Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    53:74 54:73 55:72 56:71 57:70 159:197 160:196 161:195
	    162:194 163:193 164:192 165:191 166:190 210:235 211:234 212:233
	    258:292 259:291 260:290 261:289 262:288 263:287 264:286 265:285
	Energy of Broken Structure: -46.1
	Energy of Pseudo-Helices:   -40.5
	Pseudoknot Energy Penalty:  35.5
	Total Free Energy:          -51.1
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 = -1.3  for stack of 3-353
		Stack = -2.1  for stack of 4-352
		Stack = -3.4  for stack of 5-351
		Stack = -2.4  for stack of 6-350
	Helix total = -14.0
	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 = -1.3  for stack of 23-325
		Stack = -0.6  for stack of 24-324
		Stack = -1.4  for stack of 25-323
		Stack = -1.3  for stack of 26-322
		Stack = -0.9  for stack of 27-321
	Helix total = -8.7
	Internal/bulge = 2.4  for closure of 28-320	Size = 6
		Stack = 0.3  for stack of 32-316
		Stack = -2.5  for stack of 33-315
	Helix total = -2.2
	Internal/bulge = 0.3  for closure of 34-314	Size = 4
		Stack = -2.1  for stack of 37-311
		Stack = -2.4  for stack of 38-310
		Stack = -1.4  for stack of 39-309
	Helix total = -5.9
	Internal/bulge = 3.6  for closure of 40-308	Size = 7
		Stack = -2.1  for stack of 43-302
		Stack = -1.1  for stack of 44-301
		Stack = -2.1  for stack of 45-300
		Stack = -2.5  for stack of 46-299
	Helix total = -7.8
	Multiloop = 5.6  for closure of 47-298
		Stack = -2.5  for stack of 239-277
		Stack = -3.3  for stack of 240-276
		Stack = -2.1  for stack of 241-275
		Stack = -0.6  for stack of 242-274
	Helix total = -8.5
	Internal/bulge = 3.7  for closure of 243-273	Size = 3
		Stack = -0.6  for stack of 246-271
		Stack = -0.9  for stack of 247-270
	Helix total = -1.5
	Internal/bulge = 4.6  for closure of 248-269	Size = 4
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 253-268	Size = 2
	Helix total = 0.0
	Hairpin = 6.3  for closure of 255-266
		Stack = -2.5  for stack of 199-224
		Stack = -3.3  for stack of 200-223
		Stack = -2.1  for stack of 201-222
		Stack = -1.3  for stack of 202-221
	Helix total = -9.2
	Internal/bulge = 3.7  for closure of 203-220	Size = 1 BP stack across bulge = 0.3
		Stack = -2.5  for stack of 204-218
		Stack = -2.4  for stack of 205-217
		Stack = -2.5  for stack of 206-216
		Stack = -0.6  for stack of 207-215
	Helix total = -8.0
	Hairpin = 5.5  for closure of 208-214
		Stack = -2.1  for stack of 145-181
		Stack = -1.4  for stack of 146-180
		Stack = -2.4  for stack of 147-179
		Stack = -0.9  for stack of 148-178
		Stack = -0.9  for stack of 149-177
	Helix total = -7.7
	Internal/bulge = 1.2  for closure of 150-176	Size = 2
		Stack = -0.9  for stack of 152-174
		Stack = -1.3  for stack of 153-173
		Stack = -0.9  for stack of 154-172
		Stack = -2.1  for stack of 155-171
	Helix total = -5.2
	Internal/bulge = 0.4  for closure of 156-170	Size = 1 BP stack across bulge = -3.4
	Helix total = 0.0
	Hairpin = 5.0  for closure of 158-169
		Stack = -3.4  for stack of 118-144
		Stack = -2.1  for stack of 119-143
	Helix total = -5.5
	Internal/bulge = 2.6  for closure of 120-142	Size = 3
		Stack = -0.6  for stack of 123-140
		Stack = -2.5  for stack of 124-139
		Stack = -2.1  for stack of 125-138
		Stack = -2.1  for stack of 126-137
	Helix total = -7.3
	Hairpin = 5.0  for closure of 127-136
		Stack = -2.4  for stack of 48-63
		Stack = -3.4  for stack of 49-62
		Stack = -2.1  for stack of 50-61
		Stack = -0.9  for stack of 51-60
	Helix total = -8.8
	Hairpin = 5.2  for closure of 52-59


	Total energy = -46.1



