for stack of 144-157
		Stack = -2.1  for stack of 145-156
	Helix total = -10.7
	Hairpin = 5.3  for closure of 146-155
		Stack = -1.4  for stack of 113-132
		Stack = -3.3  for stack of 114-131
		Stack = -3.4  for stack of 115-130
	Helix total = -8.1
	Internal/bulge = 0.5  for closure of 116-129	Size = 2
		Stack = -3.4  for stack of 118-127
		Stack = -3.3  for stack of 119-126
	Helix total = -6.7
	Hairpin = 3.6  for closure of 120-125
		Stack = -2.4  for stack of 49-66
		Stack = -2.4  for stack of 50-65
		Stack = -2.1  for stack of 51-64
		Stack = -3.3  for stack of 52-63
	Helix total = -10.2
	Hairpin = 4.4  for closure of 53-62


	Total energy = -90.7



