Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    13:881 14:880 431:453 432:452 433:451
	Energy of Broken Structure: -363.9
	Energy of Pseudo-Helices:   -10.0
	Pseudoknot Energy Penalty:  14.8
	Total Free Energy:          -359.1
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -9.2
		Stack = -1.0  for stack of 1420-1443
		Stack = -1.1  for stack of 1421-1442
		Stack = -2.4  for stack of 1422-1441
		Stack = -3.3  for stack of 1423-1440
		Stack = -2.4  for stack of 1424-1439
		Stack = -2.5  for stack of 1425-1438
		Stack = -1.0  for stack of 1426-1437
		Stack = -2.1  for stack of 1427-1436
		Stack = -3.3  for stack of 1428-1435
	Helix total = -19.1
	Hairpin = 4.5  for closure of 1429-1434
	Helix total = 0.0
	Internal/bulge = 2.3  for closure of 1320-1418	Size = 3
	Helix total = 0.0
	Internal/bulge = 2.6  for closure of 1322-1415	Size = 5
		Stack = -2.4  for stack of 1325-1411
	Helix total = -2.4
	Internal/bulge = -0.6  for closure of 1326-1410	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.7  for closure of 1328-1408	Size = 3
		Stack = -2.1  for stack of 1330-1405
		Stack = -2.4  for stack of 1331-1404
		Stack = -3.3  for stack of 1332-1403
		Stack = -2.1  for stack of 1333-1402
	Helix total = -9.9
	Internal/bulge = 1.2  for closure of 1334-1401	Size = 2
		Stack = -3.3  for stack of 1336-1399
	Helix total = -3.3
	Internal/bulge = -1.7  for closure of 1337-1398	Size = 4
	Helix total = 0.0
	Internal/bulge = 2.4  for closure of 1340-1395	Size = 1 BP stack across bulge = -1.4
		Stack = -2.1  for stack of 1342-1394
		Stack = -3.3  for stack of 1343-1393
		Stack = -3.4  for stack of 1344-1392
		Stack = -2.4  for stack of 1345-1391
		Stack = -3.4  for stack of 1346-1390
		Stack = -2.4  for stack of 1347-1389
		Stack = -3.3  for stack of 1348-1388
	Helix total = -20.3
	Internal/bulge = 0.5  for closure of 1349-1387	Size = 2
		Stack = -3.3  for stack of 1351-1385
		Stack = -3.4  for stack of 1352-1384
	Helix total = -6.7
	Internal/bulge = -0.7  for closure of 1353-1383	Size = 4
		Stack = -3.4  for stack of 1356-1380
		Stack = -2.4  for stack of 1357-1379
	Helix total = -5.8
	Internal/bulge = 0.5  for closure of 1358-1378	Size = 2
		Stack = -3.3  for stack of 1360-1376
		Stack = -3.3  for stack of 1361-1375
	Helix total = -6.6
	Hairpin = 4.3  for closure of 1362-1374
		Stack = -2.1  for stack of 885-1317
	Helix total = -2.1
	Internal/bulge = 1.4  for closure of 886-1316	Size = 1 BP stack across bulge = -2.4
		Stack = -2.2  for stack of 887-1314
		Stack = -1.4  for stack of 888-1313
	Helix total = -3.6
	Internal/bulge = 2.1  for closure of 889-1312	Size = 1 BP stack across bulge = -1.3
		Stack = -2.1  for stack of 891-1311
		Stack = -3.3  for stack of 892-1310
		Stack = -3.3  for stack of 893-1309
		Stack = -3.3  for stack of 894-1308
		Stack = -2.5  for stack of 895-1307
		Stack = -1.0  for stack of 896-1306
	Helix total = -15.5
	Multiloop = 8.3  for closure of 897-1305
		Stack = -3.3  for stack of 1271-1293
		Stack = -3.4  for stack of 1272-1292
		Stack = -2.4  for stack of 1273-1291
		Stack = -3.4  for stack of 1274-1290
	Helix total = -12.5
	Internal/bulge = 0.5  for closure of 1275-1289	Size = 2
		Stack = -2.4  for stack of 1277-1287
	Helix total = -2.4
	Hairpin = 5.3  for closure of 1278-1286
		Stack = -2.1  for stack of 903-1266
		Stack = -2.4  for stack of 904-1265
		Stack = -2.2  for stack of 905-1264
		Stack = -1.4  for stack of 906-1263
