Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    47:64 48:63 49:62 50:61 51:60 148:195 149:194 150:193
	    151:192 152:191 153:190 212:241 213:240 214:239 215:238 261:300
	    262:299 264:297 265:296 266:295 267:294
	Energy of Broken Structure: 1299.8
	Energy of Pseudo-Helices:   -33.7
	Pseudoknot Energy Penalty:  42.2
	Total Free Energy:          1308.3
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-360
		Stack = -1.5  for stack of 2-359
		Stack = -2.1  for stack of 3-358
		Stack = -3.3  for stack of 4-357
		Stack = -3.4  for stack of 5-356
		Stack = -2.4  for stack of 6-355
	Helix total = -16.0
	Multiloop = 5.0  for closure of 7-354
		Stack = -3.4  for stack of 337-353
		Stack = -2.4  for stack of 338-352
		Stack = -3.3  for stack of 339-351
		Stack = -3.3  for stack of 340-350
	Helix total = -12.4
	Hairpin = 4.4  for closure of 341-349
		Stack = -2.4  for stack of 19-333
		Stack = -3.4  for stack of 20-332
		Stack = -2.1  for stack of 21-331
		Stack = -2.1  for stack of 22-330
	Helix total = -10.0
	Internal/bulge = 1.2  for closure of 23-329	Size = 1 BP stack across bulge = -2.2
	Helix total = 0.0
	Internal/bulge = 0.2  for closure of 25-328	Size = 4
	Helix total = 0.0
	Internal/bulge = 1.7  for closure of 28-325	Size = 6
		Stack = -2.5  for stack of 32-321
		Stack = -3.3  for stack of 33-320
	Helix total = -5.8
	Internal/bulge = 1.1  for closure of 34-319	Size = 2
		Stack = -1.5  for stack of 36-317
		Stack = -2.4  for stack of 37-316
		Stack = -3.3  for stack of 38-315
	Helix total = -7.2
	Internal/bulge = 3.3  for closure of 39-314	Size = 7
		Stack = -2.1  for stack of 42-308
		Stack = -1.1  for stack of 43-307
		Stack = -2.1  for stack of 44-306
		Stack = -3.4  for stack of 45-305
	Helix total = -8.7
	Multiloop = 4.1  for closure of 46-304
		Stack = -2.5  for stack of 245-282
		Stack = -3.3  for stack of 246-281
	Helix total = -5.8
	Internal/bulge = 0.5  for closure of 247-280	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.2  for closure of 249-278	Size = 3
	Helix total = 0.0
	Internal/bulge = 1.7  for closure of 252-276	Size = 9
		Stack = -2.4  for stack of 257-270
		Stack = -3.3  for stack of 258-269
	Helix total = -5.7
	Hairpin = 4.1  for closure of 259-268
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 197-229	Size = 2
		Stack = -2.5  for stack of 199-227
		Stack = 0.3  for stack of 200-226
		Stack = -2.5  for stack of 201-225
		Stack = -2.4  for stack of 202-224
		Stack = -3.4  for stack of 203-223
		Stack = -2.1  for stack of 204-222
		Stack = -1.1  for stack of 205-221
		Stack = -1.3  for stack of 206-220
		Stack = -1.5  for stack of 207-219
		Stack = -2.1  for stack of 208-218
		Stack = -1.0  for stack of 209-217
	Helix total = -19.6
	Hairpin = 4.6  for closure of 210-216
		Stack = -3.3  for stack of 131-181
		Stack = -3.3  for stack of 132-180
		Stack = -2.1  for stack of 133-179
		Stack = -2.4  for stack of 134-178
		Stack = -2.1  for stack of 135-177
		Stack = -1.4  for stack of 136-176
	Helix total = -14.6
	Multiloop = 3.3  for closure of 137-175
		Stack = -3.4  for stack of 162-171
		Stack = -3.3  for stack of 163-170
	Helix total = -6.7
	Hairpin = 3.3  for closure of 164-169
		Stack = -3.3  for stack of 139-160
		Stack = -2.4  for stack of 140-159
		Stack = -3.3  for stack of 141-158
		Stack = -2.4  for stack of 142-157
		Stack = -1.1  for stack of 143-156
		Stack = -1.3  for stack of 144-155
	Helix total = -13.8
	Hairpin = 5.3  for closure of 145-154
		Stack = -2.1  for stack of 111-130
		Stack = -2.4  for stack of 112-129
		Stack = -1.4  for stack of 113-128
		Stack = -2.5  for stack of 114-127
		Stack = -2.1  for stack of 115-126
		Stack = -2.1  for stack of 116-125
		Stack = -3.4  for stack of 117-124
		Stack = -2.1  for stack of 118-123
	Helix total = -18.1
	Hairpin = 1400.5  for closure of 119-122
		Stack = -2.1  for stack of 52-78
		Stack = -3.4  for stack of 53-77
		Stack = -2.4  for stack of 54-76
		Stack = -1.5  for stack of 55-75
		Stack = 1.3  for stack of 56-74
		Stack = -0.5  for stack of 57-73
	Helix total = -8.6
	Hairpin = 6.8  for closure of 58-72


	Total energy = 1299.8



