Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:63 50:62 51:61 52:60 149:185 150:184 151:183 152:182
	    153:181 154:180 155:179 201:231 202:230 203:229 204:228 205:227
	    206:226 207:225 248:287 249:286 250:285 251:284 252:283 253:282
	    254:281
	Energy of Broken Structure: -77.9
	Energy of Pseudo-Helices:   -48.3
	Pseudoknot Energy Penalty:  35.9
	Total Free Energy:          -90.3
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 = -2.4  for stack of 4-344
		Stack = -1.1  for stack of 5-343
		Stack = -2.1  for stack of 6-342
	Helix total = -12.5
	Multiloop = 5.1  for closure of 7-341
		Stack = -3.3  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 = -13.2
	Hairpin = 4.4  for closure of 328-336
		Stack = -3.3  for stack of 20-320
		Stack = -2.4  for stack of 21-319
		Stack = -1.5  for stack of 22-318
		Stack = -1.3  for stack of 23-317
		Stack = -0.9  for stack of 24-316
		Stack = -0.9  for stack of 25-315
		Stack = -2.1  for stack of 26-314
	Helix total = -12.4
	Internal/bulge = 2.8  for closure of 27-313	Size = 2
		Stack = -3.3  for stack of 30-312
		Stack = -2.4  for stack of 31-311
		Stack = -0.6  for stack of 32-310
	Helix total = -6.3
	Internal/bulge = 1.5  for closure of 33-309	Size = 2
	Helix total = 0.0
	Internal/bulge = 0.9  for closure of 35-307	Size = 4
		Stack = -0.9  for stack of 38-304
		Stack = -2.1  for stack of 39-303
		Stack = -3.4  for stack of 40-302
	Helix total = -6.4
	Internal/bulge = 1.7  for closure of 41-301	Size = 1 BP stack across bulge = -2.1
	Helix total = 0.0
	Internal/bulge = 3.0  for closure of 42-299	Size = 4
		Stack = -2.1  for stack of 44-295
		Stack = -2.1  for stack of 45-294
		Stack = -3.3  for stack of 46-293
		Stack = -3.4  for stack of 47-292
	Helix total = -10.9
	Multiloop = 1.8  for closure of 48-291
		Stack = -1.3  for stack of 232-270
	Helix total = -1.3
	Internal/bulge = 1.2  for closure of 233-269	Size = 2
		Stack = -3.3  for stack of 235-267
		Stack = -2.4  for stack of 236-266
		Stack = -1.1  for stack of 237-265
		Stack = -1.3  for stack of 238-264
		Stack = -1.5  for stack of 239-263
		Stack = -2.4  for stack of 240-262
	Helix total = -12.0
	Internal/bulge = 1.8  for closure of 241-261	Size = 4
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 244-258	Size = 2
	Helix total = 0.0
	Hairpin = 5.5  for closure of 246-256
		Stack = -2.1  for stack of 189-217
		Stack = -0.6  for stack of 190-216
		Stack = -0.9  for stack of 191-215
		Stack = -0.9  for stack of 192-214
		Stack = -0.9  for stack of 193-213
		Stack = -1.3  for stack of 194-212
		Stack = -0.6  for stack of 195-211
		Stack = -2.5  for stack of 196-210
		Stack = -2.4  for stack of 197-209
	Helix total = -12.2
	Hairpin = 3.9  for closure of 198-208
		Stack = -2.4  for stack of 131-171
		Stack = -3.3  for stack of 132-170
		Stack = -2.4  for stack of 133-169
		Stack = -0.9  for stack of 134-168
	Helix total = -9.0
	Internal/bulge = 2.4  for closure of 135-167	Size = 1 BP stack across bulge = -1.4
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 136-165	Size = 2
		Stack = -2.1  for stack of 138-163
		Stack = -3.4  for stack of 139-162
		Stack = -2.1  for stack of 140-161
		Stack = -0.5  for stack of 141-160
		Stack = -0.5  for stack of 142-159
		Stack = -1.4  for stack of 143-158
		Stack = -3.4  for stack of 144-157
	Helix total = -13.4
	Hairpin = 5.0  for closure of 145-156
		Stack = -2.4  for stack of 106-130
		Stack = -2.4  for stack of 107-129
		Stack = -1.1  for stack of 108-128
		Stack = -0.9  for stack of 109-127
		Stack = -1.3  for stack of 110-126
	Helix total = -8.1
	Internal/bulge = 1.2  for closure of 111-125	Size = 2
		Stack = -3.4  for stack of 113-123
	Helix total = -3.4
	Hairpin = 5.2  for closure of 114-122
		Stack = -3.4  for stack of 54-72
		Stack = -3.3  for stack of 55-71
		Stack = -2.4  for stack of 56-70
		Stack = -2.4  for stack of 57-69
	Helix total = -11.5
	Hairpin = 5.2  for closure of 58-68


	Total energy = -77.9