		Stack = -1.4  for stack of 907-1262
	Helix total = -9.5
	Multiloop = 5.6  for closure of 908-1261
	Helix total = 0.0
	Internal/bulge = 1.3  for closure of 1226-1255	Size = 8
		Stack = -2.4  for stack of 1231-1250
	Helix total = -2.4
	Internal/bulge = 0.5  for closure of 1232-1249	Size = 2
		Stack = -3.3  for stack of 1234-1247
		Stack = -3.3  for stack of 1235-1246
		Stack = -3.4  for stack of 1236-1245
	Helix total = -10.0
	Hairpin = 4.0  for closure of 1237-1244
		Stack = -3.3  for stack of 1176-1219
		Stack = -3.4  for stack of 1177-1218
		Stack = -2.4  for stack of 1178-1217
		Stack = -3.3  for stack of 1179-1216
		Stack = -3.3  for stack of 1180-1215
	Helix total = -15.7
	Internal/bulge = 2.2  for closure of 1181-1214	Size = 9
		Stack = -3.3  for stack of 1187-1209
		Stack = -2.4  for stack of 1188-1208
	Helix total = -5.7
	Internal/bulge = 0.5  for closure of 1189-1207	Size = 1 BP stack across bulge = -3.3
		Stack = -3.4  for stack of 1190-1205
		Stack = -2.4  for stack of 1191-1204
	Helix total = -5.8
	Internal/bulge = -0.4  for closure of 1192-1203	Size = 4
	Helix total = 0.0
	Hairpin = 3.3  for closure of 1195-1200
		Stack = -2.1  for stack of 911-1170
		Stack = -2.5  for stack of 912-1169
	Helix total = -4.6
	Internal/bulge = 1.9  for closure of 913-1168	Size = 2
		Stack = -1.4  for stack of 915-1166
		Stack = -3.4  for stack of 916-1165
		Stack = -2.4  for stack of 917-1164
	Helix total = -7.2
	Internal/bulge = 0.5  for closure of 918-1163	Size = 1 BP stack across bulge = -3.3
		Stack = -3.4  for stack of 919-1161
	Helix total = -3.4
	Multiloop = 6.8  for closure of 920-1160
		Stack = -3.3  for stack of 948-1156
		Stack = -2.1  for stack of 949-1155
		Stack = -2.1  for stack of 950-1154
		Stack = -3.3  for stack of 951-1153
	Helix total = -10.8
	Internal/bulge = 0.5  for closure of 952-1152	Size = 2
	Helix total = 0.0
	Multiloop = 5.8  for closure of 954-1150
		Stack = -2.1  for stack of 1005-1144
	Helix total = -2.1
	Internal/bulge = 0.5  for closure of 1006-1143	Size = 1 BP stack across bulge = -3.3
		Stack = -3.3  for stack of 1008-1142
		Stack = -2.5  for stack of 1009-1141
		Stack = 0.3  for stack of 1010-1140
	Helix total = -5.5
	Internal/bulge = 3.8  for closure of 1011-1139	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.8  for closure of 1014-1138	Size = 1 BP stack across bulge = -1.0
	Helix total = 0.0
	Internal/bulge = 4.2  for closure of 1015-1136	Size = 3
		Stack = -2.5  for stack of 1016-1132
		Stack = -3.3  for stack of 1017-1131
	Helix total = -5.8
	Internal/bulge = 1.4  for closure of 1018-1130	Size = 1 BP stack across bulge = -2.4
		Stack = -3.4  for stack of 1019-1128
		Stack = -2.1  for stack of 1020-1127
	Helix total = -5.5
	Multiloop = 5.5  for closure of 1021-1126
		Stack = -3.3  for stack of 1071-1120
		Stack = -3.3  for stack of 1072-1119
		Stack = -2.4  for stack of 1073-1118
	Helix total = -9.0
	Multiloop = 4.9  for closure of 1074-1117
		Stack = -3.3  for stack of 1097-1108
		Stack = -2.4  for stack of 1098-1107
		Stack = -3.4  for stack of 1099-1106
	Helix total = -9.1
	Hairpin = 3.3  for closure of 1100-1105
		Stack = -3.3  for stack of 1076-1090
		Stack = -2.4  for stack of 1077-1089
		Stack = -3.4  for stack of 1078-1088
		Stack = -2.4  for stack of 1079-1087
		Stack = -3.3  for stack of 1080-1086
	Helix total = -14.8
	Hairpin = 5.4  for closure of 1081-1085
		Stack = -3.4  for stack of 1026-1065
	Helix total = -3.4
