Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:66 49:65 50:64 51:63 52:62 146:181 147:180 148:179
	    149:178 150:177 151:176 196:225 197:224 198:223 199:222 200:221
	    201:220 245:284 246:283 247:282 248:281 249:280 250:279 251:278
	Energy of Broken Structure: -86.5
	Energy of Pseudo-Helices:   -48.9
	Pseudoknot Energy Penalty:  31.7
	Total Free Energy:          -103.7
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-344
		Stack = -1.5  for stack of 2-343
		Stack = -2.1  for stack of 3-342
		Stack = -3.3  for stack of 4-341
		Stack = -2.2  for stack of 5-340
		Stack = -2.1  for stack of 6-339
	Helix total = -14.5
	Multiloop = 5.1  for closure of 7-338
		Stack = -3.3  for stack of 321-337
		Stack = -3.4  for stack of 322-336
		Stack = -2.4  for stack of 323-335
		Stack = -3.3  for stack of 324-334
	Helix total = -12.4
	Hairpin = 4.4  for closure of 325-333
		Stack = -2.1  for stack of 20-317
		Stack = -0.6  for stack of 21-316
		Stack = -2.1  for stack of 22-315
		Stack = -1.5  for stack of 23-314
		Stack = -2.1  for stack of 24-313
	Helix total = -8.4
	Internal/bulge = 2.3  for closure of 25-312	Size = 3
		Stack = -2.1  for stack of 28-310
	Helix total = -2.1
	Internal/bulge = 2.1  for closure of 29-309	Size = 7
		Stack = -2.1  for stack of 33-304
		Stack = -2.5  for stack of 34-303
		Stack = -1.4  for stack of 35-302
	Helix total = -6.0
	Internal/bulge = 1.6  for closure of 36-301	Size = 1 BP stack across bulge = -2.2
		Stack = -2.1  for stack of 38-300
		Stack = -3.4  for stack of 39-299
	Helix total = -5.5
	Internal/bulge = 3.9  for closure of 40-298	Size = 7
		Stack = -2.4  for stack of 43-292
		Stack = -2.2  for stack of 44-291
		Stack = -2.1  for stack of 45-290
		Stack = -2.2  for stack of 46-289
	Helix total = -8.9
	Multiloop = 3.9  for closure of 47-288
		Stack = -2.4  for stack of 229-267
		Stack = -3.3  for stack of 230-266
	Helix total = -5.7
	Internal/bulge = 2.2  for closure of 231-265	Size = 4
		Stack = -1.4  for stack of 234-262
		Stack = -3.3  for stack of 235-261
		Stack = -3.3  for stack of 236-260
	Helix total = -8.0
	Internal/bulge = 1.9  for closure of 237-259	Size = 3
	Helix total = 0.0
	Internal/bulge = -0.1  for closure of 239-256	Size = 2
		Stack = -3.4  for stack of 241-254
		Stack = -3.3  for stack of 242-253
	Helix total = -6.7
	Hairpin = 3.4  for closure of 243-252
		Stack = -3.4  for stack of 184-211
		Stack = -3.3  for stack of 185-210
	Helix total = -6.7
	Internal/bulge = 2.6  for closure of 186-209	Size = 5
		Stack = -3.3  for stack of 189-205
		Stack = -3.4  for stack of 190-204
	Helix total = -6.7
	Hairpin = 4.3  for closure of 191-203
		Stack = -2.1  for stack of 128-167
		Stack = -2.1  for stack of 129-166
		Stack = -2.2  for stack of 130-165
	Helix total = -6.4
	Internal/bulge = 1.7  for closure of 131-164	Size = 6
		Stack = -2.4  for stack of 135-160
		Stack = -3.4  for stack of 136-159
		Stack = -3.3  for stack of 137-158
	Helix total = -9.1
	Internal/bulge = 0.6  for closure of 138-157	Size = 4
		Stack = -3.4  for stack of 141-154
		Stack = -3.3  for stack of 142-153
	Helix total = -6.7
	Hairpin = 4.7  for closure of 143-152
		Stack = -2.4  for stack of 109-127
		Stack = -2.1  for stack of 110-126
		Stack = -2.4  for stack of 111-125
		Stack = -1.4  for stack of 112-124
		Stack = -2.5  for stack of 113-123
		Stack = -2.1  for stack of 114-122
	Helix total = -12.9
	Hairpin = 4.2  for closure of 115-121
		Stack = -3.4  for stack of 54-78
		Stack = -3.3  for stack of 55-77
		Stack = -2.4  for stack of 56-76
		Stack = -2.2  for stack of 57-75
		Stack = -0.9  for stack of 58-74
	Helix total = -12.2
	Hairpin = 5.3  for closure of 59-73


	Total energy = -86.5



