Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:67 50:66 51:65 52:64 53:63 149:182 150:181 151:180
	    152:179 153:178 200:228 201:227 202:226 203:225 204:224 205:223
	    231:267 234:264 239:261 241:256 243:254
	Energy of Broken Structure: -114.1
	Energy of Pseudo-Helices:   -32.9
	Pseudoknot Energy Penalty:  53.9
	Total Free Energy:          -93.1
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-347
		Stack = -1.5  for stack of 2-346
		Stack = -2.1  for stack of 3-345
		Stack = -3.3  for stack of 4-344
		Stack = -2.2  for stack of 5-343
		Stack = -2.1  for stack of 6-342
	Helix total = -14.5
	Multiloop = 5.0  for closure of 7-341
		Stack = -2.4  for stack of 324-340
		Stack = -3.3  for stack of 325-339
		Stack = -3.3  for stack of 326-338
		Stack = -3.3  for stack of 327-337
	Helix total = -12.3
	Hairpin = 4.4  for closure of 328-336
		Stack = -2.4  for stack of 20-320
		Stack = -1.5  for stack of 21-319
		Stack = -0.5  for stack of 22-318
		Stack = -2.1  for stack of 23-317
		Stack = -3.3  for stack of 24-316
		Stack = -3.4  for stack of 25-315
		Stack = -2.4  for stack of 26-314
	Helix total = -15.6
	Internal/bulge = 1.2  for closure of 27-313	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.2  for closure of 29-311	Size = 5
		Stack = -3.3  for stack of 33-308
		Stack = -2.2  for stack of 34-307
		Stack = -1.3  for stack of 35-306
		Stack = -0.9  for stack of 36-305
		Stack = -0.9  for stack of 37-304
		Stack = -0.9  for stack of 38-303
		Stack = -2.1  for stack of 39-302
		Stack = -2.5  for stack of 40-301
	Helix total = -14.1
	Internal/bulge = 3.6  for closure of 41-300	Size = 7
		Stack = -2.4  for stack of 44-294
		Stack = -2.4  for stack of 45-293
		Stack = -2.1  for stack of 46-292
		Stack = -3.4  for stack of 47-291
	Helix total = -10.3
	Multiloop = 2.9  for closure of 48-290
		Stack = -2.2  for stack of 247-286
		Stack = -2.4  for stack of 248-285
		Stack = -2.4  for stack of 249-284
		Stack = -3.4  for stack of 250-283
		Stack = -2.1  for stack of 251-282
		Stack = -2.1  for stack of 252-281
	Helix total = -14.6
	Hairpin = 5.0  for closure of 253-280
		Stack = -2.1  for stack of 186-217
		Stack = -1.4  for stack of 187-216
		Stack = -3.3  for stack of 188-215
		Stack = -2.2  for stack of 189-214
		Stack = -0.9  for stack of 190-213
		Stack = -0.9  for stack of 191-212
		Stack = -0.9  for stack of 192-211
		Stack = -2.1  for stack of 193-210
		Stack = -3.4  for stack of 194-209
		Stack = -3.3  for stack of 195-208
	Helix total = -20.5
	Hairpin = 5.5  for closure of 196-207
		Stack = -2.4  for stack of 133-169
		Stack = -2.5  for stack of 134-168
		Stack = -1.5  for stack of 135-167
		Stack = -3.3  for stack of 136-166
		Stack = -2.1  for stack of 137-165
		Stack = -2.1  for stack of 138-164
	Helix total = -13.9
	Internal/bulge = 0.4  for closure of 139-163	Size = 1 BP stack across bulge = -3.4
		Stack = -3.3  for stack of 140-161
		Stack = -2.1  for stack of 141-160
		Stack = -2.1  for stack of 142-159
		Stack = -2.4  for stack of 143-158
		Stack = -0.9  for stack of 144-157
		Stack = -0.9  for stack of 145-156
		Stack = -1.4  for stack of 146-155
	Helix total = -13.1
	Hairpin = 5.1  for closure of 147-154
		Stack = -3.4  for stack of 113-132
		Stack = -2.1  for stack of 114-131
		Stack = -1.4  for stack of 115-130
		Stack = -3.4  for stack of 116-129
		Stack = -3.3  for stack of 117-128
		Stack = -2.1  for stack of 118-127
	Helix total = -15.7
	Hairpin = 4.9  for closure of 119-126
		Stack = -2.4  for stack of 56-80
		Stack = -3.3  for stack of 57-79
		Stack = -2.1  for stack of 58-78
		Stack = -2.2  for stack of 59-77
		Stack = -3.3  for stack of 60-76
	Helix total = -13.3
	Hairpin = 5.3  for closure of 61-75


	Total energy = -114.1