	Internal/bulge = 0.3  for closure of 1027-1064	Size = 2
		Stack = -2.4  for stack of 1029-1062
		Stack = -2.2  for stack of 1030-1061
	Helix total = -4.6
	Multiloop = 7.2  for closure of 1031-1060
		Stack = -1.4  for stack of 1045-1056
		Stack = -3.4  for stack of 1046-1055
	Helix total = -4.8
	Hairpin = 3.3  for closure of 1047-1054
		Stack = -3.3  for stack of 1032-1041
		Stack = -3.4  for stack of 1033-1040
	Helix total = -6.7
	Hairpin = 3.3  for closure of 1034-1039
		Stack = -3.4  for stack of 960-1000
		Stack = -2.4  for stack of 961-999
		Stack = -3.4  for stack of 962-998
		Stack = -2.4  for stack of 963-997
	Helix total = -11.6
	Internal/bulge = 3.7  for closure of 964-996	Size = 10
		Stack = -2.4  for stack of 971-991
		Stack = -2.4  for stack of 972-990
	Helix total = -4.8
	Internal/bulge = 1.9  for closure of 973-989	Size = 2
		Stack = -2.1  for stack of 975-987
		Stack = -3.4  for stack of 976-986
	Helix total = -5.5
	Hairpin = 4.9  for closure of 977-985
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 925-940	Size = 2
		Stack = -1.4  for stack of 927-938
	Helix total = -1.4
	Hairpin = 4.2  for closure of 928-937
		Stack = -2.1  for stack of 858-869
		Stack = -3.4  for stack of 859-868
		Stack = -3.3  for stack of 860-867
	Helix total = -8.8
	Hairpin = 3.3  for closure of 861-866
		Stack = -2.1  for stack of 494-847
		Stack = -2.1  for stack of 495-846
	Helix total = -4.2
	Internal/bulge = 4.5  for closure of 496-845	Size = 5
	Helix total = 0.0
	Multiloop = 4.9  for closure of 502-844
		Stack = -3.4  for stack of 782-843
		Stack = -3.3  for stack of 783-842
	Helix total = -6.7
	Internal/bulge = 3.6  for closure of 784-841	Size = 4
		Stack = -3.4  for stack of 785-836
		Stack = -3.3  for stack of 786-835
	Helix total = -6.7
	Multiloop = 5.0  for closure of 787-834
		Stack = -3.3  for stack of 822-829
	Helix total = -3.3
	Hairpin = 3.1  for closure of 823-828
		Stack = -3.4  for stack of 790-818
		Stack = -2.4  for stack of 791-817
		Stack = -3.3  for stack of 792-816
		Stack = -3.4  for stack of 793-815
		Stack = -3.3  for stack of 794-814
		Stack = -2.4  for stack of 795-813
		Stack = -3.3  for stack of 796-812
		Stack = -3.4  for stack of 797-811
		Stack = -2.4  for stack of 798-810
	Helix total = -27.3
	Hairpin = 5.7  for closure of 799-809
		Stack = -3.4  for stack of 730-771
		Stack = -3.3  for stack of 731-770
		Stack = -2.4  for stack of 732-769
		Stack = -3.3  for stack of 733-768
		Stack = -3.3  for stack of 734-767
		Stack = -1.5  for stack of 735-766
	Helix total = -17.2
	Internal/bulge = 4.2  for closure of 736-765	Size = 3
	Helix total = 0.0
	Internal/bulge = 0.7  for closure of 740-764	Size = 6
		Stack = -3.3  for stack of 744-760
	Helix total = -3.3
	Internal/bulge = -0.4  for closure of 745-759	Size = 2
	Helix total = 0.0
	Hairpin = 4.9  for closure of 747-757
		Stack = -3.4  for stack of 504-725
		Stack = -3.3  for stack of 505-724
		Stack = -3.3  for stack of 506-723
	Helix total = -10.0
	Internal/bulge = 1.7  for closure of 507-722	Size = 6
		Stack = -1.4  for stack of 511-718
		Stack = -0.9  for stack of 512-717
		Stack = -2.1  for stack of 513-716
	Helix total = -4.4
	Multiloop = 8.2  for closure of 514-715
		Stack = -2.1  for stack of 616-712
		Stack = -2.4  for stack of 617-711
	Helix total = -4.5
	Internal/bulge = 0.4  for closure of 618-710	Size = 1 BP stack across bulge = -2.1
		Stack = -3.4  for stack of 619-708
