Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    12:278 13:277 14:276 15:275 16:274 17:273 18:272 66:215
	    67:214 68:213 69:212
	Energy of Broken Structure: 2668.0
	Energy of Pseudo-Helices:   -22.5
	Pseudoknot Energy Penalty:  17.5
	Total Free Energy:          2663.0
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -0.2
		Stack = -0.9  for stack of 1-337
		Stack = -0.9  for stack of 2-336
		Stack = -2.1  for stack of 3-335
		Stack = -3.4  for stack of 4-334
		Stack = -2.1  for stack of 5-333
		Stack = -2.1  for stack of 6-332
		Stack = -3.3  for stack of 7-331
		Stack = -3.4  for stack of 8-330
		Stack = -3.3  for stack of 9-329
	Helix total = -21.5
	Internal/bulge = 1.7  for closure of 10-328	Size = 1 BP stack across bulge = -2.1
	Helix total = 0.0
	Multiloop = 6.3  for closure of 11-326
		Stack = -0.9  for stack of 50-324
		Stack = -2.1  for stack of 51-323
	Helix total = -3.0
	Internal/bulge = 0.4  for closure of 52-322	Size = 1 BP stack across bulge = -3.4
		Stack = -3.3  for stack of 54-321
		Stack = -2.4  for stack of 55-320
		Stack = -3.3  for stack of 56-319
		Stack = -2.4  for stack of 57-318
	Helix total = -11.4
	Multiloop = 5.1  for closure of 58-317
		Stack = -3.4  for stack of 281-308
	Helix total = -3.4
	Internal/bulge = 0.5  for closure of 282-307	Size = 2
		Stack = -3.3  for stack of 284-305
		Stack = -2.4  for stack of 285-304
		Stack = -2.5  for stack of 286-303
		Stack = -0.5  for stack of 287-302
		Stack = -0.5  for stack of 288-301
		Stack = -1.4  for stack of 289-300
		Stack = -3.4  for stack of 290-299
		Stack = -3.3  for stack of 291-298
	Helix total = -17.3
	Hairpin = 3.3  for closure of 292-297
		Stack = -3.4  for stack of 242-261
		Stack = -3.3  for stack of 243-260
		Stack = -2.4  for stack of 244-259
		Stack = -3.3  for stack of 245-258
		Stack = -3.4  for stack of 246-257
		Stack = -2.1  for stack of 247-256
		Stack = -2.1  for stack of 248-255
	Helix total = -20.0
	Hairpin = 3.1  for closure of 249-254
		Stack = -2.4  for stack of 187-235
		Stack = -3.3  for stack of 188-234
		Stack = -3.3  for stack of 189-233
	Helix total = -9.0
	Internal/bulge = 2.2  for closure of 190-232	Size = 11
		Stack = -3.4  for stack of 197-226
		Stack = -2.1  for stack of 198-225
		Stack = -2.1  for stack of 199-224
		Stack = -1.5  for stack of 200-223
		Stack = -2.5  for stack of 201-222
	Helix total = -11.6
	Internal/bulge = 3.2  for closure of 202-221	Size = 3
		Stack = 1400.0  for stack of 206-220
		Stack = 1400.0  for stack of 207-219
		Stack = -2.1  for stack of 208-218
		Stack = -3.4  for stack of 209-217
	Helix total = 2794.5
	Hairpin = 4.2  for closure of 210-216
		Stack = -2.1  for stack of 59-183
		Stack = -2.4  for stack of 60-182
		Stack = -3.3  for stack of 61-181
	Helix total = -7.8
	Internal/bulge = 5.2  for closure of 62-180	Size = 8
		Stack = -2.1  for stack of 71-179
		Stack = -3.3  for stack of 72-178
		Stack = -2.2  for stack of 73-177
		Stack = -2.1  for stack of 74-176
	Helix total = -9.7
	Multiloop = 1.6  for closure of 75-175
		Stack = -2.4  for stack of 106-174
	Helix total = -2.4
	Internal/bulge = 3.7  for closure of 107-173	Size = 3
		Stack = -3.3  for stack of 111-172
	Helix total = -3.3
	Internal/bulge = 2.3  for closure of 112-171	Size = 28
		Stack = -1.5  for stack of 127-156
		Stack = -2.1  for stack of 128-155
		Stack = -0.9  for stack of 129-154
	Helix total = -4.5
	Internal/bulge = -1.4  for closure of 130-153	Size = 2
		Stack = -3.3  for stack of 132-151
		Stack = -2.4  for stack of 133-150
		Stack = -3.4  for stack of 134-149
		Stack = -3.3  for stack of 135-148
		Stack = -2.4  for stack of 136-147
		Stack = -3.3  for stack of 137-146
		Stack = -3.3  for stack of 138-145
	Helix total = -21.4
	Hairpin = 4.5  for closure of 139-144
	Helix total = 0.0
	Internal/bulge = 0.5  for closure of 91-105	Size = 1 BP stack across bulge = -3.3
		Stack = -2.1  for stack of 92-103
		Stack = -2.2  for stack of 93-102
		Stack = -2.4  for stack of 94-101
	Helix total = -6.7
	Hairpin = 3.1  for closure of 95-100
		Stack = -2.1  for stack of 77-89
		Stack = -3.3  for stack of 78-88
		Stack = -3.4  for stack of 79-87
	Helix total = -8.8
	Hairpin = 4.7  for closure of 80-86
		Stack = -2.1  for stack of 20-45
	Helix total = -2.1
	Internal/bulge = -1.4  for closure of 21-44	Size = 2
		Stack = -3.3  for stack of 23-42
		Stack = -2.1  for stack of 24-41
		Stack = -2.1  for stack of 25-40
		Stack = -3.4  for stack of 26-39
		Stack = -2.1  for stack of 27-38
		Stack = -2.2  for stack of 28-37
		Stack = -3.3  for stack of 29-36
	Helix total = -18.5
	Hairpin = 3.3  for closure of 30-35


	Total energy = 2668.0



