Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:67 50:66 51:65 52:64 53:63 158:197 159:196 160:195
	    161:194 162:193 214:245 215:244 216:243 217:242 218:241 263:300
	    264:299 265:298 266:297 267:295 268:294 269:293
	Energy of Broken Structure: -88.0
	Energy of Pseudo-Helices:   -40.0
	Pseudoknot Energy Penalty:  31.9
	Total Free Energy:          -96.1
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 = -3.4  for stack of 4-357
		Stack = -2.1  for stack of 5-356
		Stack = -2.1  for stack of 6-355
	Helix total = -14.5
	Multiloop = 5.2  for closure of 7-354
		Stack = -3.3  for stack of 337-353
		Stack = -3.3  for stack of 338-352
		Stack = -3.3  for stack of 339-351
		Stack = -3.3  for stack of 340-350
	Helix total = -13.2
	Hairpin = 4.4  for closure of 341-349
		Stack = -2.4  for stack of 21-333
		Stack = -1.5  for stack of 22-332
		Stack = -0.5  for stack of 23-331
		Stack = -1.3  for stack of 24-330
		Stack = -1.1  for stack of 25-329
		Stack = -0.9  for stack of 26-328
	Helix total = -7.7
	Internal/bulge = 3.0  for closure of 27-327	Size = 11
		Stack = -2.5  for stack of 34-321
		Stack = -3.3  for stack of 35-320
	Helix total = -5.8
	Internal/bulge = 1.2  for closure of 36-319	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 38-317	Size = 2
		Stack = -3.3  for stack of 40-315
	Helix total = -3.3
	Internal/bulge = 1.0  for closure of 41-314	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.7  for closure of 43-312	Size = 3
		Stack = -2.1  for stack of 44-308
		Stack = -1.1  for stack of 45-307
		Stack = -2.1  for stack of 46-306
		Stack = -3.4  for stack of 47-305
	Helix total = -8.7
	Multiloop = 1.4  for closure of 48-304
		Stack = -2.5  for stack of 248-283
		Stack = -1.5  for stack of 249-282
	Helix total = -4.0
	Internal/bulge = 0.5  for closure of 250-281	Size = 2
		Stack = -2.5  for stack of 252-279
		Stack = -1.5  for stack of 253-278
		Stack = -2.1  for stack of 254-277
		Stack = -2.1  for stack of 255-276
		Stack = -2.5  for stack of 256-275
	Helix total = -10.7
	Internal/bulge = 2.2  for closure of 257-274	Size = 2
		Stack = -3.4  for stack of 259-272
		Stack = -2.4  for stack of 260-271
	Helix total = -5.8
	Hairpin = 4.5  for closure of 261-270
		Stack = -2.4  for stack of 202-229
		Stack = -2.5  for stack of 203-228
	Helix total = -4.9
	Internal/bulge = 1.4  for closure of 204-227	Size = 8
		Stack = -2.5  for stack of 209-222
		Stack = -1.5  for stack of 210-221
		Stack = -3.3  for stack of 211-220
	Helix total = -7.3
	Hairpin = 4.4  for closure of 212-219
		Stack = -3.3  for stack of 139-182
		Stack = -2.1  for stack of 140-181
		Stack = -2.4  for stack of 141-180
		Stack = -2.1  for stack of 142-179
		Stack = -2.4  for stack of 143-178
		Stack = -2.1  for stack of 144-177
	Helix total = -14.4
	Internal/bulge = 4.1  for closure of 145-176	Size = 4
		Stack = -3.3  for stack of 146-171
		Stack = -3.3  for stack of 147-170
		Stack = -2.1  for stack of 148-169
	Helix total = -8.7
	Internal/bulge = 0.7  for closure of 149-168	Size = 4
		Stack = -3.3  for stack of 152-165
		Stack = -2.1  for stack of 153-164
	Helix total = -5.4
	Hairpin = 5.5  for closure of 154-163
		Stack = -3.4  for stack of 109-138
		Stack = -2.1  for stack of 110-137
		Stack = -1.3  for stack of 111-136
		Stack = -0.6  for stack of 112-135
		Stack = -1.3  for stack of 113-134
	Helix total = -8.7
	Internal/bulge = 1.3  for closure of 114-133	Size = 1 BP stack across bulge = -2.1
		Stack = -3.4  for stack of 115-131
		Stack = -2.1  for stack of 116-130
		Stack = -2.1  for stack of 117-129
	Helix total = -7.6
	Hairpin = 5.7  for closure of 118-128
		Stack = -3.4  for stack of 55-78
		Stack = -2.4  for stack of 56-77
		Stack = -3.3  for stack of 57-76
		Stack = -2.5  for stack of 58-75
		Stack = -0.6  for stack of 59-74
	Helix total = -12.2
	Hairpin = 5.2  for closure of 60-73


	Total energy = -88.0