		Stack = -2.4  for stack of 620-707
		Stack = -3.3  for stack of 621-706
	Helix total = -9.1
	Internal/bulge = 0.5  for closure of 622-705	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.0  for closure of 624-703	Size = 5
		Stack = -3.3  for stack of 628-700
		Stack = -3.4  for stack of 629-699
		Stack = -2.1  for stack of 630-698
	Helix total = -8.8
	Multiloop = 6.1  for closure of 631-697
		Stack = -3.4  for stack of 686-693
	Helix total = -3.4
	Hairpin = 3.2  for closure of 687-692
		Stack = -3.3  for stack of 634-678
		Stack = -2.2  for stack of 635-677
	Helix total = -5.5
	Internal/bulge = 0.9  for closure of 636-676	Size = 4
		Stack = -2.4  for stack of 639-673
		Stack = -3.3  for stack of 640-672
		Stack = -3.4  for stack of 641-671
	Helix total = -9.1
	Internal/bulge = 0.5  for closure of 642-670	Size = 2
		Stack = -3.3  for stack of 644-668
	Helix total = -3.3
	Internal/bulge = 3.2  for closure of 645-667	Size = 9
	Helix total = 0.0
	Internal/bulge = 0.5  for closure of 649-660	Size = 2
	Helix total = 0.0
	Hairpin = 2.9  for closure of 651-658
		Stack = -2.4  for stack of 521-581
	Helix total = -2.4
	Internal/bulge = 1.0  for closure of 522-580	Size = 6
		Stack = -3.3  for stack of 526-576
		Stack = -2.1  for stack of 527-575
		Stack = -2.2  for stack of 528-574
		Stack = -2.4  for stack of 529-573
	Helix total = -10.0
	Hairpin = 6.7  for closure of 530-572
		Stack = -3.4  for stack of 22-483
		Stack = -2.4  for stack of 23-482
		Stack = -3.4  for stack of 24-481
		Stack = -2.4  for stack of 25-480
		Stack = -2.4  for stack of 26-479
		Stack = -2.2  for stack of 27-478
		Stack = -2.4  for stack of 28-477
		Stack = -3.4  for stack of 29-476
		Stack = -2.1  for stack of 30-475
	Helix total = -24.1
	Multiloop = 0.5  for closure of 31-474
		Stack = -3.4  for stack of 425-472
		Stack = -3.3  for stack of 426-471
		Stack = -2.4  for stack of 427-470
		Stack = -2.4  for stack of 428-469
		Stack = -2.1  for stack of 429-468
	Helix total = -13.6
	Internal/bulge = 4.7  for closure of 430-467	Size = 8
		Stack = -2.1  for stack of 439-466
		Stack = -2.1  for stack of 440-465
		Stack = -3.3  for stack of 441-464
	Helix total = -7.5
	Internal/bulge = 0.7  for closure of 442-463	Size = 2
	Helix total = 0.0
	Hairpin = 6.9  for closure of 444-461
		Stack = -3.3  for stack of 399-419
		Stack = -3.4  for stack of 400-418
		Stack = -2.4  for stack of 401-417
		Stack = -3.3  for stack of 402-416
		Stack = -3.3  for stack of 403-415
	Helix total = -15.7
	Hairpin = 5.7  for closure of 404-414
		Stack = -3.4  for stack of 389-396
	Helix total = -3.4
	Hairpin = 3.3  for closure of 390-395
		Stack = -2.4  for stack of 33-386
		Stack = -3.3  for stack of 34-385
		Stack = -3.3  for stack of 35-384
		Stack = -3.3  for stack of 36-383
	Helix total = -12.3
	Internal/bulge = 1.5  for closure of 37-382	Size = 5
	Helix total = 0.0
	Multiloop = 4.2  for closure of 40-378
		Stack = -2.1  for stack of 350-377
	Helix total = -2.1
	Internal/bulge = 1.3  for closure of 351-376	Size = 1 BP stack across bulge = -2.1
		Stack = -3.4  for stack of 353-375
		Stack = -3.3  for stack of 354-374
	Helix total = -6.7
	Internal/bulge = 3.0  for closure of 355-373	Size = 4
		Stack = -1.4  for stack of 359-371
		Stack = -3.4  for stack of 360-370
		Stack = -2.4  for stack of 361-369
		Stack = -3.4  for stack of 362-368
	Helix total = -10.6
	Hairpin = 5.4  for closure of 363-367
	Helix total = 0.0
