Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:66 49:65 50:64 51:63 52:62 153:193 154:192 155:191
	    156:190 157:189 158:188 209:240 210:239 211:238 212:237 213:236
	    259:295 260:294 261:293 262:292 263:291 264:290 265:289
	Energy of Broken Structure: -44.9
	Energy of Pseudo-Helices:   -44.1
	Pseudoknot Energy Penalty:  31.4
	Total Free Energy:          -57.6
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -0.8
		Stack = -1.5  for stack of 1-354
		Stack = -2.1  for stack of 2-353
	Helix total = -3.6
	Multiloop = 6.3  for closure of 3-352
		Stack = -3.4  for stack of 332-348
		Stack = -2.4  for stack of 333-347
		Stack = -3.3  for stack of 334-346
		Stack = -3.3  for stack of 335-345
	Helix total = -12.4
	Hairpin = 4.4  for closure of 336-344
		Stack = -2.4  for stack of 20-328
	Helix total = -2.4
	Internal/bulge = -1.4  for closure of 21-327	Size = 2
		Stack = -1.3  for stack of 23-325
		Stack = -1.1  for stack of 24-324
		Stack = -1.3  for stack of 25-323
		Stack = -2.2  for stack of 26-322
	Helix total = -5.9
	Internal/bulge = 1.9  for closure of 27-321	Size = 9
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 33-316	Size = 2
		Stack = -3.3  for stack of 35-314
	Helix total = -3.3
	Internal/bulge = 0.2  for closure of 36-313	Size = 4
		Stack = -3.3  for stack of 39-310
		Stack = -2.2  for stack of 40-309
	Helix total = -5.5
	Internal/bulge = 4.5  for closure of 41-308	Size = 5
		Stack = -2.1  for stack of 43-303
		Stack = -1.1  for stack of 44-302
		Stack = -2.1  for stack of 45-301
		Stack = -3.4  for stack of 46-300
	Helix total = -8.7
	Multiloop = 5.8  for closure of 47-299
		Stack = -1.4  for stack of 243-279
		Stack = -2.4  for stack of 244-278
		Stack = -2.1  for stack of 245-277
		Stack = -2.1  for stack of 246-276
		Stack = -2.2  for stack of 247-275
	Helix total = -10.2
	Internal/bulge = 4.1  for closure of 248-274	Size = 7
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 253-270	Size = 2
		Stack = -3.4  for stack of 255-268
		Stack = -3.3  for stack of 256-267
	Helix total = -6.7
	Hairpin = 4.1  for closure of 257-266
		Stack = -2.5  for stack of 196-225
		Stack = -2.4  for stack of 197-224
		Stack = -2.5  for stack of 198-223
	Helix total = -7.4
	Internal/bulge = 2.1  for closure of 199-222	Size = 7
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 204-218	Size = 2
		Stack = -0.6  for stack of 206-216
		Stack = -1.3  for stack of 207-215
	Helix total = -1.9
	Hairpin = 4.6  for closure of 208-214
		Stack = -3.3  for stack of 136-176
		Stack = -2.1  for stack of 137-175
		Stack = -1.1  for stack of 138-174
		Stack = -2.4  for stack of 139-173
	Helix total = -8.9
	Internal/bulge = 3.9  for closure of 140-172	Size = 7
		Stack = -3.3  for stack of 143-166
		Stack = -2.4  for stack of 144-165
	Helix total = -5.7
	Internal/bulge = 3.9  for closure of 145-164	Size = 6
		Stack = -0.6  for stack of 150-161
		Stack = -1.3  for stack of 151-160
	Helix total = -1.9
	Hairpin = 5.1  for closure of 152-159
	Helix total = 0.0
	Internal/bulge = 1.3  for closure of 111-134	Size = 1 BP stack across bulge = -2.1
		Stack = -1.3  for stack of 112-132
		Stack = -2.1  for stack of 113-131
		Stack = -3.4  for stack of 114-130
		Stack = -2.4  for stack of 115-129
		Stack = -3.3  for stack of 116-128
	Helix total = -12.5
	Hairpin = 5.7  for closure of 117-127
		Stack = -2.1  for stack of 53-78
		Stack = -2.4  for stack of 54-77
		Stack = -2.1  for stack of 55-76
		Stack = -3.3  for stack of 56-75
		Stack = -3.4  for stack of 57-74
	Helix total = -13.3
	Hairpin = 5.4  for closure of 58-73


	Total energy = -44.9



