Alignment of IL_69229.3 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 3 2	5 3 I	6 3 3	7 3 I	8 3 4	10 5 5	12 6 6	14 7 7	16 8	18 7 8	20 6 9	22 5 10	24 3 11	26 2 12	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_69229.3_Instance_1 IL_69229.3,IL_3NVI_002,G15_C8	G	C		G	U	G	A	U	G		C	U	G	A	C
IL_69229.3_Sequence_1 IL_69229.33NVI_G15_C8	G	C		G	U	G	A	U	G	*	C	U	G	A	C	true	100	0	0	0.00
IL_69229.3_Instance_2 IL_69229.3,IL_5GIP_001,U8_A34	U	U		G	U	G	A	U	G		C	U	G	A	A
IL_69229.3_Sequence_2 IL_69229.35GIP_U8_A34	U	U		G	U	G	A	U	G	*	C	U	G	A	A	true	99	0	0	0.24
IL_69229.3_Instance_3 IL_69229.3,IL_5GIP_003,U8_A34	U	U		G	U	G	A	U	G		C	U	G	A	A
IL_69229.3_Sequence_3 IL_69229.35GIP_U8_A34	U	U		G	U	G	A	U	G	*	C	U	G	A	A	true	99	0	0	0.24
IL_69229.3_Instance_4 IL_69229.3,IL_3NMU_004,G24_C17	G	C		G	U	G	A	U	G		C	U	G	A	C
IL_69229.3_Sequence_4 IL_69229.33NMU_G24_C17	G	C		G	U	G	A	U	G	*	C	U	G	A	C	true	100	0	0	0.00
IL_69229.3_Instance_5 IL_69229.3,IL_1RLG_004,G15_C8	G	C		G	U	G	A	U	G		C	U	G	A	C
IL_69229.3_Sequence_5 IL_69229.31RLG_G15_C8	G	C		G	U	G	A	U	G	*	C	U	G	A	C	true	100	0	0	0.00
IL_69229.3_Instance_6 IL_69229.3,IL_3Q3Z_002,C16_G58	C	A		A	U	G	A	U	G		U	U	G	A	G
IL_69229.3_Sequence_6 IL_69229.33Q3Z_C16_G58	C	A		A	U	G	A	U	G	*	U	U	G	A	G	true	89	0	0	2.15
IL_69229.3_Instance_7 IL_69229.3,IL_6DVK_002,C68_G22	C	G		U	UU	G	A	C	G		C	C	G	A	G
IL_69229.3_Sequence_7 IL_69229.36DVK_C68_G22	C	G		U	UU	G	A	C	G	*	C	C	G	A	G	true	75	0	0	5.00
IL_69229.3_Instance_8 IL_69229.3,IL_7A0S_050,C1598_G1430	C	G	U	U		G	A	A	A		U	G	G	A	G
IL_69229.3_Sequence_8 IL_69229.37A0S_C_1598_G_1430	C	G		U	U	G	A	A	A	*	U	G	G	A	G	true	83	0	0	3.40

Conserved interactions between motif group positions in IL_69229.3:

1 2 s35 
1 12 cWW 
2 11 tSS 
2 12 s55 
3 4 s35 
3 11 s33 
4 10 s33 
4 11 tSH 
5 6 s35 
5 10 tHS 
5 11 s55 
5 12 perp 
6 7 s35 
6 9 cWW 
7 8 cWW 
7 9 s55 
8 9 s35 
9 10 s35 
11 12 perp 
10 4 6BR
11 4 6BR
4 10 6BR
5 10 6BR

JAR3D SCFG/MRF model for IL_69229.3:

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 [12] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008957994,0.017378845,0.010148388,0.188059271,0.000000000],[0.018441409,0.009141765,0.220204749,0.012196759,0.000000000],[0.010152962,0.219609041,0.001962745,0.023232061,0.000000000],[0.208491401,0.012038445,0.030373981,0.009610184,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair G15 - C8 cWW 
ClusterNode  | Deletion Probability [0.0000000000015373] | Num Left Bases [3] | Num Right Bases [1] | Left Index [2] | Right Index [11] | Norm Constant [0.419423571192567] // Cluster node 3NVI|1|F|C|16:3NVI|1|F|G|19 and 3NVI|1|F|A|7:3NVI|1|F|A|7
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.211158828,0.039489841,0.039905912,0.038865149,0.000000000],[0.155364558,0.022023296,0.023744397,0.022023296,0.000000000],[0.170324966,0.022023296,0.023421606,0.036949968,0.000000000],[0.128634998,0.022023296,0.022023296,0.022023296,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3NVI|1|F|C|16 - 3NVI|1|F|A|7 tSS 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.051125900,0.054123656,0.000613732,0.002892522,0.000000000],[0.051505729,0.053998327,0.000613732,0.000613732,0.000000000],[0.393981458,0.003068662,0.015001713,0.260456406,0.000000000],[0.057070158,0.053706807,0.000613732,0.000613732,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3NVI|1|F|G|19 - 3NVI|1|F|A|7 tSH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.150000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.050000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.550000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3NVI|1|F|G|17
Insertion    | Location [1] | Length Distribution [0.869396619,0.129517605,0.001046999,0.000038778] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 2, position 1 in cluster node
Insertion    | Location [2] | Length Distribution [0.128145746,0.742627760,0.128184345,0.001003551,0.000038598] | Letter Distribution [0.050000000,0.050000000,0.050000000,0.850000000,0.000000000]// Insertion after nucleotide 3, position 2 in cluster node
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [10] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.051125900,0.051505729,0.393981458,0.057070158,0.000000000],[0.054123656,0.053998327,0.003068662,0.053706807,0.000000000],[0.000613732,0.000613732,0.015001713,0.000613732,0.000000000],[0.002892522,0.000613732,0.260456406,0.000613732,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [10] // Basepair A20 - G6 tHS 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.014100605,0.258622283,0.036783010,0.021988284,0.000000000],[0.015584515,0.040997510,0.018794731,0.013820321,0.000000000],[0.012326511,0.019146131,0.003886384,0.049649293,0.000000000],[0.019208232,0.014967397,0.015930823,0.444193970,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair U21 - U5 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009860579,0.052006811,0.010711944,0.185943858,0.000000000],[0.015798891,0.009401807,0.171033885,0.012333004,0.000000000],[0.010586262,0.231672514,0.002103895,0.072801947,0.000000000],[0.168237118,0.012925649,0.021034647,0.013547190,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [8] // Basepair G22 - C4 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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_69229.3:> IL_69229.3 3NVI G 15 C 8 GCGUGAUG*CUGAC > IL_69229.3 5GIP U 8 A 34 UUGUGAUG*CUGAA > IL_69229.3 5GIP U 8 A 34 UUGUGAUG*CUGAA > IL_69229.3 3NMU G 24 C 17 GCGUGAUG*CUGAC > IL_69229.3 1RLG G 15 C 8 GCGUGAUG*CUGAC > IL_69229.3 3Q3Z C 16 G 58 CAAUGAUG*UUGAG > IL_69229.3 6DVK C 68 G 22 CGUUUGACG*CCGAG > IL_69229.3 7A0S C 1598 G 1430 CGUUGAAA*UGGAG