Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    35:63 36:62 38:60 142:179 143:178 144:177 145:176 146:175
	    147:174 197:228 198:227 199:226 200:225 201:224 202:223 246:286
	    247:285 248:284 249:283 250:282 251:281 252:280
	Energy of Broken Structure: -42.4
	Energy of Pseudo-Helices:   -39.5
	Pseudoknot Energy Penalty:  32.2
	Total Free Energy:          -49.7
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.3
		Stack = -2.1  for stack of 1-320
		Stack = -2.1  for stack of 2-319
		Stack = -1.5  for stack of 3-318
		Stack = -0.5  for stack of 4-317
		Stack = -1.3  for stack of 5-316
		Stack = -1.1  for stack of 6-315
		Stack = -1.3  for stack of 7-314
	Helix total = -9.9
	Internal/bulge = 2.4  for closure of 8-313	Size = 7
	Helix total = 0.0
	Internal/bulge = 1.0  for closure of 13-309	Size = 2
		Stack = -2.5  for stack of 15-307
		Stack = -2.1  for stack of 16-306
		Stack = -0.9  for stack of 17-305
		Stack = -1.0  for stack of 18-304
		Stack = -1.3  for stack of 19-303
		Stack = -0.6  for stack of 20-302
		Stack = -1.4  for stack of 21-301
	Helix total = -9.8
	Internal/bulge = 4.0  for closure of 22-300	Size = 7
		Stack = -2.4  for stack of 25-294
		Stack = -2.4  for stack of 26-293
		Stack = -2.1  for stack of 27-292
		Stack = -2.5  for stack of 28-291
	Helix total = -9.4
	Multiloop = 5.2  for closure of 29-290
		Stack = -3.4  for stack of 231-267
	Helix total = -3.4
	Internal/bulge = 1.7  for closure of 232-266	Size = 1 BP stack across bulge = -2.1
		Stack = -1.0  for stack of 233-264
	Helix total = -1.0
	Internal/bulge = 2.1  for closure of 234-263	Size = 1 BP stack across bulge = -1.3
	Helix total = 0.0
	Internal/bulge = 1.7  for closure of 236-262	Size = 4
	Helix total = 0.0
	Internal/bulge = 2.6  for closure of 239-259	Size = 3
		Stack = -2.1  for stack of 241-256
		Stack = -3.4  for stack of 242-255
		Stack = -3.3  for stack of 243-254
	Helix total = -8.8
	Hairpin = 4.5  for closure of 244-253
		Stack = -2.1  for stack of 184-212
		Stack = -1.3  for stack of 185-211
		Stack = -0.9  for stack of 186-210
	Helix total = -4.3
	Internal/bulge = 1.9  for closure of 187-209	Size = 2
		Stack = -1.3  for stack of 189-207
		Stack = -0.9  for stack of 190-206
		Stack = -1.4  for stack of 191-205
		Stack = -1.5  for stack of 192-204
	Helix total = -5.1
	Hairpin = 5.4  for closure of 193-203
		Stack = -2.4  for stack of 127-164
		Stack = -1.4  for stack of 128-163
		Stack = -1.5  for stack of 129-162
		Stack = -3.3  for stack of 130-161
		Stack = -2.1  for stack of 131-160
	Helix total = -10.7
	Internal/bulge = 3.3  for closure of 132-159	Size = 2
		Stack = -3.3  for stack of 133-156
		Stack = -2.4  for stack of 134-155
		Stack = -2.2  for stack of 135-154
	Helix total = -7.9
	Internal/bulge = 1.7  for closure of 136-153	Size = 1 BP stack across bulge = -2.1
		Stack = -3.4  for stack of 137-151
		Stack = -2.1  for stack of 138-150
		Stack = -1.4  for stack of 139-149
	Helix total = -6.9
	Hairpin = 6.0  for closure of 140-148
		Stack = -0.6  for stack of 97-124
	Helix total = -0.6
	Internal/bulge = 1.5  for closure of 98-123	Size = 4
		Stack = -3.4  for stack of 101-120
		Stack = -2.1  for stack of 102-119
		Stack = -1.0  for stack of 103-118
		Stack = -2.5  for stack of 104-117
	Helix total = -9.0
	Hairpin = 5.5  for closure of 105-116
		Stack = -2.4  for stack of 30-46
		Stack = -1.5  for stack of 31-45
		Stack = -2.1  for stack of 32-44
		Stack = -3.3  for stack of 33-43
	Helix total = -9.3
	Hairpin = 4.5  for closure of 34-42


	Total energy = -42.4



