Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    54:80 55:79 56:78 57:77 58:76 147:178 148:177 149:176
	    151:174 196:227 197:226 198:225 199:224 200:223 201:222 246:277
	    247:276 248:275 249:274 250:273 251:272 252:271 253:270
	Energy of Broken Structure: -42.7
	Energy of Pseudo-Helices:   -36.6
	Pseudoknot Energy Penalty:  32.1
	Total Free Energy:          -47.2
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-337
		Stack = -1.5  for stack of 2-336
		Stack = -2.1  for stack of 3-335
		Stack = -3.3  for stack of 4-334
		Stack = -2.2  for stack of 5-333
		Stack = -2.1  for stack of 6-332
	Helix total = -14.5
	Multiloop = 5.0  for closure of 7-331
		Stack = -2.4  for stack of 314-330
		Stack = -3.3  for stack of 315-329
		Stack = -3.3  for stack of 316-328
		Stack = -3.3  for stack of 317-327
	Helix total = -12.3
	Hairpin = 4.4  for closure of 318-326
		Stack = -2.1  for stack of 20-310
		Stack = -0.9  for stack of 21-309
		Stack = -0.9  for stack of 22-308
	Helix total = -3.9
	Internal/bulge = 1.9  for closure of 23-307	Size = 2
		Stack = -0.9  for stack of 25-305
		Stack = -2.1  for stack of 26-304
		Stack = -3.4  for stack of 27-303
	Helix total = -6.4
	Internal/bulge = 1.5  for closure of 28-302	Size = 5
		Stack = -3.3  for stack of 32-299
		Stack = -2.1  for stack of 33-298
	Helix total = -5.4
	Internal/bulge = 0.8  for closure of 34-297	Size = 4
		Stack = -2.1  for stack of 37-294
		Stack = -2.1  for stack of 38-293
		Stack = -2.5  for stack of 39-292
	Helix total = -6.7
	Internal/bulge = 3.6  for closure of 40-291	Size = 7
		Stack = -2.4  for stack of 43-285
		Stack = -2.4  for stack of 44-284
		Stack = -2.1  for stack of 45-283
		Stack = -3.4  for stack of 46-282
	Helix total = -10.3
	Multiloop = 6.7  for closure of 47-281
		Stack = -2.2  for stack of 229-266
		Stack = -2.1  for stack of 230-265
		Stack = -1.3  for stack of 231-264
		Stack = -1.1  for stack of 232-263
	Helix total = -6.7
	Internal/bulge = 4.0  for closure of 233-262	Size = 5
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 237-259	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.7  for closure of 239-257	Size = 3
	Helix total = 0.0
	Hairpin = 5.1  for closure of 243-256
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 180-214	Size = 2
		Stack = -1.5  for stack of 182-212
		Stack = -1.3  for stack of 183-211
	Helix total = -2.8
	Internal/bulge = 0.8  for closure of 184-210	Size = 2
		Stack = -3.4  for stack of 186-208
		Stack = -2.1  for stack of 187-207
	Helix total = -5.5
	Internal/bulge = 2.1  for closure of 188-206	Size = 1 BP stack across bulge = -1.3
		Stack = -2.1  for stack of 190-205
		Stack = -2.5  for stack of 191-204
		Stack = -0.5  for stack of 192-203
	Helix total = -5.1
	Hairpin = 5.2  for closure of 193-202
		Stack = -2.4  for stack of 133-171
		Stack = -2.5  for stack of 134-170
		Stack = -1.5  for stack of 135-169
		Stack = -2.4  for stack of 136-168
		Stack = -2.4  for stack of 137-167
	Helix total = -11.2
	Internal/bulge = 3.3  for closure of 138-166	Size = 2
		Stack = -2.1  for stack of 139-163
		Stack = -1.3  for stack of 140-162
		Stack = -1.1  for stack of 141-161
		Stack = -2.4  for stack of 142-160
	Helix total = -6.9
	Internal/bulge = 1.0  for closure of 143-159	Size = 1 BP stack across bulge = -2.4
		Stack = -1.5  for stack of 144-157
		Stack = -2.1  for stack of 145-156
	Helix total = -3.6
	Hairpin = 4.0  for closure of 146-155
	Helix total = 0.0
	Internal/bulge = 2.3  for closure of 113-132	Size = 4
	Helix total = 0.0
	Internal/bulge = 2.3  for closure of 116-129	Size = 4
	Helix total = 0.0
	Hairpin = 5.2  for closure of 119-126
		Stack = -2.1  for stack of 48-66
		Stack = -2.4  for stack of 49-65
		Stack = -2.1  for stack of 50-64
		Stack = -3.3  for stack of 51-63
	Helix total = -9.9
	Hairpin = 4.2  for closure of 52-62


	Total energy = -42.7



