Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:66 50:65 51:64 52:63 53:62 156:197 157:196 158:195
	    159:194 160:193 161:192 214:243 215:242 216:241 217:240 262:299
	    263:298 264:297 265:296 266:294 267:293 268:292
	Energy of Broken Structure: -86.8
	Energy of Pseudo-Helices:   -40.0
	Pseudoknot Energy Penalty:  32.1
	Total Free Energy:          -94.7
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 = -3.4  for stack of 4-356
		Stack = -2.1  for stack of 5-355
		Stack = -2.1  for stack of 6-354
	Helix total = -14.5
	Multiloop = 5.2  for closure of 7-353
		Stack = -3.3  for stack of 336-352
		Stack = -3.3  for stack of 337-351
		Stack = -3.3  for stack of 338-350
		Stack = -3.3  for stack of 339-349
	Helix total = -13.2
	Hairpin = 4.4  for closure of 340-348
		Stack = -2.4  for stack of 21-332
		Stack = -1.5  for stack of 22-331
		Stack = -0.5  for stack of 23-330
		Stack = -1.3  for stack of 24-329
		Stack = -1.1  for stack of 25-328
		Stack = -0.9  for stack of 26-327
	Helix total = -7.7
	Internal/bulge = 3.6  for closure of 27-326	Size = 11
		Stack = -2.2  for stack of 34-320
		Stack = -3.3  for stack of 35-319
	Helix total = -5.5
	Internal/bulge = 1.0  for closure of 36-318	Size = 6
		Stack = -3.3  for stack of 40-314
		Stack = -2.2  for stack of 41-313
		Stack = -1.0  for stack of 42-312
	Helix total = -6.5
	Internal/bulge = 3.7  for closure of 43-311	Size = 3
		Stack = -2.1  for stack of 44-307
		Stack = -1.1  for stack of 45-306
		Stack = -2.1  for stack of 46-305
		Stack = -3.4  for stack of 47-304
	Helix total = -8.7
	Multiloop = 3.8  for closure of 48-303
		Stack = -2.5  for stack of 247-282
		Stack = -0.5  for stack of 248-281
	Helix total = -3.0
	Internal/bulge = 1.2  for closure of 249-280	Size = 2
		Stack = -2.5  for stack of 251-278
		Stack = -1.5  for stack of 252-277
		Stack = -2.1  for stack of 253-276
		Stack = -2.1  for stack of 254-275
		Stack = -2.5  for stack of 255-274
	Helix total = -10.7
	Internal/bulge = 1.2  for closure of 256-273	Size = 2
		Stack = -3.4  for stack of 258-271
		Stack = -2.4  for stack of 259-270
	Helix total = -5.8
	Hairpin = 4.5  for closure of 260-269
		Stack = -2.1  for stack of 201-228
		Stack = -2.5  for stack of 202-227
	Helix total = -4.6
	Internal/bulge = 1.7  for closure of 203-226	Size = 8
		Stack = -2.2  for stack of 208-221
		Stack = -3.3  for stack of 209-220
		Stack = -2.1  for stack of 210-219
	Helix total = -7.6
	Hairpin = 5.2  for closure of 211-218
		Stack = -3.3  for stack of 138-181
		Stack = -2.1  for stack of 139-180
		Stack = -2.4  for stack of 140-179
		Stack = -2.1  for stack of 141-178
		Stack = -2.4  for stack of 142-177
		Stack = -2.1  for stack of 143-176
	Helix total = -14.4
	Internal/bulge = 4.1  for closure of 144-175	Size = 4
		Stack = -3.3  for stack of 145-170
		Stack = -3.3  for stack of 146-169
		Stack = -2.1  for stack of 147-168
	Helix total = -8.7
	Internal/bulge = 0.7  for closure of 148-167	Size = 4
		Stack = -3.3  for stack of 151-164
		Stack = -2.1  for stack of 152-163
	Helix total = -5.4
	Hairpin = 5.5  for closure of 153-162
		Stack = -3.4  for stack of 108-137
	Helix total = -3.4
	Internal/bulge = 0.9  for closure of 109-136	Size = 2
		Stack = -2.1  for stack of 111-134
		Stack = -1.3  for stack of 112-133
	Helix total = -3.4
	Internal/bulge = 1.3  for closure of 113-132	Size = 1 BP stack across bulge = -2.1
		Stack = -3.4  for stack of 114-130
		Stack = -2.1  for stack of 115-129
		Stack = -2.1  for stack of 116-128
	Helix total = -7.6
	Hairpin = 5.7  for closure of 117-127
		Stack = -2.1  for stack of 54-78
		Stack = -3.4  for stack of 55-77
		Stack = -2.4  for stack of 56-76
		Stack = -3.3  for stack of 57-75
		Stack = -2.2  for stack of 58-74
	Helix total = -13.4
	Hairpin = 5.3  for closure of 59-73


	Total energy = -86.8



