Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    53:74 54:73 55:72 56:71 57:70 160:198 161:197 162:196
	    163:195 164:194 165:193 166:192 167:191 211:236 212:235 213:234
	    258:292 259:291 260:290 261:289 262:288 263:287 264:286 265:285
	Energy of Broken Structure: -53.1
	Energy of Pseudo-Helices:   -38.9
	Pseudoknot Energy Penalty:  47.4
	Total Free Energy:          -44.6
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 = -2.2  for stack of 5-351
		Stack = -2.4  for stack of 6-350
	Helix total = -13.9
	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 = -0.6  for stack of 27-321
		Stack = -1.3  for stack of 28-320
	Helix total = -9.7
	Internal/bulge = 2.6  for closure of 29-319	Size = 4
		Stack = -0.5  for stack of 32-316
		Stack = -2.5  for stack of 33-315
		Stack = -3.3  for stack of 34-314
	Helix total = -6.3
	Internal/bulge = 1.1  for closure of 35-313	Size = 2
		Stack = -1.4  for stack of 37-311
		Stack = -3.3  for stack of 38-310
		Stack = -2.5  for stack of 39-309
		Stack = 0.3  for stack of 40-308
	Helix total = -6.9
	Internal/bulge = 4.5  for closure of 41-307	Size = 5
		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 = 5.7  for closure of 47-298
		Stack = -1.4  for stack of 240-277
		Stack = -2.4  for stack of 241-276
		Stack = -2.1  for stack of 242-275
		Stack = -1.3  for stack of 243-274
	Helix total = -7.2
	Internal/bulge = 3.7  for closure of 244-273	Size = 3
		Stack = -0.5  for stack of 247-271
	Helix total = -0.5
	Internal/bulge = 2.8  for closure of 248-270	Size = 1 BP stack across bulge = -1.0
		Stack = -0.9  for stack of 250-269
		Stack = -0.9  for stack of 251-268
		Stack = -1.4  for stack of 252-267
	Helix total = -3.2
	Hairpin = 6.5  for closure of 253-266
		Stack = -1.3  for stack of 200-224
		Stack = -1.1  for stack of 201-223
		Stack = -0.9  for stack of 202-222
		Stack = -1.0  for stack of 203-221
		Stack = -1.3  for stack of 204-220
		Stack = -0.9  for stack of 205-219
		Stack = -0.9  for stack of 206-218
		Stack = -1.1  for stack of 207-217
		Stack = -0.9  for stack of 208-216
	Helix total = -9.4
	Hairpin = 5.5  for closure of 209-215
		Stack = -2.1  for stack of 146-182
		Stack = 0.3  for stack of 147-181
		Stack = -1.3  for stack of 148-180
		Stack = -0.9  for stack of 149-179
		Stack = -1.1  for stack of 150-178
		Stack = -0.9  for stack of 151-177
		Stack = -1.3  for stack of 152-176
		Stack = -0.6  for stack of 153-175
		Stack = -1.3  for stack of 154-174
		Stack = -0.9  for stack of 155-173
		Stack = -2.1  for stack of 156-172
		Stack = -2.5  for stack of 157-171
	Helix total = -14.7
	Hairpin = 5.7  for closure of 158-170
		Stack = -3.4  for stack of 119-145
		Stack = -2.1  for stack of 120-144
	Helix total = -5.5
	Internal/bulge = 2.6  for closure of 121-143	Size = 3
		Stack = -0.6  for stack of 124-141
		Stack = -2.5  for stack of 125-140
		Stack = -2.1  for stack of 126-139
		Stack = -2.1  for stack of 127-138
	Helix total = -7.3
	Hairpin = 5.0  for closure of 128-137
		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 = -53.1