	Internal/bulge = 4.4  for closure of 41-345	Size = 6
		Stack = -3.4  for stack of 47-343
		Stack = -3.3  for stack of 48-342
	Helix total = -6.7
	Internal/bulge = 1.7  for closure of 49-341	Size = 1 BP stack across bulge = -2.1
		Stack = -2.1  for stack of 51-340
		Stack = -3.4  for stack of 52-339
	Helix total = -5.5
	Multiloop = 0.1  for closure of 53-338
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 323-334	Size = 2
		Stack = -2.4  for stack of 325-332
	Helix total = -2.4
	Hairpin = 3.3  for closure of 326-331
		Stack = -3.4  for stack of 300-321
		Stack = -2.4  for stack of 301-320
		Stack = -3.3  for stack of 302-319
		Stack = -3.3  for stack of 303-318
		Stack = -3.4  for stack of 304-317
		Stack = -3.3  for stack of 305-316
	Helix total = -19.1
	Hairpin = 4.1  for closure of 306-315
		Stack = -2.1  for stack of 84-298
		Stack = -2.4  for stack of 85-297
	Helix total = -4.5
	Multiloop = 2.0  for closure of 86-296
		Stack = -2.4  for stack of 273-295
		Stack = -3.3  for stack of 274-294
		Stack = -2.4  for stack of 275-293
	Helix total = -8.1
	Internal/bulge = 3.7  for closure of 276-292	Size = 3
		Stack = -2.4  for stack of 277-288
		Stack = -0.9  for stack of 278-287
		Stack = -1.4  for stack of 279-286
	Helix total = -4.7
	Hairpin = 5.4  for closure of 280-285
		Stack = -3.3  for stack of 223-269
		Stack = -3.4  for stack of 224-268
	Helix total = -6.7
	Internal/bulge = 3.7  for closure of 225-267	Size = 10
		Stack = -3.3  for stack of 230-260
		Stack = -3.3  for stack of 231-259
	Helix total = -6.6
	Internal/bulge = 3.3  for closure of 232-258	Size = 2
		Stack = -2.4  for stack of 235-257
		Stack = -2.4  for stack of 236-256
		Stack = -3.3  for stack of 237-255
		Stack = -3.4  for stack of 238-254
		Stack = -2.4  for stack of 239-253
		Stack = -3.4  for stack of 240-252
		Stack = -2.4  for stack of 241-251
	Helix total = -19.7
	Hairpin = 3.8  for closure of 242-250
		Stack = -2.4  for stack of 94-221
		Stack = -3.3  for stack of 95-220
	Helix total = -5.7
	Internal/bulge = -0.6  for closure of 96-219	Size = 4
	Helix total = 0.0
	Internal/bulge = 2.3  for closure of 99-216	Size = 4
		Stack = -3.3  for stack of 103-214
	Helix total = -3.3
	Internal/bulge = 2.6  for closure of 104-213	Size = 5
		Stack = -3.4  for stack of 108-210
		Stack = -2.4  for stack of 109-209
		Stack = -3.3  for stack of 110-208
	Helix total = -9.1
	Internal/bulge = 7.5  for closure of 111-207	Size = 64
		Stack = -2.4  for stack of 126-156
	Helix total = -2.4
	Internal/bulge = 2.2  for closure of 127-155	Size = 11
		Stack = -2.4  for stack of 133-148
		Stack = -3.4  for stack of 134-147
		Stack = -2.1  for stack of 135-146
		Stack = -1.4  for stack of 136-145
		Stack = -3.3  for stack of 137-144
	Helix total = -12.6
	Hairpin = 4.9  for closure of 138-143
		Stack = -3.4  for stack of 56-77
	Helix total = -3.4
	Internal/bulge = -1.0  for closure of 57-76	Size = 1 BP stack across bulge = -3.3
		Stack = -2.4  for stack of 59-75
		Stack = -3.4  for stack of 60-74
	Helix total = -5.8
	Internal/bulge = 1.7  for closure of 61-73	Size = 1 BP stack across bulge = -2.1
		Stack = -2.4  for stack of 62-71
	Helix total = -2.4
	Hairpin = 4.0  for closure of 63-70
		Stack = -3.3  for stack of 4-20
		Stack = -2.4  for stack of 5-19
		Stack = -3.3  for stack of 6-18
		Stack = -2.5  for stack of 7-17
	Helix total = -11.5
	Hairpin = 6.0  for closure of 8-16


	Total energy = -363.9



