Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    12:309 13:308 14:307 15:306 16:305 17:304 18:303
	Energy of Broken Structure: -136.6
	Energy of Pseudo-Helices:   -12.3
	Pseudoknot Energy Penalty:  8.7
	Total Free Energy:          -140.2
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -0.8
		Stack = -3.3  for stack of 1-356
		Stack = -2.4  for stack of 2-355
		Stack = -2.1  for stack of 3-354
		Stack = -2.2  for stack of 4-353
		Stack = -2.4  for stack of 5-352
		Stack = -2.4  for stack of 6-351
		Stack = -3.3  for stack of 7-350
		Stack = -2.4  for stack of 8-349
		Stack = -2.2  for stack of 9-348
	Helix total = -22.7
	Internal/bulge = 1.4  for closure of 10-347	Size = 1 BP stack across bulge = -2.4
	Helix total = 0.0
	Multiloop = 5.2  for closure of 11-345
		Stack = -0.9  for stack of 44-343
		Stack = -2.1  for stack of 45-342
	Helix total = -3.0
	Internal/bulge = 0.4  for closure of 46-341	Size = 1 BP stack across bulge = -3.4
		Stack = -3.3  for stack of 48-340
		Stack = -2.4  for stack of 49-339
		Stack = -3.3  for stack of 50-338
		Stack = -3.3  for stack of 51-337
	Helix total = -12.3
	Multiloop = 4.9  for closure of 52-336
		Stack = -2.2  for stack of 312-327
		Stack = -1.4  for stack of 313-326
		Stack = -2.5  for stack of 314-325
		Stack = -2.4  for stack of 315-324
		Stack = -3.3  for stack of 316-323
	Helix total = -11.8
	Hairpin = 3.1  for closure of 317-322
		Stack = -1.5  for stack of 273-292
		Stack = -2.1  for stack of 274-291
		Stack = -2.2  for stack of 275-290
		Stack = -2.1  for stack of 276-289
		Stack = -2.5  for stack of 277-288
		Stack = -1.4  for stack of 278-287
		Stack = -3.3  for stack of 279-286
	Helix total = -15.1
	Hairpin = 3.1  for closure of 280-285
		Stack = -1.3  for stack of 218-266
		Stack = -2.2  for stack of 219-265
		Stack = -3.3  for stack of 220-264
	Helix total = -6.8
	Internal/bulge = 2.2  for closure of 221-263	Size = 11
		Stack = -3.3  for stack of 228-257
		Stack = -2.4  for stack of 229-256
		Stack = -0.9  for stack of 230-255
		Stack = -2.1  for stack of 231-254
		Stack = -3.3  for stack of 232-253
	Helix total = -12.0
	Internal/bulge = 3.2  for closure of 233-252	Size = 3
		Stack = -2.4  for stack of 234-248
		Stack = -3.3  for stack of 235-247
		Stack = -3.4  for stack of 236-246
		Stack = -3.3  for stack of 237-245
	Helix total = -12.4
	Hairpin = 4.2  for closure of 238-244
		Stack = -2.1  for stack of 53-214
		Stack = -2.4  for stack of 54-213
		Stack = -3.3  for stack of 55-212
	Helix total = -7.8
	Internal/bulge = 4.7  for closure of 56-211	Size = 8
		Stack = -2.4  for stack of 65-210
		Stack = -0.9  for stack of 66-209
		Stack = -2.2  for stack of 67-208
		Stack = -2.4  for stack of 68-207
	Helix total = -7.9
	Multiloop = 0.3  for closure of 69-206
		Stack = -3.3  for stack of 99-205
	Helix total = -3.3
	Internal/bulge = 3.2  for closure of 100-204	Size = 3
	Helix total = 0.0
	Multiloop = 5.2  for closure of 104-203
		Stack = -1.1  for stack of 173-192
		Stack = -2.1  for stack of 174-191
		Stack = -3.4  for stack of 175-190
		Stack = -3.3  for stack of 176-189
		Stack = -2.4  for stack of 177-188
		Stack = -2.2  for stack of 178-187
		Stack = -2.1  for stack of 179-186
	Helix total = -16.6
	Hairpin = 3.1  for closure of 180-185
		Stack = -3.3  for stack of 152-170
		Stack = -2.2  for stack of 153-169
		Stack = -2.1  for stack of 154-168
		Stack = -3.3  for stack of 155-167
		Stack = -2.2  for stack of 156-166
	Helix total = -13.1
	Hairpin = 4.5  for closure of 157-165
		Stack = -3.3  for stack of 121-144
	Helix total = -3.3
	Internal/bulge = 3.3  for closure of 122-143	Size = 2
		Stack = -2.5  for stack of 123-140
		Stack = -3.3  for stack of 124-139
		Stack = -3.3  for stack of 125-138
		Stack = -2.4  for stack of 126-137
		Stack = -3.3  for stack of 127-136
		Stack = -3.4  for stack of 128-135
	Helix total = -18.2
	Hairpin = 2.5  for closure of 129-134
		Stack = -3.3  for stack of 85-98
		Stack = -2.4  for stack of 86-97
		Stack = -2.1  for stack of 87-96
		Stack = -3.3  for stack of 88-95
	Helix total = -11.1
	Hairpin = 3.1  for closure of 89-94
		Stack = -2.1  for stack of 70-84
		Stack = -2.1  for stack of 71-83
		Stack = -3.3  for stack of 72-82
		Stack = -2.4  for stack of 73-81
	Helix total = -9.9
	Hairpin = 5.6  for closure of 74-80
		Stack = -3.3  for stack of 20-39
	Helix total = -3.3
	Internal/bulge = -2.2  for closure of 21-38	Size = 2
		Stack = -2.4  for stack of 23-36
		Stack = -3.3  for stack of 24-35
		Stack = -1.5  for stack of 25-34
		Stack = -2.1  for stack of 26-33
	Helix total = -9.3
	Hairpin = 3.1  for closure of 27-32


	Total energy = -136.6



