Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:64 50:63 51:62 52:61 53:60 156:192 157:191 158:190
	    159:189 160:188 161:187 209:242 210:241 211:240 212:239 213:238
	    214:237 259:296 260:295 261:294 262:293 263:292 264:291 265:290
	Energy of Broken Structure: -61.8
	Energy of Pseudo-Helices:   -39.2
	Pseudoknot Energy Penalty:  37.3
	Total Free Energy:          -63.7
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-357
		Stack = -1.5  for stack of 2-356
		Stack = -2.1  for stack of 3-355
		Stack = -2.4  for stack of 4-354
		Stack = -2.2  for stack of 5-353
		Stack = -2.4  for stack of 6-352
	Helix total = -13.9
	Multiloop = 5.2  for closure of 7-351
		Stack = -3.4  for stack of 334-350
		Stack = -2.4  for stack of 335-349
		Stack = -3.3  for stack of 336-348
		Stack = -3.3  for stack of 337-347
	Helix total = -12.4
	Hairpin = 4.4  for closure of 338-346
		Stack = -2.1  for stack of 21-330
		Stack = -2.1  for stack of 22-329
		Stack = -1.5  for stack of 23-328
		Stack = -2.1  for stack of 24-327
		Stack = -3.3  for stack of 25-326
		Stack = -2.2  for stack of 26-325
		Stack = -2.4  for stack of 27-324
		Stack = -3.3  for stack of 28-323
	Helix total = -19.0
	Internal/bulge = 1.9  for closure of 29-322	Size = 4
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 32-319	Size = 2
		Stack = -2.5  for stack of 34-317
	Helix total = -2.5
	Internal/bulge = 0.3  for closure of 35-316	Size = 4
		Stack = -1.1  for stack of 38-313
		Stack = -1.3  for stack of 39-312
	Helix total = -2.4
	Internal/bulge = 4.9  for closure of 40-311	Size = 9
		Stack = -2.4  for stack of 44-304
		Stack = -2.2  for stack of 45-303
		Stack = -2.1  for stack of 46-302
		Stack = -2.2  for stack of 47-301
	Helix total = -8.9
	Multiloop = 4.9  for closure of 48-300
		Stack = -2.5  for stack of 245-279
		Stack = -1.0  for stack of 246-278
		Stack = -1.1  for stack of 247-277
		Stack = -2.4  for stack of 248-276
		Stack = -2.1  for stack of 249-275
		Stack = -1.1  for stack of 250-274
		Stack = -2.1  for stack of 251-273
		Stack = -2.5  for stack of 252-272
		Stack = -0.6  for stack of 253-271
	Helix total = -15.4
	Internal/bulge = 2.4  for closure of 254-270	Size = 1 BP stack across bulge = -1.0
		Stack = -2.1  for stack of 255-268
		Stack = -2.5  for stack of 256-267
	Helix total = -4.6
	Hairpin = 4.6  for closure of 257-266
		Stack = -2.1  for stack of 197-225
		Stack = -1.3  for stack of 198-224
		Stack = -0.9  for stack of 199-223
		Stack = -0.9  for stack of 200-222
		Stack = -2.2  for stack of 201-221
		Stack = -2.1  for stack of 202-220
	Helix total = -9.5
	Hairpin = 6.7  for closure of 203-219
		Stack = -1.1  for stack of 140-177
	Helix total = -1.1
	Internal/bulge = 1.2  for closure of 141-176	Size = 2
		Stack = -3.4  for stack of 143-174
	Helix total = -3.4
	Internal/bulge = 1.2  for closure of 144-173	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.1  for closure of 146-171	Size = 1 BP stack across bulge = -1.3
		Stack = -0.9  for stack of 147-169
		Stack = -2.2  for stack of 148-168
		Stack = -2.1  for stack of 149-167
		Stack = -2.1  for stack of 150-166
		Stack = -3.4  for stack of 151-165
		Stack = -2.1  for stack of 152-164
		Stack = -1.4  for stack of 153-163
	Helix total = -14.2
	Hairpin = 5.9  for closure of 154-162
		Stack = -2.5  for stack of 118-139
		Stack = -1.0  for stack of 119-138
		Stack = -2.1  for stack of 120-137
	Helix total = -5.6
	Internal/bulge = 1.2  for closure of 121-136	Size = 4
		Stack = -3.4  for stack of 124-133
	Helix total = -3.4
	Hairpin = 3.1  for closure of 125-132
		Stack = -0.5  for stack of 54-83
		Stack = 1.3  for stack of 55-82
		Stack = -0.5  for stack of 56-81
		Stack = -1.4  for stack of 57-80
		Stack = -1.5  for stack of 58-79
	Helix total = -2.6
	Hairpin = 6.9  for closure of 59-78


	Total energy = -61.8



