Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:68 50:67 51:66 52:65 53:64 153:192 154:191 155:190
	    156:189 157:188 158:187 210:238 211:237 212:236 213:235 256:295
	    259:292 260:289 261:288 262:287
	Energy of Broken Structure: -45.8
	Energy of Pseudo-Helices:   -30.9
	Pseudoknot Energy Penalty:  50.9
	Total Free Energy:          -25.8
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 = -2.4  for stack of 4-352
		Stack = -1.1  for stack of 5-351
		Stack = -2.1  for stack of 6-350
	Helix total = -12.5
	Multiloop = 5.1  for closure of 7-349
		Stack = -3.4  for stack of 332-348
		Stack = -2.4  for stack of 333-347
		Stack = -3.3  for stack of 334-346
		Stack = -3.3  for stack of 335-345
	Helix total = -12.4
	Hairpin = 4.4  for closure of 336-344
		Stack = -2.4  for stack of 20-328
		Stack = -3.4  for stack of 21-327
		Stack = -2.1  for stack of 22-326
		Stack = 0.3  for stack of 23-325
		Stack = -2.1  for stack of 24-324
		Stack = -2.5  for stack of 25-323
		Stack = 0.3  for stack of 26-322
	Helix total = -11.9
	Internal/bulge = 1.9  for closure of 27-321	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.4  for closure of 29-319	Size = 7
		Stack = -2.1  for stack of 34-315
		Stack = -2.4  for stack of 35-314
		Stack = -2.1  for stack of 36-313
	Helix total = -6.6
	Internal/bulge = 2.8  for closure of 37-312	Size = 4
		Stack = -1.3  for stack of 40-309
		Stack = -1.1  for stack of 41-308
	Helix total = -2.4
	Internal/bulge = 3.0  for closure of 42-307	Size = 4
		Stack = -2.1  for stack of 44-303
		Stack = -1.1  for stack of 45-302
		Stack = -2.1  for stack of 46-301
		Stack = -2.2  for stack of 47-300
	Helix total = -7.5
	Multiloop = 6.6  for closure of 48-299
		Stack = -2.2  for stack of 242-276
		Stack = -2.4  for stack of 243-275
		Stack = -3.3  for stack of 244-274
	Helix total = -7.9
	Internal/bulge = 3.0  for closure of 245-273	Size = 3
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 248-271	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 250-269	Size = 7
		Stack = -2.1  for stack of 254-264
	Helix total = -2.1
	Hairpin = 5.7  for closure of 255-263
		Stack = -2.5  for stack of 196-225
		Stack = -3.3  for stack of 197-224
	Helix total = -5.8
	Internal/bulge = 2.8  for closure of 198-223	Size = 5
		Stack = -2.1  for stack of 202-220
		Stack = -2.5  for stack of 203-219
		Stack = 0.3  for stack of 204-218
		Stack = -1.3  for stack of 205-217
		Stack = -1.1  for stack of 206-216
	Helix total = -6.7
	Hairpin = 5.8  for closure of 207-215
		Stack = -2.2  for stack of 137-173
		Stack = -2.1  for stack of 138-172
		Stack = -0.9  for stack of 139-171
		Stack = -1.0  for stack of 140-170
		Stack = -2.1  for stack of 141-169
		Stack = -2.2  for stack of 142-168
		Stack = -0.9  for stack of 143-167
		Stack = -2.1  for stack of 144-166
	Helix total = -13.5
	Internal/bulge = 0.4  for closure of 145-165	Size = 1 BP stack across bulge = -3.4
		Stack = -2.1  for stack of 146-163
		Stack = 0.3  for stack of 147-162
		Stack = -1.3  for stack of 148-161
		Stack = -1.4  for stack of 149-160
	Helix total = -4.5
	Hairpin = 5.3  for closure of 150-159
		Stack = -0.6  for stack of 118-135
		Stack = -2.5  for stack of 119-134
		Stack = -2.1  for stack of 120-133
		Stack = -2.1  for stack of 121-132
	Helix total = -7.3
	Hairpin = 4.8  for closure of 122-131
		Stack = -1.1  for stack of 56-82
		Stack = -1.3  for stack of 57-81
		Stack = -1.1  for stack of 58-80
		Stack = -2.1  for stack of 59-79
		Stack = -2.2  for stack of 60-78
	Helix total = -7.8
	Hairpin = 6.7  for closure of 61-77


	Total energy = -45.8



