Alignment of IL_63596.11 sequences from 3D to the JAR3D model

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The correspondence between sequences from 3D structures and the motif group is shown in blue and the JAR3D alignment of the sequences to the motif group is shown in black. Occasionally the two disagree, in which case the JAR3D alignment is shown in red.

Column number: Node in JAR3D model: Insertion positions indicated by I: Position in motif group:	2 2 1	4 2 2	6 2 3	8 2 4	10 2 5	12 4	14 2 6	15 2 I	16 2 7	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_63596.11_Instance_1 IL_63596.11,IL_5J7L_347,U2680_A2727	U	C	A	C	U		A	A	A
IL_63596.11_Sequence_1 IL_63596.115J7L_U_2680_A_2727	U	C	A	C	U	*	A	A	A	true	75	0	0	3.06
IL_63596.11_Instance_2 IL_63596.11,IL_7A0S_095,C2659_G2707	C	C	G	C	U		A	U	G
IL_63596.11_Sequence_2 IL_63596.117A0S_C_2659_G_2707	C	C	G	C	U	*	A	U	G	true	83	0	0	2.12
IL_63596.11_Instance_3 IL_63596.11,IL_4WF9_101,C2707_G2754	C	C	U	C	U		A	U	G
IL_63596.11_Sequence_3 IL_63596.114WF9_C_2707_G_2754	C	C	U	C	U	*	A	U	G	true	99	0	0	0.13
IL_63596.11_Instance_4 IL_63596.11,IL_9DFE_103,C2680_G2727	C	C	U	C	U		A	U	G
IL_63596.11_Sequence_4 IL_63596.119DFE_C_2680_G_2727	C	C	U	C	U	*	A	U	G	true	99	0	0	0.13
IL_63596.11_Instance_5 IL_63596.11,IL_1KOG_007,C96_G76	C	C	A	C	U		A	U	G
IL_63596.11_Sequence_5 IL_63596.111KOG_C96_G76	C	C	A	C	U	*	A	U	G	true	99	0	0	0.13
IL_63596.11_Instance_6 IL_63596.11,IL_8HNT_002,G87_C122	G	C	U	C	U		A	U	C
IL_63596.11_Sequence_6 IL_63596.118HNT_G87_C122	G	C	U	C	U	*	A	U	C	true	89	0	0	1.37
IL_63596.11_Instance_7 IL_63596.11,IL_6XJQ_001,G5_C54	G	C	U	C	C		G	U	C
IL_63596.11_Sequence_7 IL_63596.116XJQ_G5_C54	G	C	U	C	C	*	G	U	C	true	69	0	0	3.84
IL_63596.11_Instance_8 IL_63596.11,IL_4V9F_093,C2717_G2763	C	C	A	C	U		A	C	G
IL_63596.11_Sequence_8 IL_63596.114V9F_C_2717_G_2763	C	C	A	C	U	*	A	C	G	true	100	0	0	0.00
IL_63596.11_Instance_9 IL_63596.11,IL_4MGN_001,C29_G75	C	C	U	C	U		A	C	G
IL_63596.11_Sequence_9 IL_63596.114MGN_C29_G75	C	C	U	C	U	*	A	C	G	true	100	0	0	0.00
IL_63596.11_Instance_10 IL_63596.11,IL_8P9A_431,U1617_A1160	U	C	C	C	U		A	CC	A
IL_63596.11_Sequence_10 IL_63596.118P9A_U_1617_A_1160	U	C	C	C	U	*	A	CC	A	true	53	0	0	5.79
IL_63596.11_Instance_11 IL_63596.11,IL_4V9F_051,G1425_C1439	G	C	A	C	U		A	G	C
IL_63596.11_Sequence_11 IL_63596.114V9F_G_1425_C_1439	G	C	A	C	U	*	A	G	C	true	86	0	0	1.68
IL_63596.11_Instance_12 IL_63596.11,IL_5B2P_003,C76_G90	C	C	U	C	U		A	C	G
IL_63596.11_Sequence_12 IL_63596.115B2P_C76_G90	C	C	U	C	U	*	A	C	G	true	100	0	0	0.00
IL_63596.11_Instance_13 IL_63596.11,IL_8CRE_445,U1604_A1145	U	C	C	C	U		A	CC	A
IL_63596.11_Sequence_13 IL_63596.118CRE_U_1604_A_1145	U	C	C	C	U	*	A	CC	A	true	53	0	0	5.79
IL_63596.11_Instance_14 IL_63596.11,IL_4JRC_003,C29_G75	C	C	U	C	U		A	C	G
IL_63596.11_Sequence_14 IL_63596.114JRC_C29_G75	C	C	U	C	U	*	A	C	G	true	100	0	0	0.00
IL_63596.11_Instance_15 IL_63596.11,IL_6JDV_004,G105_C140	G	C	U	C	U		A	U	C
IL_63596.11_Sequence_15 IL_63596.116JDV_G105_C140	G	C	U	C	U	*	A	U	C	true	89	0	0	1.37
IL_63596.11_Instance_16 IL_63596.11,IL_5J7L_291,C1319_G1333	C	C	A	A	C		G	G	G
IL_63596.11_Sequence_16 IL_63596.115J7L_C_1319_G_1333	C	C	A	A	C	*	G	G	G	true	55	0	0	5.47
IL_63596.11_Instance_17 IL_63596.11,IL_9DFE_050,G1319_C1333	G	C	A	A	U		A	G	C
IL_63596.11_Sequence_17 IL_63596.119DFE_G_1319_C_1333	G	C	A	A	U	*	A	G	C	true	74	0	0	3.13
IL_63596.11_Instance_18 IL_63596.11,IL_8P9A_290,U1501_A1515	U	C	A	A	C		G	G	A
IL_63596.11_Sequence_18 IL_63596.118P9A_U_1501_A_1515	U	C	A	A	C	*	G	G	A	true	55	0	0	5.47
IL_63596.11_Instance_19 IL_63596.11,IL_8CRE_066,U1497_A1511	U	C	A	A	C		G	G	A
IL_63596.11_Sequence_19 IL_63596.118CRE_U_1497_A_1511	U	C	A	A	C	*	G	G	A	true	55	0	0	5.47

