Alignment of IL_13404.2 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	6 4 3	8 5 4	10 6	12 5 5	13 4 I	14 4 6	16 3 7	18 2 8	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_13404.2_Instance_1 IL_13404.2,IL_422D_001,U7_G22	U	U	C	G		U		U	C	G
IL_13404.2_Sequence_1 IL_13404.2422D_U7_G22	U	U	C	G	*	U		U	C	G	true	100	0	0	0.00
IL_13404.2_Instance_2 IL_13404.2,IL_4ERD_002,U127_G142	U	U	C	G		U		U	C	G
IL_13404.2_Sequence_2 IL_13404.24ERD_U127_G142	U	U	C	G	*	U		U	C	G	true	100	0	0	0.00
IL_13404.2_Instance_3 IL_13404.2,IL_1IHA_001,U3_G6	U	U	C	G		U		U	C	G
IL_13404.2_Sequence_3 IL_13404.21IHA_U3_G6	U	U	C	G	*	U		U	C	G	true	100	0	0	0.00
IL_13404.2_Instance_4 IL_13404.2,IL_1ICG_001,U3_G6	U	U	C	G		U		U	C	G
IL_13404.2_Sequence_4 IL_13404.21ICG_U3_G6	U	U	C	G	*	U		U	C	G	true	100	0	0	0.00
IL_13404.2_Instance_5 IL_13404.2,IL_255D_001,U5_G8	U	U	C	G		U		U	C	G
IL_13404.2_Sequence_5 IL_13404.2255D_U5_G8	U	U	C	G	*	U		U	C	G	true	100	0	0	0.00
IL_13404.2_Instance_6 IL_13404.2,IL_6L0Y_002,U10_G13	U	U	C	G		U		U	C	G
IL_13404.2_Sequence_6 IL_13404.26L0Y_U10_G13	U	U	C	G	*	U		U	C	G	true	100	0	0	0.00
IL_13404.2_Instance_7 IL_13404.2,IL_1QBP_002,U22_G10	U	U	C	G		U		U	C	G
IL_13404.2_Sequence_7 IL_13404.21QBP_U22_G10	U	U	C	G	*	U		U	C	G	true	100	0	0	0.00
IL_13404.2_Instance_8 IL_13404.2,IL_413D_001,U6_G9	U	U	C	G		U		U	C	G
IL_13404.2_Sequence_8 IL_13404.2413D_U6_G9	U	U	C	G	*	U		U	C	G	true	100	0	0	0.00
IL_13404.2_Instance_9 IL_13404.2,IL_8CRE_458,A1368_U1328	A	G	A	G		C	U	A	C	U
IL_13404.2_Sequence_9 IL_13404.28CRE_A_1368_U_1328	A	G	A	G	*	C	U	A	C	U	true	24	0	0	9.62
IL_13404.2_Instance_10 IL_13404.2,IL_4WF9_124,G2217_C2126	G	G	C	U		A		U	U	C
IL_13404.2_Sequence_10 IL_13404.24WF9_G_2217_C_2126	G	G	C	U	*	A		U	U	C	true	58	0	0	5.35

Conserved interactions between motif group positions in IL_13404.2:

1 8 cWW 
2 3 s35 
2 7 cWW 
2 8 s55 
3 4 s35 
3 6 cWW 
4 5 cWW 
4 6 s55 
6 7 s35 
7 8 s35

JAR3D SCFG/MRF model for IL_13404.2:

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 [8] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.010105956,0.014294290,0.012538510,0.074336848,0.000000000],[0.227638118,0.022507790,0.068249640,0.014086747,0.000000000],[0.012757176,0.074242340,0.002835564,0.018300194,0.000000000],[0.100545145,0.013190349,0.322292680,0.012078652,0.000000000],[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 [8] // Basepair U7 - G22 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.016741257,0.014897014,0.041955243,0.018198591,0.000000000],[0.013575875,0.010812137,0.021416189,0.285830786,0.000000000],[0.039708464,0.042405319,0.003368294,0.036512912,0.000000000],[0.017094082,0.409556656,0.014955075,0.012972107,0.000000000],[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 [2] | Right Index [7] // Basepair U8 - C21 cWW 
BasepairNode | Deletion Probability [0.0000141488146644] | Pair Probability [[0.078067699,0.015118939,0.041287581,0.018317064,0.000000000],[0.015492012,0.011752380,0.023072419,0.395686323,0.000000000],[0.042288810,0.022374564,0.003666644,0.016524013,0.000000000],[0.019267313,0.267022936,0.016982566,0.013078738,0.000000000],[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 [0.895351728,0.103902560,0.000720855,0.000024857] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair C9 - U20 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.013490579,0.223742772,0.012567813,0.099617307,0.000000000],[0.013809273,0.011284142,0.064117464,0.012941809,0.000000000],[0.012330652,0.077328212,0.002790039,0.318021113,0.000000000],[0.073610163,0.013912715,0.017797981,0.032637965,0.000000000],[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 [4] | Right Index [5] // Basepair G10 - U19 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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_13404.2:> IL_13404.2 422D U 7 G 22 UUCG*UUCG > IL_13404.2 4ERD U 127 G 142 UUCG*UUCG > IL_13404.2 1IHA U 3 G 6 UUCG*UUCG > IL_13404.2 1ICG U 3 G 6 UUCG*UUCG > IL_13404.2 255D U 5 G 8 UUCG*UUCG > IL_13404.2 6L0Y U 10 G 13 UUCG*UUCG > IL_13404.2 1QBP U 22 G 10 UUCG*UUCG > IL_13404.2 413D U 6 G 9 UUCG*UUCG > IL_13404.2 8CRE A 1368 U 1328 AGAG*CUACU > IL_13404.2 4WF9 G 2217 C 2126 GGCU*AUUC