Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:69 50:68 51:67 52:66 53:65 203:241 204:240 205:239
	    206:238 207:237 208:236 209:235 254:284 255:283 256:282 257:281
	    258:280 259:279 301:338 302:337 303:336 304:335 305:334
	Energy of Broken Structure: -53.5
	Energy of Pseudo-Helices:   -44.6
	Pseudoknot Energy Penalty:  32.3
	Total Free Energy:          -65.8
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-400
		Stack = -1.5  for stack of 2-399
		Stack = -2.1  for stack of 3-398
		Stack = -2.2  for stack of 4-397
		Stack = -2.4  for stack of 5-396
		Stack = -2.4  for stack of 6-395
	Helix total = -13.9
	Multiloop = 5.0  for closure of 7-394
		Stack = -2.4  for stack of 377-393
		Stack = -2.1  for stack of 378-392
		Stack = -2.4  for stack of 379-391
		Stack = -2.1  for stack of 380-390
	Helix total = -9.0
	Hairpin = 4.4  for closure of 381-389
		Stack = -2.1  for stack of 19-373
		Stack = -2.1  for stack of 20-372
		Stack = -1.5  for stack of 21-371
	Helix total = -5.7
	Internal/bulge = 3.1  for closure of 22-370	Size = 4
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 25-367	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.7  for closure of 27-365	Size = 3
		Stack = -0.5  for stack of 31-364
		Stack = -1.0  for stack of 32-363
		Stack = -2.2  for stack of 33-362
	Helix total = -3.7
	Internal/bulge = 2.4  for closure of 34-361	Size = 1 BP stack across bulge = -1.4
	Helix total = 0.0
	Internal/bulge = 5.1  for closure of 35-359	Size = 1 BP stack across bulge = 1.3
		Stack = -1.4  for stack of 36-357
	Helix total = -1.4
	Internal/bulge = 0.7  for closure of 37-356	Size = 2
		Stack = -1.4  for stack of 39-354
	Helix total = -1.4
	Internal/bulge = 4.1  for closure of 40-353	Size = 9
		Stack = -2.1  for stack of 44-346
		Stack = -1.1  for stack of 45-345
		Stack = -2.1  for stack of 46-344
		Stack = -3.4  for stack of 47-343
	Helix total = -8.7
	Multiloop = 4.6  for closure of 48-342
		Stack = -2.1  for stack of 287-320
		Stack = -2.5  for stack of 288-319
		Stack = -0.6  for stack of 289-318
	Helix total = -5.2
	Internal/bulge = 1.9  for closure of 290-317	Size = 2
		Stack = -1.3  for stack of 292-315
		Stack = -2.1  for stack of 293-314
		Stack = -2.5  for stack of 294-313
	Helix total = -5.9
	Internal/bulge = 1.1  for closure of 295-312	Size = 2
		Stack = -3.3  for stack of 297-310
	Helix total = -3.3
	Hairpin = 4.0  for closure of 298-309
	Helix total = 0.0
	Internal/bulge = -2.2  for closure of 244-270	Size = 2
		Stack = -1.5  for stack of 246-268
		Stack = -1.3  for stack of 247-267
		Stack = -2.1  for stack of 248-266
		Stack = -2.5  for stack of 249-265
		Stack = -1.0  for stack of 250-264
		Stack = -2.2  for stack of 251-263
	Helix total = -10.6
	Hairpin = 5.0  for closure of 252-262
		Stack = -2.1  for stack of 186-227
		Stack = -1.1  for stack of 187-226
		Stack = -2.4  for stack of 188-225
		Stack = -2.1  for stack of 189-224
		Stack = -2.4  for stack of 190-223
	Helix total = -10.1
	Internal/bulge = 3.8  for closure of 191-222	Size = 5
		Stack = -2.1  for stack of 193-217
		Stack = -2.2  for stack of 194-216
	Helix total = -4.3
	Internal/bulge = 1.4  for closure of 195-215	Size = 1 BP stack across bulge = -2.4
	Helix total = 0.0
	Internal/bulge = -2.3  for closure of 196-213	Size = 2
		Stack = -2.1  for stack of 198-211
	Helix total = -2.1
	Hairpin = 6.4  for closure of 199-210
		Stack = -2.1  for stack of 114-185
		Stack = -3.3  for stack of 115-184
		Stack = -3.4  for stack of 116-183
		Stack = -2.1  for stack of 117-182
		Stack = -1.4  for stack of 118-181
	Helix total = -12.3
	Multiloop = 6.3  for closure of 119-180
		Stack = -3.3  for stack of 159-179
	Helix total = -3.3
	Internal/bulge = 0.9  for closure of 160-178	Size = 2
		Stack = -3.4  for stack of 162-176
		Stack = -2.1  for stack of 163-175
		Stack = -2.1  for stack of 164-174
		Stack = -2.2  for stack of 165-173
		Stack = -0.9  for stack of 166-172
	Helix total = -10.7
	Hairpin = 5.9  for closure of 167-171
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 122-146	Size = 2
		Stack = -1.1  for stack of 124-144
		Stack = -0.9  for stack of 125-143
		Stack = -1.3  for stack of 126-142
		Stack = -2.2  for stack of 127-141
		Stack = -1.4  for stack of 128-140
		Stack = -1.3  for stack of 129-139
		Stack = -0.9  for stack of 130-138
		Stack = -2.2  for stack of 131-137
	Helix total = -11.3
	Hairpin = 5.4  for closure of 132-136
		Stack = -1.4  for stack of 56-84
		Stack = -3.3  for stack of 57-83
		Stack = -1.5  for stack of 58-82
		Stack = -1.3  for stack of 59-81
		Stack = -1.4  for stack of 60-80
	Helix total = -8.9
	Hairpin = 6.2  for closure of 61-79


	Total energy = -53.5