Conserved interactions between motif group positions in IL_63596.11:

1 2 s35 
1 7 cWW 
2 4 cSH 
2 6 tWH 
2 7 s55 
3 4 s35 
4 5 s35 
4 7 cWS 
5 6 cWW 
6 7 s35 
3 2 7BR

JAR3D SCFG/MRF model for IL_63596.11:

Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [7] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000223328457280071460584722431189528970159112] | Num Left Bases [5] | Num Right Bases [2] | Left Index [1] | Right Index [7] | Norm Constant [0.008748336697488] // Cluster node 5J7L|1|DA|U|2680:5J7L|1|DA|U|2684 and 5J7L|1|DA|A|2725:5J7L|1|DA|A|2727
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.031843204,0.013485512,0.080527687,0.013485512,0.000000000],[0.379953218,0.028749934,0.047098957,0.013485512,0.000000000],[0.013485512,0.019535492,0.032895086,0.033442083,0.000000000],[0.035478394,0.013485512,0.021975449,0.221072936,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|2681 - 5J7L|1|DA|A|2725 tWH 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.007834346,0.014958357,0.008684444,0.168720670,0.000000000],[0.018575859,0.008405686,0.204619178,0.009962529,0.000000000],[0.008719741,0.168234648,0.001760426,0.019830586,0.000000000],[0.300719926,0.009418038,0.040894884,0.008660681,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|2684 - 5J7L|1|DA|A|2725 cWW 
Interaction  | Interacting Bases [1,7] | Pair Probability [[0.008105384,0.015473466,0.009186860,0.170405132,0.000000000],[0.017061420,0.008314162,0.250704869,0.011086930,0.000000000],[0.009213444,0.215457325,0.001780847,0.020763584,0.000000000],[0.214715044,0.010844820,0.028182785,0.008703929,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|2680 - 5J7L|1|DA|A|2727 cWW 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.063781716,0.055522707,0.054477794,0.046285617,0.000000000],[0.111493036,0.120168446,0.358827972,0.085221023,0.000000000],[0.018344455,0.010636512,0.018102324,0.015634134,0.000000000],[0.010691600,0.012588458,0.007964435,0.010259772,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|2683 - 5J7L|1|DA|A|2727 cWS 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.074156057,0.073555679,0.004043079,0.058987560,0.000000000],[0.110216985,0.217363980,0.000846835,0.044424285,0.000000000],[0.046981489,0.000846835,0.072885912,0.069571402,0.000000000],[0.075914703,0.074005313,0.000846835,0.075353051,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|2681 - 5J7L|1|DA|C|2683 cSH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.417525773,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.108247423,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.056701031,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.417525773,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|DA|A|2682
Insertion    | Location [6] | Length Distribution [0.002341937,0.890211394,0.107040274,0.000392619,0.000013776] | Letter Distribution [0.065217391,0.369565217,0.239130435,0.326086957,0.000000000]// Insertion after nucleotide 6, position 6 in cluster node
InitialNode  | Left Length Distribution [0.997221289,0.002647563,0.000131149] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997221289,0.002647563,0.000131149] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [5] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node type *
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncation

Sequences of instances from IL_63596.11:> IL_63596.11 5J7L U 2680 A 2727 UCACU*AAA > IL_63596.11 7A0S C 2659 G 2707 CCGCU*AUG > IL_63596.11 4WF9 C 2707 G 2754 CCUCU*AUG > IL_63596.11 9DFE C 2680 G 2727 CCUCU*AUG > IL_63596.11 1KOG C 96 G 76 CCACU*AUG > IL_63596.11 8HNT G 87 C 122 GCUCU*AUC > IL_63596.11 6XJQ G 5 C 54 GCUCC*GUC > IL_63596.11 4V9F C 2717 G 2763 CCACU*ACG > IL_63596.11 4MGN C 29 G 75 CCUCU*ACG > IL_63596.11 8P9A U 1617 A 1160 UCCCU*ACCA > IL_63596.11 4V9F G 1425 C 1439 GCACU*AGC > IL_63596.11 5B2P C 76 G 90 CCUCU*ACG > IL_63596.11 8CRE U 1604 A 1145 UCCCU*ACCA > IL_63596.11 4JRC C 29 G 75 CCUCU*ACG > IL_63596.11 6JDV G 105 C 140 GCUCU*AUC > IL_63596.11 5J7L C 1319 G 1333 CCAAC*GGG > IL_63596.11 9DFE G 1319 C 1333 GCAAU*AGC > IL_63596.11 8P9A U 1501 A 1515 UCAAC*GGA > IL_63596.11 8CRE U 1497 A 1511 UCAAC*GGA