Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    35:62 36:61 38:59 41:56 141:179 142:178 143:177 144:176
	    145:175 146:174 197:228 198:227 199:226 200:225 201:224 202:223
	    246:286 249:283 250:282 251:281 252:280
	Energy of Broken Structure: -32.0
	Energy of Pseudo-Helices:   -34.5
	Pseudoknot Energy Penalty:  32.8
	Total Free Energy:          -33.7
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 = -2.1  for stack of 18-304
		Stack = -2.4  for stack of 19-303
		Stack = -2.1  for stack of 20-302
		Stack = -2.5  for stack of 21-301
	Helix total = -14.6
	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 = -3.4  for stack of 28-291
	Helix total = -10.3
	Multiloop = 2.7  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 = -1.3  for stack of 233-264
	Helix total = -1.3
	Internal/bulge = 3.4  for closure of 234-263	Size = 7
	Helix total = 0.0
	Internal/bulge = 2.7  for closure of 239-259	Size = 7
		Stack = -3.3  for stack of 243-254
	Helix total = -3.3
	Hairpin = 4.5  for closure of 244-253
		Stack = -2.1  for stack of 184-212
	Helix total = -2.1
	Internal/bulge = -1.4  for closure of 185-211	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 187-209	Size = 2
		Stack = -0.9  for stack of 189-207
	Helix total = -0.9
	Internal/bulge = 1.9  for closure of 190-206	Size = 2
		Stack = -1.5  for stack of 192-204
	Helix total = -1.5
	Hairpin = 5.4  for closure of 193-203
		Stack = -2.4  for stack of 126-163
		Stack = -1.4  for stack of 127-162
		Stack = -1.5  for stack of 128-161
		Stack = -3.3  for stack of 129-160
		Stack = -2.1  for stack of 130-159
	Helix total = -10.7
	Internal/bulge = 3.3  for closure of 131-158	Size = 2
		Stack = -3.3  for stack of 132-155
		Stack = -2.4  for stack of 133-154
		Stack = -2.2  for stack of 134-153
	Helix total = -7.9
	Internal/bulge = 1.7  for closure of 135-152	Size = 1 BP stack across bulge = -2.1
		Stack = -3.4  for stack of 136-150
		Stack = -2.1  for stack of 137-149
		Stack = -1.4  for stack of 138-148
	Helix total = -6.9
	Hairpin = 6.0  for closure of 139-147
		Stack = -0.6  for stack of 96-123
	Helix total = -0.6
	Internal/bulge = 1.3  for closure of 97-122	Size = 6
	Helix total = 0.0
	Internal/bulge = 0.4  for closure of 101-118	Size = 2
	Helix total = 0.0
	Hairpin = 6.2  for closure of 103-116
		Stack = -2.4  for stack of 30-45
		Stack = -3.3  for stack of 31-44
		Stack = -3.3  for stack of 32-43
	Helix total = -9.0
	Hairpin = 3.3  for closure of 33-42


	Total energy = -32.0



