Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    54:82 55:81 57:79 161:198 162:197 163:196 164:195 165:194
	    166:193 216:247 217:246 218:245 219:244 220:243 221:242 265:305
	    266:304 267:303 268:302 269:301 270:300 271:299
	Energy of Broken Structure: -51.4
	Energy of Pseudo-Helices:   -39.5
	Pseudoknot Energy Penalty:  32.3
	Total Free Energy:          -58.6
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-366
		Stack = -1.5  for stack of 2-365
		Stack = -2.1  for stack of 3-364
		Stack = -2.4  for stack of 4-363
		Stack = -1.1  for stack of 5-362
		Stack = -2.1  for stack of 6-361
	Helix total = -12.5
	Multiloop = 5.1  for closure of 7-360
		Stack = -2.2  for stack of 343-359
		Stack = -2.1  for stack of 344-358
		Stack = -3.3  for stack of 345-357
		Stack = -3.3  for stack of 346-356
	Helix total = -10.9
	Hairpin = 4.4  for closure of 347-355
		Stack = -2.1  for stack of 20-339
		Stack = -2.1  for stack of 21-338
		Stack = -1.5  for stack of 22-337
		Stack = -0.5  for stack of 23-336
		Stack = -1.3  for stack of 24-335
		Stack = -1.1  for stack of 25-334
		Stack = -1.3  for stack of 26-333
	Helix total = -9.9
	Internal/bulge = 1.9  for closure of 27-332	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.0  for closure of 29-330	Size = 3
	Helix total = 0.0
	Internal/bulge = 1.0  for closure of 32-328	Size = 2
		Stack = -2.5  for stack of 34-326
		Stack = -2.1  for stack of 35-325
		Stack = -0.9  for stack of 36-324
		Stack = -1.0  for stack of 37-323
		Stack = -1.3  for stack of 38-322
		Stack = -0.6  for stack of 39-321
		Stack = -1.4  for stack of 40-320
	Helix total = -9.8
	Internal/bulge = 4.0  for closure of 41-319	Size = 7
		Stack = -2.4  for stack of 44-313
		Stack = -2.4  for stack of 45-312
		Stack = -2.1  for stack of 46-311
		Stack = -2.5  for stack of 47-310
	Helix total = -9.4
	Multiloop = 5.2  for closure of 48-309
		Stack = -3.4  for stack of 250-286
	Helix total = -3.4
	Internal/bulge = 1.7  for closure of 251-285	Size = 1 BP stack across bulge = -2.1
		Stack = -1.0  for stack of 252-283
	Helix total = -1.0
	Internal/bulge = 2.1  for closure of 253-282	Size = 1 BP stack across bulge = -1.3
	Helix total = 0.0
	Internal/bulge = 1.7  for closure of 255-281	Size = 4
	Helix total = 0.0
	Internal/bulge = 3.3  for closure of 258-278	Size = 5
		Stack = -3.4  for stack of 261-274
		Stack = -3.3  for stack of 262-273
	Helix total = -6.7
	Hairpin = 4.5  for closure of 263-272
		Stack = -2.1  for stack of 203-231
		Stack = -1.3  for stack of 204-230
	Helix total = -3.4
	Internal/bulge = 1.9  for closure of 205-229	Size = 2
		Stack = -0.9  for stack of 207-227
		Stack = -1.3  for stack of 208-226
		Stack = -0.9  for stack of 209-225
		Stack = -1.4  for stack of 210-224
		Stack = -1.5  for stack of 211-223
	Helix total = -6.0
	Hairpin = 5.4  for closure of 212-222
		Stack = -2.4  for stack of 146-183
		Stack = -1.4  for stack of 147-182
		Stack = -1.5  for stack of 148-181
		Stack = -3.3  for stack of 149-180
		Stack = -2.1  for stack of 150-179
	Helix total = -10.7
	Internal/bulge = 3.3  for closure of 151-178	Size = 2
		Stack = -3.3  for stack of 152-175
		Stack = -2.4  for stack of 153-174
		Stack = -2.2  for stack of 154-173
	Helix total = -7.9
	Internal/bulge = 1.7  for closure of 155-172	Size = 1 BP stack across bulge = -2.1
		Stack = -3.4  for stack of 156-170
		Stack = -2.1  for stack of 157-169
		Stack = -1.4  for stack of 158-168
	Helix total = -6.9
	Hairpin = 6.0  for closure of 159-167
		Stack = -0.6  for stack of 116-143
	Helix total = -0.6
	Internal/bulge = 1.5  for closure of 117-142	Size = 4
		Stack = -3.4  for stack of 120-139
		Stack = -2.1  for stack of 121-138
		Stack = -1.0  for stack of 122-137
		Stack = -2.5  for stack of 123-136
	Helix total = -9.0
	Hairpin = 5.5  for closure of 124-135
		Stack = -2.4  for stack of 49-65
		Stack = -1.5  for stack of 50-64
		Stack = -2.1  for stack of 51-63
		Stack = -3.3  for stack of 52-62
	Helix total = -9.3
	Hairpin = 4.5  for closure of 53-61


	Total energy = -51.4



