Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    47:67 48:66 49:65 50:64 51:63 216:250 217:249 218:248
	    219:247 220:246 221:245 269:303 270:302 271:301 272:300 273:299
	    274:298 275:297 322:360 323:359 324:358 325:357 326:356 327:355
	    328:354
	Energy of Broken Structure: -69.7
	Energy of Pseudo-Helices:   -45.1
	Pseudoknot Energy Penalty:  33.5
	Total Free Energy:          -81.3
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-422
		Stack = -1.5  for stack of 2-421
		Stack = -2.1  for stack of 3-420
		Stack = -3.3  for stack of 4-419
		Stack = -2.2  for stack of 5-418
		Stack = -2.1  for stack of 6-417
	Helix total = -14.5
	Multiloop = 5.1  for closure of 7-416
		Stack = -2.4  for stack of 399-415
		Stack = -2.1  for stack of 400-414
		Stack = -2.4  for stack of 401-413
		Stack = -2.1  for stack of 402-412
	Helix total = -9.0
	Hairpin = 4.4  for closure of 403-411
		Stack = -2.1  for stack of 20-395
		Stack = -0.9  for stack of 21-394
		Stack = -2.1  for stack of 22-393
		Stack = -2.4  for stack of 23-392
	Helix total = -7.5
	Internal/bulge = 1.9  for closure of 24-391	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.3  for closure of 26-389	Size = 1 BP stack across bulge = -0.9
		Stack = -1.4  for stack of 27-387
	Helix total = -1.4
	Internal/bulge = 1.7  for closure of 28-386	Size = 8
		Stack = -2.1  for stack of 33-381
		Stack = -2.5  for stack of 34-380
		Stack = -0.6  for stack of 35-379
		Stack = -1.3  for stack of 36-378
		Stack = -0.9  for stack of 37-377
		Stack = -1.4  for stack of 38-376
		Stack = -0.5  for stack of 39-375
	Helix total = -9.3
	Internal/bulge = 4.5  for closure of 40-374	Size = 5
		Stack = -2.1  for stack of 42-369
		Stack = -1.1  for stack of 43-368
		Stack = -2.1  for stack of 44-367
		Stack = -3.4  for stack of 45-366
	Helix total = -8.7
	Multiloop = 4.5  for closure of 46-365
		Stack = -2.1  for stack of 304-344
		Stack = -1.1  for stack of 305-343
		Stack = -0.9  for stack of 306-342
		Stack = -2.1  for stack of 307-341
	Helix total = -6.2
	Internal/bulge = 1.0  for closure of 308-340	Size = 1 BP stack across bulge = -1.5
		Stack = -2.5  for stack of 309-338
		Stack = -2.1  for stack of 310-337
	Helix total = -4.6
	Internal/bulge = -1.4  for closure of 311-336	Size = 2
		Stack = -2.1  for stack of 313-334
	Helix total = -2.1
	Internal/bulge = 1.9  for closure of 314-333	Size = 2
		Stack = -1.3  for stack of 316-331
		Stack = -2.1  for stack of 317-330
	Helix total = -3.4
	Hairpin = 5.2  for closure of 318-329
	Helix total = 0.0
	Internal/bulge = -1.4  for closure of 251-290	Size = 2
		Stack = -2.4  for stack of 253-288
		Stack = -0.9  for stack of 254-287
		Stack = -2.2  for stack of 255-286
	Helix total = -5.5
	Internal/bulge = 1.2  for closure of 256-285	Size = 4
		Stack = -2.2  for stack of 259-282
		Stack = -2.1  for stack of 260-281
		Stack = -0.9  for stack of 261-280
		Stack = -1.3  for stack of 262-279
		Stack = -1.5  for stack of 263-278
		Stack = -2.1  for stack of 264-277
	Helix total = -10.1
	Hairpin = 6.3  for closure of 265-276
		Stack = -2.4  for stack of 199-237
		Stack = -3.3  for stack of 200-236
		Stack = -2.2  for stack of 201-235
		Stack = -1.3  for stack of 202-234
	Helix total = -9.2
	Internal/bulge = 1.9  for closure of 203-233	Size = 1 BP stack across bulge = -1.1
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 204-231	Size = 2
		Stack = -2.1  for stack of 206-229
		Stack = -3.4  for stack of 207-228
		Stack = -1.4  for stack of 208-227
		Stack = -1.3  for stack of 209-226
		Stack = -2.1  for stack of 210-225
		Stack = -3.4  for stack of 211-224
		Stack = -2.1  for stack of 212-223
	Helix total = -15.8
	Hairpin = 5.3  for closure of 213-222
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 130-196	Size = 2
		Stack = -2.2  for stack of 132-194
		Stack = -2.1  for stack of 133-193
	Helix total = -4.3
	Internal/bulge = 1.9  for closure of 134-192	Size = 2
		Stack = -2.1  for stack of 136-190
	Helix total = -2.1
	Internal/bulge = 1.1  for closure of 137-189	Size = 4
	Helix total = 0.0
	Internal/bulge = 3.7  for closure of 140-186	Size = 4
	Helix total = 0.0
	Internal/bulge = 3.4  for closure of 143-183	Size = 6
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 147-179	Size = 2
		Stack = -2.1  for stack of 149-177
		Stack = -1.3  for stack of 150-176
		Stack = -0.6  for stack of 151-175
		Stack = -2.5  for stack of 152-174
	Helix total = -6.5
	Internal/bulge = 1.1  for closure of 153-173	Size = 2
		Stack = -2.5  for stack of 155-171
		Stack = -2.1  for stack of 156-170
		Stack = -0.9  for stack of 157-169
	Helix total = -5.5
	Hairpin = 5.9  for closure of 158-168
		Stack = -2.2  for stack of 54-79
		Stack = -0.9  for stack of 55-78
		Stack = -2.1  for stack of 56-77
		Stack = -3.3  for stack of 57-76
		Stack = -3.4  for stack of 58-75
		Stack = -2.1  for stack of 59-74
	Helix total = -14.0
	Hairpin = 5.2  for closure of 60-73


	Total energy = -69.7



