Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:60 50:59 51:58 156:192 157:191 158:190 159:189 160:188
	    161:187 205:238 207:236 208:235 209:234 210:233 211:232 258:293
	    259:292 260:291 261:290 264:287
	Energy of Broken Structure: -56.3
	Energy of Pseudo-Helices:   -31.0
	Pseudoknot Energy Penalty:  33.6
	Total Free Energy:          -53.7
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-355
		Stack = -1.5  for stack of 2-354
		Stack = -2.1  for stack of 3-353
		Stack = -3.3  for stack of 4-352
		Stack = -3.4  for stack of 5-351
		Stack = -2.4  for stack of 6-350
	Helix total = -16.0
	Multiloop = 6.5  for closure of 7-349
		Stack = -2.1  for stack of 332-348
		Stack = -3.3  for stack of 333-347
		Stack = -3.3  for stack of 334-346
		Stack = -3.3  for stack of 335-345
	Helix total = -12.0
	Hairpin = 4.4  for closure of 336-344
		Stack = -2.1  for stack of 20-328
		Stack = -0.6  for stack of 21-327
		Stack = -0.5  for stack of 22-326
		Stack = -2.5  for stack of 23-325
		Stack = -2.1  for stack of 24-324
		Stack = -1.4  for stack of 25-323
		Stack = -0.5  for stack of 26-322
	Helix total = -9.7
	Internal/bulge = 2.9  for closure of 27-321	Size = 10
		Stack = -2.5  for stack of 33-315
		Stack = -2.1  for stack of 34-314
		Stack = -1.1  for stack of 35-313
	Helix total = -5.7
	Internal/bulge = -0.7  for closure of 36-312	Size = 2
		Stack = -0.9  for stack of 38-310
		Stack = -2.2  for stack of 39-309
	Helix total = -3.1
	Internal/bulge = 3.9  for closure of 40-308	Size = 7
		Stack = -2.1  for stack of 43-302
		Stack = -0.9  for stack of 44-301
		Stack = -2.2  for stack of 45-300
		Stack = -2.1  for stack of 46-299
	Helix total = -7.3
	Multiloop = 6.3  for closure of 47-298
		Stack = -2.5  for stack of 239-277
		Stack = -2.1  for stack of 240-276
		Stack = -0.9  for stack of 241-275
		Stack = -0.9  for stack of 242-274
		Stack = -0.9  for stack of 243-273
		Stack = -1.1  for stack of 244-272
		Stack = -2.1  for stack of 245-271
		Stack = -2.5  for stack of 246-270
		Stack = -1.5  for stack of 247-269
	Helix total = -14.5
	Internal/bulge = 3.0  for closure of 248-268	Size = 4
	Helix total = 0.0
	Hairpin = 5.8  for closure of 252-266
		Stack = -0.9  for stack of 197-221
		Stack = -2.1  for stack of 198-220
		Stack = -2.5  for stack of 199-219
		Stack = -0.6  for stack of 200-218
		Stack = -2.1  for stack of 201-217
		Stack = -2.5  for stack of 202-216
		Stack = -1.4  for stack of 203-215
	Helix total = -12.1
	Hairpin = 3.9  for closure of 204-214
	Helix total = 0.0
	Internal/bulge = 0.5  for closure of 141-176	Size = 2
		Stack = -2.1  for stack of 143-174
		Stack = -1.4  for stack of 144-173
	Helix total = -3.5
	Internal/bulge = 3.1  for closure of 145-172	Size = 9
		Stack = -0.9  for stack of 150-166
		Stack = -2.1  for stack of 151-165
		Stack = -3.4  for stack of 152-164
		Stack = -2.1  for stack of 153-163
	Helix total = -8.5
	Hairpin = 6.0  for closure of 154-162
		Stack = -2.2  for stack of 110-140
		Stack = -2.4  for stack of 111-139
		Stack = -3.4  for stack of 112-138
		Stack = -2.1  for stack of 113-137
	Helix total = -10.1
	Internal/bulge = 2.3  for closure of 114-136	Size = 1 BP stack across bulge = -1.1
		Stack = -2.1  for stack of 116-135
		Stack = -3.3  for stack of 117-134
	Helix total = -5.4
	Hairpin = 5.8  for closure of 118-133
		Stack = -3.3  for stack of 54-71
		Stack = -2.4  for stack of 55-70
		Stack = -1.1  for stack of 56-69
	Helix total = -6.8
	Hairpin = 6.4  for closure of 57-68


	Total energy = -56.3



