Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:68 49:67 50:66 51:65 52:64 162:196 163:195 164:194
	    165:193 166:192 167:191 211:244 212:243 213:242 214:241 215:240
	    216:239 217:238 263:301 264:300 265:299 266:298 267:297 269:295
	    270:294
	Energy of Broken Structure: -108.3
	Energy of Pseudo-Helices:   -44.7
	Pseudoknot Energy Penalty:  31.8
	Total Free Energy:          -121.2
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-362
		Stack = -1.5  for stack of 2-361
		Stack = -2.1  for stack of 3-360
		Stack = -2.4  for stack of 4-359
		Stack = -1.1  for stack of 5-358
		Stack = -2.1  for stack of 6-357
	Helix total = -12.5
	Multiloop = 5.0  for closure of 7-356
		Stack = -3.4  for stack of 339-355
		Stack = -2.4  for stack of 340-354
		Stack = -3.3  for stack of 341-353
		Stack = -3.3  for stack of 342-352
	Helix total = -12.4
	Hairpin = 4.4  for closure of 343-351
		Stack = -2.4  for stack of 19-335
		Stack = -2.2  for stack of 20-334
		Stack = -1.3  for stack of 21-333
		Stack = 0.3  for stack of 22-332
		Stack = -2.1  for stack of 23-331
		Stack = -2.5  for stack of 24-330
	Helix total = -10.2
	Internal/bulge = 3.4  for closure of 25-329	Size = 7
	Helix total = 0.0
	Internal/bulge = 1.6  for closure of 30-325	Size = 2
		Stack = -2.5  for stack of 32-323
		Stack = -3.3  for stack of 33-322
		Stack = -2.1  for stack of 34-321
		Stack = -2.1  for stack of 35-320
		Stack = -3.3  for stack of 36-319
		Stack = -3.3  for stack of 37-318
	Helix total = -16.6
	Internal/bulge = 1.7  for closure of 38-317	Size = 10
		Stack = -2.4  for stack of 43-310
		Stack = -3.3  for stack of 44-309
		Stack = -3.3  for stack of 45-308
		Stack = -2.2  for stack of 46-307
	Helix total = -11.2
	Multiloop = 4.9  for closure of 47-306
		Stack = -3.3  for stack of 246-282
		Stack = -3.4  for stack of 247-281
		Stack = -3.3  for stack of 248-280
		Stack = -3.3  for stack of 249-279
	Helix total = -13.3
	Internal/bulge = 2.8  for closure of 250-278	Size = 2
		Stack = -2.4  for stack of 253-277
		Stack = -2.4  for stack of 254-276
		Stack = -1.1  for stack of 255-275
		Stack = -2.1  for stack of 256-274
	Helix total = -8.0
	Hairpin = 5.6  for closure of 257-273
		Stack = -3.3  for stack of 200-228
		Stack = -2.1  for stack of 201-227
		Stack = -2.4  for stack of 202-226
		Stack = -2.1  for stack of 203-225
		Stack = -2.4  for stack of 204-224
		Stack = -2.1  for stack of 205-223
		Stack = -2.2  for stack of 206-222
		Stack = -3.3  for stack of 207-221
	Helix total = -19.9
	Hairpin = 4.3  for closure of 208-220
		Stack = -2.1  for stack of 147-183
		Stack = -2.5  for stack of 148-182
		Stack = -1.5  for stack of 149-181
		Stack = -2.1  for stack of 150-180
		Stack = -2.1  for stack of 151-179
	Helix total = -10.3
	Internal/bulge = 2.3  for closure of 152-178	Size = 4
		Stack = -3.3  for stack of 154-174
		Stack = -2.4  for stack of 155-173
		Stack = -3.3  for stack of 156-172
		Stack = -3.3  for stack of 157-171
	Helix total = -12.3
	Hairpin = 5.6  for closure of 158-170
		Stack = -2.4  for stack of 113-146
		Stack = -2.1  for stack of 114-145
	Helix total = -4.5
	Internal/bulge = 1.2  for closure of 115-144	Size = 1 BP stack across bulge = -2.2
		Stack = -2.4  for stack of 117-143
		Stack = -2.4  for stack of 118-142
		Stack = -3.4  for stack of 119-141
	Helix total = -8.2
	Internal/bulge = 0.5  for closure of 120-140	Size = 2
		Stack = -2.1  for stack of 122-138
		Stack = -2.4  for stack of 123-137
		Stack = -2.4  for stack of 124-136
		Stack = -3.4  for stack of 125-135
	Helix total = -10.3
	Hairpin = 5.0  for closure of 126-134
		Stack = -2.1  for stack of 54-83
		Stack = -3.4  for stack of 55-82
		Stack = -2.1  for stack of 56-81
		Stack = -1.1  for stack of 57-80
		Stack = -2.1  for stack of 58-79
	Helix total = -10.8
	Hairpin = 5.6  for closure of 59-78


	Total energy = -108.3



