Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    55:72 56:71 57:70 159:193 160:192 161:191 162:190 163:189
	    164:188 209:238 210:237 211:236 212:235 213:234 256:297 257:296
	    258:295 260:293 261:292 262:291
	Energy of Broken Structure: -79.1
	Energy of Pseudo-Helices:   -38.3
	Pseudoknot Energy Penalty:  31.5
	Total Free Energy:          -85.9
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-359
		Stack = -1.5  for stack of 2-358
		Stack = -2.1  for stack of 3-357
		Stack = -2.4  for stack of 4-356
		Stack = -2.2  for stack of 5-355
		Stack = -2.4  for stack of 6-354
	Helix total = -13.9
	Multiloop = 5.1  for closure of 7-353
		Stack = -2.2  for stack of 336-352
		Stack = -2.1  for stack of 337-351
		Stack = -3.3  for stack of 338-350
		Stack = -3.3  for stack of 339-349
	Helix total = -10.9
	Hairpin = 4.4  for closure of 340-348
		Stack = -2.1  for stack of 20-332
		Stack = -2.1  for stack of 21-331
		Stack = -1.5  for stack of 22-330
		Stack = -0.5  for stack of 23-329
		Stack = -1.3  for stack of 24-328
		Stack = -1.4  for stack of 25-327
		Stack = 0.3  for stack of 26-326
	Helix total = -8.6
	Internal/bulge = 3.1  for closure of 27-325	Size = 12
		Stack = -2.5  for stack of 34-318
		Stack = -2.1  for stack of 35-317
		Stack = -0.9  for stack of 36-316
		Stack = -1.0  for stack of 37-315
		Stack = -1.3  for stack of 38-314
		Stack = -2.1  for stack of 39-313
		Stack = -3.4  for stack of 40-312
	Helix total = -13.3
	Internal/bulge = 3.9  for closure of 41-311	Size = 7
		Stack = -2.4  for stack of 44-305
		Stack = -2.4  for stack of 45-304
		Stack = -2.1  for stack of 46-303
		Stack = -3.4  for stack of 47-302
	Helix total = -10.3
	Multiloop = 2.3  for closure of 48-301
		Stack = -2.5  for stack of 241-277
		Stack = -2.1  for stack of 242-276
		Stack = -2.4  for stack of 243-275
	Helix total = -7.0
	Internal/bulge = 2.1  for closure of 244-274	Size = 15
		Stack = -3.4  for stack of 252-265
		Stack = -3.3  for stack of 253-264
	Helix total = -6.7
	Hairpin = 4.5  for closure of 254-263
		Stack = -2.1  for stack of 198-223
		Stack = -0.9  for stack of 199-222
		Stack = -1.0  for stack of 200-221
		Stack = -2.5  for stack of 201-220
		Stack = -2.4  for stack of 202-219
		Stack = -2.2  for stack of 203-218
		Stack = -0.9  for stack of 204-217
		Stack = -2.4  for stack of 205-216
	Helix total = -14.4
	Hairpin = 4.5  for closure of 206-215
		Stack = -3.4  for stack of 144-179
		Stack = -2.1  for stack of 145-178
		Stack = -2.4  for stack of 146-177
		Stack = -2.1  for stack of 147-176
		Stack = -0.9  for stack of 148-175
		Stack = -2.4  for stack of 149-174
	Helix total = -13.3
	Internal/bulge = 1.2  for closure of 150-173	Size = 2
		Stack = 0.3  for stack of 152-171
	Helix total = 0.3
	Internal/bulge = 2.5  for closure of 153-170	Size = 1 BP stack across bulge = -1.3
		Stack = -2.2  for stack of 154-168
		Stack = -2.1  for stack of 155-167
		Stack = -1.4  for stack of 156-166
	Helix total = -5.7
	Hairpin = 5.1  for closure of 157-165
		Stack = -3.4  for stack of 123-141
		Stack = -2.1  for stack of 124-140
		Stack = -2.1  for stack of 125-139
		Stack = -3.4  for stack of 126-138
	Helix total = -11.0
	Internal/bulge = 0.5  for closure of 127-137	Size = 1 BP stack across bulge = -3.3
		Stack = -2.1  for stack of 128-135
	Helix total = -2.1
	Hairpin = 5.1  for closure of 129-134
		Stack = -2.4  for stack of 49-63
		Stack = -2.4  for stack of 50-62
		Stack = -2.1  for stack of 51-61
		Stack = -2.4  for stack of 52-60
	Helix total = -9.3
	Hairpin = 4.5  for closure of 53-59


	Total energy = -79.1



