Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:67 50:66 51:65 52:64 53:63 159:194 161:192 162:191
	    163:190 211:242 212:241 213:240 214:239 215:238 260:296 261:295
	    262:294 264:292 265:291 266:290
	Energy of Broken Structure: -57.0
	Energy of Pseudo-Helices:   -33.4
	Pseudoknot Energy Penalty:  31.5
	Total Free Energy:          -58.9
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-356
		Stack = -1.5  for stack of 2-355
		Stack = -2.1  for stack of 3-354
		Stack = -3.4  for stack of 4-353
		Stack = -2.1  for stack of 5-352
		Stack = -2.1  for stack of 6-351
	Helix total = -14.5
	Multiloop = 5.2  for closure of 7-350
		Stack = -3.3  for stack of 333-349
		Stack = -3.3  for stack of 334-348
		Stack = -3.3  for stack of 335-347
		Stack = -3.3  for stack of 336-346
	Helix total = -13.2
	Hairpin = 4.4  for closure of 337-345
		Stack = -2.1  for stack of 21-329
		Stack = -0.9  for stack of 22-328
		Stack = -0.6  for stack of 23-327
		Stack = -1.3  for stack of 24-326
		Stack = -1.1  for stack of 25-325
		Stack = -0.9  for stack of 26-324
	Helix total = -6.9
	Internal/bulge = 3.6  for closure of 27-323	Size = 11
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 34-317	Size = 2
		Stack = -3.3  for stack of 36-315
	Helix total = -3.3
	Internal/bulge = 1.2  for closure of 37-314	Size = 4
		Stack = -3.3  for stack of 40-311
		Stack = -2.5  for stack of 41-310
		Stack = 0.3  for stack of 42-309
	Helix total = -5.5
	Internal/bulge = 3.7  for closure of 43-308	Size = 3
		Stack = -2.1  for stack of 44-304
		Stack = -1.1  for stack of 45-303
		Stack = -2.1  for stack of 46-302
		Stack = -3.4  for stack of 47-301
	Helix total = -8.7
	Multiloop = 3.7  for closure of 48-300
		Stack = -2.5  for stack of 245-280
		Stack = -1.5  for stack of 246-279
		Stack = -2.1  for stack of 247-278
		Stack = -0.9  for stack of 248-277
	Helix total = -7.0
	Internal/bulge = 2.0  for closure of 249-276	Size = 1 BP stack across bulge = -1.4
		Stack = -1.5  for stack of 251-275
	Helix total = -1.5
	Internal/bulge = 0.9  for closure of 252-274	Size = 7
		Stack = -3.4  for stack of 256-269
		Stack = -2.4  for stack of 257-268
	Helix total = -5.8
	Hairpin = 4.5  for closure of 258-267
		Stack = -1.4  for stack of 198-227
		Stack = -2.1  for stack of 199-226
		Stack = -2.5  for stack of 200-225
	Helix total = -6.0
	Internal/bulge = 1.0  for closure of 201-224	Size = 8
		Stack = -2.5  for stack of 206-219
		Stack = -1.5  for stack of 207-218
		Stack = -3.3  for stack of 208-217
	Helix total = -7.3
	Hairpin = 4.4  for closure of 209-216
		Stack = -3.3  for stack of 140-180
		Stack = -2.1  for stack of 141-179
		Stack = -0.9  for stack of 142-178
		Stack = -2.4  for stack of 143-177
		Stack = -2.1  for stack of 144-176
	Helix total = -10.8
	Internal/bulge = 3.4  for closure of 145-175	Size = 7
		Stack = -2.1  for stack of 149-170
	Helix total = -2.1
	Internal/bulge = 3.3  for closure of 150-169	Size = 2
		Stack = -2.1  for stack of 153-168
	Helix total = -2.1
	Internal/bulge = 1.2  for closure of 154-167	Size = 2
	Helix total = 0.0
	Hairpin = 4.8  for closure of 156-165
		Stack = -3.4  for stack of 110-139
	Helix total = -3.4
	Internal/bulge = 0.9  for closure of 111-138	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.3  for closure of 113-136	Size = 5
		Stack = -3.4  for stack of 116-132
		Stack = -2.1  for stack of 117-131
		Stack = -2.1  for stack of 118-130
	Helix total = -7.6
	Hairpin = 5.7  for closure of 119-129
		Stack = -2.1  for stack of 54-80
		Stack = -3.4  for stack of 55-79
		Stack = -2.4  for stack of 56-78
		Stack = -3.3  for stack of 57-77
		Stack = -2.2  for stack of 58-76
	Helix total = -13.4
	Hairpin = 6.4  for closure of 59-75


	Total energy = -57.0



