Alignment of IL_30730.1 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	5 2 I	6 2 3	8 2 4	10 4 5	11 5 I	12 8 6	14 9	16 8 7	18 6 8	20 2 9	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_30730.1_Instance_1 IL_30730.1,IL_7WIE_002,U17_A45	U	U	C	A	A	C	UC	G		C	U	A
IL_30730.1_Sequence_1 IL_30730.17WIE_U17_A45	U	U	C	A	A	C	UC	G	*	C	U	A	true	100	0	0	0.00
IL_30730.1_Instance_2 IL_30730.1,IL_8XZL_002,U13_A42	U	U	C	A	A	C	UC	G		C	U	A
IL_30730.1_Sequence_2 IL_30730.18XZL_U13_A42	U	U	C	A	A	C	UC	G	*	C	U	A	true	100	0	0	0.00

Conserved interactions between motif group positions in IL_30730.1:

1 3 cSH 
1 9 cWW 
2 3 s53 
2 4 cWH 
2 5 s35 
2 9 tHS 
3 4 s35 
4 5 s35 
4 9 cWS 
6 7 cWW 
6 8 s55 
7 8 s35 
8 9 s35

JAR3D SCFG/MRF model for IL_30730.1:

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 [9] // Initial node
ClusterNode  | Deletion Probability [0.000000000000015429359482326747228196069233951473250875292831] | Num Left Bases [4] | Num Right Bases [1] | Left Index [1] | Right Index [9] | Norm Constant [0.005304893250626] // Cluster node 7WIE|1|V|U|17:7WIE|1|V|A|21 and 7WIE|1|V|A|45:7WIE|1|V|A|45
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.009034335,0.017544761,0.009910087,0.196321162,0.000000000],[0.022043953,0.009831675,0.196981684,0.011044900,0.000000000],[0.009929415,0.194460696,0.002044250,0.023047545,0.000000000],[0.224032836,0.010374563,0.053294552,0.010103588,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7WIE|1|V|U|17 - 7WIE|1|V|A|45 cWW 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.023021455,0.018776188,0.017792908,0.018571381,0.000000000],[0.015676229,0.015711894,0.003775280,0.017882434,0.000000000],[0.003775280,0.003775280,0.340741106,0.003775280,0.000000000],[0.486262445,0.003775280,0.022912277,0.003775280,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7WIE|1|V|U|18 - 7WIE|1|V|A|45 tHS 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.308644650,0.183882729,0.194324745,0.187834025,0.000000000],[0.014692188,0.011983187,0.001999102,0.012161323,0.000000000],[0.019866299,0.001999102,0.025462132,0.009509275,0.000000000],[0.007136885,0.007528516,0.005957773,0.007018068,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7WIE|1|V|A|21 - 7WIE|1|V|A|45 cWS 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.112170041,0.106237908,0.005429695,0.015149071,0.000000000],[0.109559296,0.102527757,0.001165664,0.009760361,0.000000000],[0.009949550,0.001165664,0.098199110,0.095425674,0.000000000],[0.136174205,0.100030487,0.001165664,0.095889854,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7WIE|1|V|U|17 - 7WIE|1|V|A|20 cSH 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.002789345,0.002789345,0.012020284,0.012076678,0.000000000],[0.002789345,0.013413702,0.002789345,0.264197884,0.000000000],[0.010276482,0.002789345,0.009640600,0.002789345,0.000000000],[0.387668875,0.002789345,0.258095325,0.013084758,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7WIE|1|V|U|18 - 7WIE|1|V|A|21 cWH 
Insertion    | Location [2] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 2, position 2 in cluster node
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Initial node 7WIE|1|V|C|22 - 7WIE|1|V|U|44 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [5] | Right Index [8] // Fixed node on left for 7WIE|1|V|A|21
InitialNode  | Left Length Distribution [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.083333333,0.416666667,0.083333333,0.416666667,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Position [2] | Left Index [6] | Right Index [8] // Fixed node on right for 7WIE|1|V|C|24
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [7] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[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 [6] | Right Index [7] // Basepair G25 - C43 cWW 
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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_30730.1:> IL_30730.1 7WIE U 17 A 45 UUCAACUCG*CUA > IL_30730.1 8XZL U 13 A 42 UUCAACUCG*CUA