Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:68 49:67 50:66 51:65 52:64 210:245 211:244 212:243
	    213:242 214:241 215:240 216:239 256:291 258:289 259:288 260:287
	    261:286 262:285 263:284 264:283 293:327 294:326 295:325 296:324
	    297:323 299:322 301:320 306:317
	Energy of Broken Structure: -50.3
	Energy of Pseudo-Helices:   -31.1
	Pseudoknot Energy Penalty:  32.8
	Total Free Energy:          -48.6
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-404
		Stack = -1.5  for stack of 2-403
		Stack = -2.1  for stack of 3-402
		Stack = -2.4  for stack of 4-401
		Stack = -1.1  for stack of 5-400
		Stack = -2.1  for stack of 6-399
	Helix total = -12.5
	Multiloop = 5.1  for closure of 7-398
		Stack = -2.2  for stack of 381-397
		Stack = -2.1  for stack of 382-396
		Stack = -3.3  for stack of 383-395
		Stack = -3.3  for stack of 384-394
	Helix total = -10.9
	Hairpin = 4.4  for closure of 385-393
		Stack = -2.1  for stack of 20-377
		Stack = -0.6  for stack of 21-376
		Stack = -0.5  for stack of 22-375
		Stack = -1.3  for stack of 23-374
		Stack = -1.1  for stack of 24-373
		Stack = -1.3  for stack of 25-372
		Stack = -2.2  for stack of 26-371
		Stack = -2.1  for stack of 27-370
	Helix total = -11.2
	Internal/bulge = 3.7  for closure of 28-369	Size = 3
		Stack = -0.5  for stack of 31-367
		Stack = -1.4  for stack of 32-366
		Stack = -2.4  for stack of 33-365
		Stack = -2.1  for stack of 34-364
		Stack = -1.1  for stack of 35-363
		Stack = -1.3  for stack of 36-362
		Stack = -1.1  for stack of 37-361
	Helix total = -9.9
	Internal/bulge = 1.9  for closure of 38-360	Size = 1 BP stack across bulge = -1.3
		Stack = -0.9  for stack of 39-358
		Stack = -1.1  for stack of 40-357
	Helix total = -2.0
	Internal/bulge = 3.7  for closure of 41-356	Size = 4
		Stack = -2.5  for stack of 43-352
		Stack = -2.1  for stack of 44-351
		Stack = -2.1  for stack of 45-350
		Stack = -2.2  for stack of 46-349
	Helix total = -8.9
	Multiloop = 6.8  for closure of 47-348
		Stack = -2.4  for stack of 308-344
		Stack = -1.1  for stack of 309-343
		Stack = -1.3  for stack of 310-342
		Stack = -0.9  for stack of 311-341
		Stack = -1.1  for stack of 312-340
		Stack = -0.9  for stack of 313-339
		Stack = -0.9  for stack of 314-338
		Stack = -0.9  for stack of 315-337
	Helix total = -9.5
	Hairpin = 6.7  for closure of 316-336
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 246-276	Size = 2
		Stack = -1.3  for stack of 248-274
		Stack = -0.9  for stack of 249-273
		Stack = -0.9  for stack of 250-272
		Stack = -1.1  for stack of 251-271
		Stack = -0.9  for stack of 252-270
		Stack = -1.3  for stack of 253-269
		Stack = -1.1  for stack of 254-268
	Helix total = -7.5
	Hairpin = 5.1  for closure of 255-267
		Stack = -1.3  for stack of 178-231
		Stack = -2.2  for stack of 179-230
		Stack = -2.1  for stack of 180-229
		Stack = -0.9  for stack of 181-228
	Helix total = -6.5
	Internal/bulge = 7.1  for closure of 182-227	Size = 21
		Stack = -0.9  for stack of 201-223
		Stack = -1.3  for stack of 202-222
		Stack = -0.9  for stack of 203-221
		Stack = -1.4  for stack of 204-220
		Stack = -1.0  for stack of 205-219
		Stack = -2.1  for stack of 206-218
	Helix total = -7.6
	Hairpin = 4.8  for closure of 207-217
		Stack = -0.9  for stack of 148-169
		Stack = -0.9  for stack of 149-168
		Stack = -1.1  for stack of 150-167
		Stack = -0.9  for stack of 151-166
		Stack = -1.3  for stack of 152-165
	Helix total = -5.1
	Internal/bulge = 1.2  for closure of 153-164	Size = 2
		Stack = -3.4  for stack of 155-162
	Helix total = -3.4
	Hairpin = 4.2  for closure of 156-161
		Stack = -2.4  for stack of 118-142
		Stack = -3.3  for stack of 119-141
		Stack = -2.1  for stack of 120-140
	Helix total = -7.8
	Internal/bulge = 1.2  for closure of 121-139	Size = 2
		Stack = -2.1  for stack of 123-137
		Stack = -1.1  for stack of 124-136
		Stack = -0.9  for stack of 125-135
		Stack = -0.9  for stack of 126-134
		Stack = -1.3  for stack of 127-133
	Helix total = -6.3
	Hairpin = 5.9  for closure of 128-132
		Stack = -1.0  for stack of 55-78
		Stack = -0.6  for stack of 56-77
		Stack = -1.3  for stack of 57-76
		Stack = -2.2  for stack of 58-75
		Stack = -3.3  for stack of 59-74
	Helix total = -8.4
	Hairpin = 5.2  for closure of 60-73


	Total energy = -50.3



