Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    54:77 58:73 59:72 205:240 206:239 207:238 208:237 209:236
	    210:235 211:234 257:294 258:293 259:292 260:291 261:290 262:289
	    263:288 264:287 265:286 266:285 313:350 314:349 315:348 316:347
	    317:346 318:345 319:344 320:343
	Energy of Broken Structure: -31.0
	Energy of Pseudo-Helices:   -31.0
	Pseudoknot Energy Penalty:  41.1
	Total Free Energy:          -20.9
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-409
		Stack = -1.5  for stack of 2-408
		Stack = -2.1  for stack of 3-407
		Stack = -2.4  for stack of 4-406
		Stack = -1.1  for stack of 5-405
		Stack = -2.1  for stack of 6-404
	Helix total = -12.5
	Multiloop = 6.5  for closure of 7-403
		Stack = -2.1  for stack of 386-402
		Stack = -3.3  for stack of 387-401
		Stack = -3.3  for stack of 388-400
		Stack = -3.3  for stack of 389-399
	Helix total = -12.0
	Hairpin = 4.4  for closure of 390-398
		Stack = -2.4  for stack of 20-382
		Stack = -2.5  for stack of 21-381
		Stack = 0.3  for stack of 22-380
		Stack = -1.3  for stack of 23-379
		Stack = -2.2  for stack of 24-378
		Stack = -2.1  for stack of 25-377
		Stack = -2.2  for stack of 26-376
		Stack = -2.1  for stack of 27-375
	Helix total = -14.5
	Internal/bulge = 2.3  for closure of 28-374	Size = 1 BP stack across bulge = -1.1
		Stack = -1.3  for stack of 30-373
		Stack = -0.9  for stack of 31-372
		Stack = -1.1  for stack of 32-371
		Stack = -0.9  for stack of 33-370
	Helix total = -4.2
	Internal/bulge = 0.8  for closure of 34-369	Size = 4
		Stack = -1.3  for stack of 37-366
		Stack = -0.9  for stack of 38-365
		Stack = -1.1  for stack of 39-364
	Helix total = -3.3
	Internal/bulge = 5.2  for closure of 40-363	Size = 5
		Stack = -2.5  for stack of 42-358
		Stack = -2.1  for stack of 43-357
		Stack = -2.1  for stack of 44-356
		Stack = -2.2  for stack of 45-355
	Helix total = -8.9
	Multiloop = 7.7  for closure of 46-354
		Stack = -1.3  for stack of 296-332
		Stack = -2.1  for stack of 297-331
		Stack = -2.2  for stack of 298-330
		Stack = -0.9  for stack of 299-329
	Helix total = -6.5
	Internal/bulge = 2.1  for closure of 300-328	Size = 1 BP stack across bulge = -1.3
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 302-327	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.8  for closure of 304-325	Size = 2
		Stack = -0.9  for stack of 307-324
	Helix total = -0.9
	Internal/bulge = 1.9  for closure of 308-323	Size = 2
	Helix total = 0.0
	Hairpin = 5.6  for closure of 310-321
		Stack = -0.9  for stack of 241-278
		Stack = -0.9  for stack of 242-277
		Stack = -1.3  for stack of 243-276
		Stack = -0.9  for stack of 244-275
		Stack = -0.9  for stack of 245-274
		Stack = -1.1  for stack of 246-273
		Stack = -0.9  for stack of 247-272
		Stack = -0.9  for stack of 248-271
		Stack = -1.3  for stack of 249-270
		Stack = -0.9  for stack of 250-269
		Stack = -0.9  for stack of 251-268
	Helix total = -10.9
	Hairpin = 6.6  for closure of 252-267
		Stack = -2.5  for stack of 189-225
		Stack = -0.5  for stack of 190-224
		Stack = -1.5  for stack of 191-223
		Stack = -2.1  for stack of 192-222
	Helix total = -6.6
	Internal/bulge = 0.8  for closure of 193-221	Size = 4
		Stack = -0.9  for stack of 196-218
		Stack = -2.2  for stack of 197-217
	Helix total = -3.1
	Internal/bulge = 1.7  for closure of 198-216	Size = 1 BP stack across bulge = -2.1
		Stack = -1.0  for stack of 200-215
		Stack = -0.9  for stack of 201-214
		Stack = -1.4  for stack of 202-213
	Helix total = -3.3
	Hairpin = 5.3  for closure of 203-212
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 156-188	Size = 2
		Stack = -0.9  for stack of 158-186
		Stack = -1.3  for stack of 159-185
		Stack = -0.6  for stack of 160-184
		Stack = -1.0  for stack of 161-183
		Stack = -2.5  for stack of 162-182
	Helix total = -6.3
	Internal/bulge = 1.7  for closure of 163-181	Size = 1 BP stack across bulge = -2.1
		Stack = -1.3  for stack of 165-180
	Helix total = -1.3
	Internal/bulge = 1.9  for closure of 166-179	Size = 2
		Stack = -1.3  for stack of 168-177
		Stack = -0.9  for stack of 169-176
	Helix total = -2.2
	Hairpin = 5.5  for closure of 170-175
		Stack = -0.5  for stack of 47-68
		Stack = -0.5  for stack of 48-67
		Stack = -2.1  for stack of 49-66
		Stack = -2.5  for stack of 50-65
	Helix total = -5.6
	Hairpin = 6.6  for closure of 51-64


	Total energy = -31.0



