Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    258:333 260:332 261:331 262:330 263:329 264:328
	Energy of Broken Structure: -80.2
	Energy of Pseudo-Helices:   -8.0
	Pseudoknot Energy Penalty:  8.0
	Total Free Energy:          -80.2
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -7.4
	Helix total = 0.0
	Internal/bulge = 3.2  for closure of 334-360	Size = 7
		Stack = -2.1  for stack of 337-354
		Stack = -2.4  for stack of 338-353
		Stack = -2.1  for stack of 339-352
		Stack = -0.9  for stack of 340-351
		Stack = -0.9  for stack of 341-350
		Stack = -2.4  for stack of 342-349
	Helix total = -10.8
	Hairpin = 3.3  for closure of 343-348
		Stack = -2.5  for stack of 276-319
		Stack = -1.0  for stack of 277-318
		Stack = -1.1  for stack of 278-317
		Stack = -0.9  for stack of 279-316
		Stack = -2.1  for stack of 280-315
		Stack = -2.2  for stack of 281-314
		Stack = -1.3  for stack of 282-313
		Stack = -2.1  for stack of 283-312
		Stack = -2.4  for stack of 284-311
	Helix total = -15.6
	Internal/bulge = 4.6  for closure of 285-310	Size = 4
		Stack = -1.0  for stack of 290-309
		Stack = -0.5  for stack of 291-308
		Stack = -2.1  for stack of 292-307
		Stack = -3.3  for stack of 293-306
		Stack = -2.5  for stack of 294-305
		Stack = -0.5  for stack of 295-304
		Stack = -1.0  for stack of 296-303
	Helix total = -10.9
	Hairpin = 5.5  for closure of 297-302
		Stack = -2.1  for stack of 78-274
		Stack = -2.2  for stack of 79-273
		Stack = -2.1  for stack of 80-272
		Stack = -2.1  for stack of 81-271
		Stack = -2.5  for stack of 82-270
		Stack = -1.5  for stack of 83-269
	Helix total = -12.5
	Multiloop = 8.8  for closure of 84-268
		Stack = -2.5  for stack of 216-254
	Helix total = -2.5
	Internal/bulge = 1.7  for closure of 217-253	Size = 6
		Stack = -1.1  for stack of 221-249
		Stack = -2.4  for stack of 222-248
		Stack = -3.3  for stack of 223-247
	Helix total = -6.8
	Internal/bulge = 2.1  for closure of 224-246	Size = 7
		Stack = -2.4  for stack of 229-242
		Stack = -2.2  for stack of 230-241
		Stack = -2.1  for stack of 231-240
	Helix total = -6.7
	Hairpin = 4.2  for closure of 232-239
		Stack = -2.1  for stack of 89-215
		Stack = -3.4  for stack of 90-214
		Stack = -2.4  for stack of 91-213
		Stack = -3.3  for stack of 92-212
		Stack = -1.5  for stack of 93-211
	Helix total = -12.7
	Internal/bulge = 1.8  for closure of 94-210	Size = 7
		Stack = -3.3  for stack of 99-206
		Stack = -3.3  for stack of 100-205
	Helix total = -6.6
	Multiloop = 5.8  for closure of 101-204
	Helix total = 0.0
	Internal/bulge = -0.9  for closure of 184-201	Size = 4
		Stack = -2.1  for stack of 187-198
		Stack = -2.4  for stack of 188-197
	Helix total = -4.5
	Hairpin = 3.3  for closure of 189-196
		Stack = -1.1  for stack of 107-182
		Stack = -0.9  for stack of 108-181
		Stack = -2.4  for stack of 109-180
		Stack = -2.1  for stack of 110-179
		Stack = -0.9  for stack of 111-178
		Stack = -2.2  for stack of 112-177
	Helix total = -9.6
	Internal/bulge = 1.7  for closure of 113-176	Size = 1 BP stack across bulge = -2.1
	Helix total = 0.0
	Internal/bulge = 4.6  for closure of 114-174	Size = 4
		Stack = -2.2  for stack of 115-169
		Stack = -2.1  for stack of 116-168
	Helix total = -4.3
	Multiloop = 6.8  for closure of 117-167
		Stack = -3.3  for stack of 145-162
		Stack = -1.4  for stack of 146-161
	Helix total = -4.7
	Internal/bulge = 3.0  for closure of 147-160	Size = 3
		Stack = -2.5  for stack of 149-157
		Stack = -0.6  for stack of 150-156
	Helix total = -3.1
	Hairpin = 5.9  for closure of 151-155
		Stack = -2.5  for stack of 120-142
		Stack = -2.1  for stack of 121-141
		Stack = -0.6  for stack of 122-140
	Helix total = -5.2
	Internal/bulge = 5.1  for closure of 123-139	Size = 1 BP stack across bulge = 1.3
		Stack = -0.6  for stack of 125-138
		Stack = -2.1  for stack of 126-137
		Stack = -2.2  for stack of 127-136
		Stack = -2.1  for stack of 128-135
	Helix total = -7.0
	Hairpin = 3.1  for closure of 129-134
		Stack = -2.5  for stack of 49-75
		Stack = 0.3  for stack of 50-74
		Stack = -1.3  for stack of 51-73
		Stack = -1.4  for stack of 52-72
		Stack = -1.5  for stack of 53-71
		Stack = -3.3  for stack of 54-70
		Stack = -2.4  for stack of 55-69
		Stack = -2.4  for stack of 56-68
		Stack = -0.9  for stack of 57-67
	Helix total = -15.4
	Hairpin = 5.7  for closure of 58-66
		Stack = -2.1  for stack of 27-47
		Stack = -3.4  for stack of 28-46
	Helix total = -5.5
	Internal/bulge = 2.4  for closure of 29-45	Size = 1 BP stack across bulge = -1.4
		Stack = -0.5  for stack of 30-43
		Stack = -2.5  for stack of 31-42
		Stack = -1.4  for stack of 32-41
		Stack = -2.5  for stack of 33-40
	Helix total = -6.9
	Hairpin = 3.3  for closure of 34-39
		Stack = -1.1  for stack of 1-23
		Stack = -2.1  for stack of 2-22
		Stack = -2.4  for stack of 3-21
		Stack = -2.2  for stack of 4-20
		Stack = -2.1  for stack of 5-19
		Stack = -1.5  for stack of 6-18
	Helix total = -11.4
	Hairpin = 4.9  for closure of 7-17


	Total energy = -80.2



