Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    88:143 89:142 90:141 91:140 92:139 93:138 94:136 95:135
	    96:134
	Energy of Broken Structure: -129.4
	Energy of Pseudo-Helices:   -14.0
	Pseudoknot Energy Penalty:  8.6
	Total Free Energy:          -134.8
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -4.5
		Stack = -2.4  for stack of 339-402
		Stack = -2.1  for stack of 340-401
		Stack = -3.4  for stack of 341-400
		Stack = -2.4  for stack of 342-399
	Helix total = -10.3
	Internal/bulge = 2.3  for closure of 343-398	Size = 1 BP stack across bulge = -1.5
	Helix total = 0.0
	Internal/bulge = 3.3  for closure of 344-396	Size = 2
		Stack = -3.4  for stack of 347-395
		Stack = -3.3  for stack of 348-394
		Stack = -3.3  for stack of 349-393
		Stack = -3.3  for stack of 350-392
	Helix total = -13.3
	Internal/bulge = 5.4  for closure of 351-391	Size = 9
		Stack = -3.3  for stack of 359-388
		Stack = -2.4  for stack of 360-387
		Stack = -3.4  for stack of 361-386
	Helix total = -9.1
	Internal/bulge = 2.0  for closure of 362-385	Size = 6
		Stack = -3.3  for stack of 366-381
		Stack = -3.3  for stack of 367-380
		Stack = -3.3  for stack of 368-379
	Helix total = -9.9
	Hairpin = 3.4  for closure of 369-378
		Stack = -2.1  for stack of 170-326
	Helix total = -2.1
	Internal/bulge = 1.8  for closure of 171-325	Size = 1 BP stack across bulge = -1.4
		Stack = -3.3  for stack of 173-324
		Stack = -3.4  for stack of 174-323
		Stack = -3.3  for stack of 175-322
	Helix total = -10.0
	Internal/bulge = 4.5  for closure of 176-321	Size = 13
		Stack = -1.4  for stack of 182-312
		Stack = -3.3  for stack of 183-311
		Stack = -3.3  for stack of 184-310
		Stack = -1.5  for stack of 185-309
		Stack = -2.5  for stack of 186-308
		Stack = -3.3  for stack of 187-307
		Stack = -3.3  for stack of 188-306
		Stack = -2.4  for stack of 189-305
		Stack = -3.4  for stack of 190-304
		Stack = -3.3  for stack of 191-303
	Helix total = -27.7
	Internal/bulge = 2.7  for closure of 192-302	Size = 15
		Stack = -3.3  for stack of 201-294
		Stack = -3.3  for stack of 202-293
	Helix total = -6.6
	Internal/bulge = 0.5  for closure of 203-292	Size = 2
		Stack = -3.4  for stack of 205-290
		Stack = -3.3  for stack of 206-289
		Stack = -2.4  for stack of 207-288
		Stack = -3.4  for stack of 208-287
	Helix total = -12.5
	Internal/bulge = -0.4  for closure of 209-286	Size = 1 BP stack across bulge = -3.3
		Stack = -3.3  for stack of 210-284
		Stack = -3.3  for stack of 211-283
		Stack = -2.4  for stack of 212-282
	Helix total = -9.0
	Multiloop = 6.7  for closure of 213-281
		Stack = -2.1  for stack of 260-272
		Stack = -2.4  for stack of 261-271
		Stack = -2.1  for stack of 262-270
	Helix total = -6.6
	Hairpin = 4.1  for closure of 263-269
		Stack = -2.4  for stack of 226-258
		Stack = -3.4  for stack of 227-257
		Stack = -2.4  for stack of 228-256
		Stack = -3.3  for stack of 229-255
	Helix total = -11.5
	Internal/bulge = 0.4  for closure of 230-254	Size = 1 BP stack across bulge = -3.4
		Stack = -2.1  for stack of 232-253
		Stack = -2.1  for stack of 233-252
		Stack = -3.4  for stack of 234-251
	Helix total = -7.6
	Internal/bulge = 2.3  for closure of 235-250	Size = 4
		Stack = -3.3  for stack of 237-246
		Stack = -3.4  for stack of 238-245
	Helix total = -6.7
	Hairpin = 4.2  for closure of 239-244
	Helix total = 0.0
	Internal/bulge = 0.5  for closure of 4-167	Size = 2
		Stack = -3.4  for stack of 6-165
		Stack = -2.4  for stack of 7-164
	Helix total = -5.8
	Internal/bulge = 0.7  for closure of 8-163	Size = 4
	Helix total = 0.0
	Internal/bulge = 3.0  for closure of 11-160	Size = 4
		Stack = -2.1  for stack of 15-158
	Helix total = -2.1
	Internal/bulge = 0.6  for closure of 16-157	Size = 2
		Stack = -3.3  for stack of 18-155
	Helix total = -3.3
	Internal/bulge = 0.5  for closure of 19-154	Size = 2
		Stack = -3.3  for stack of 21-152
	Helix total = -3.3
	Internal/bulge = -1.1  for closure of 22-151	Size = 1 BP stack across bulge = -3.4
		Stack = -2.1  for stack of 23-149
		Stack = -1.5  for stack of 24-148
	Helix total = -3.6
	Internal/bulge = 5.5  for closure of 25-147	Size = 65
		Stack = -2.1  for stack of 57-112
		Stack = -2.4  for stack of 58-111
		Stack = -3.3  for stack of 59-110
	Helix total = -7.8
	Internal/bulge = 5.8  for closure of 60-109	Size = 13
		Stack = -2.4  for stack of 71-105
		Stack = -2.2  for stack of 72-104
		Stack = -2.4  for stack of 73-103
		Stack = -3.3  for stack of 74-102
		Stack = -2.4  for stack of 75-101
		Stack = -3.4  for stack of 76-100
		Stack = -2.1  for stack of 77-99
		Stack = -2.1  for stack of 78-98
	Helix total = -20.3
	Hairpin = 5.5  for closure of 79-97


	Total energy = -129.4



