Alignment of IL_33886.1 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 3 2	6 5 3	7 6 I	8 7 4	9 7 I	10 7 5	12 9 6	14 10	16 9 7	18 7 8	20 7 9	22 7 10	24 2 11	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_33886.1_Instance_1 IL_33886.1,IL_4V9F_108,C260_G249	C	A	A	U	G		U	G		C	G	A	A	G
IL_33886.1_Sequence_1 IL_33886.14V9F_C260_G249	C	A	A	U	G		U	G	*	C	G	A	A	G	true	100	0	0	0.00
IL_33886.1_Instance_2 IL_33886.1,IL_1NTA_006,A105_U19	A	C	C		A	C	G	G		C	U	U	C	U
IL_33886.1_Sequence_2 IL_33886.11NTA_A105_U19	A	C	C		A	C	G	G	*	C	U	U	C	U	true	94	0	0	1.03

Conserved interactions between motif group positions in IL_33886.1:

1 2 s35 
1 11 cWW 
3 4 s35 
3 9 s53 
4 5 cSH 
4 8 s33 
4 9 tSH 
5 6 s35 
5 8 tHS 
5 9 s55 
5 10 cWW 
5 11 perp 
6 7 cWW 
6 10 s55 
7 8 s35 
9 10 s53 
9 11 perp 
10 8 7BR

JAR3D SCFG/MRF model for IL_33886.1:

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 [11] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009409752,0.019555960,0.010438919,0.211256183,0.000000000],[0.018897284,0.009646494,0.211374635,0.012074740,0.000000000],[0.010490831,0.199877935,0.002065453,0.038339992,0.000000000],[0.198695040,0.012157589,0.024891932,0.010827262,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [1] | Right Index [11] // Basepair C260 - G249 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [2] | Right Index [10] // Fixed node on left for 4V9F|1|0|G|246
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [3] | Right Index [10] // Fixed node on left for 4V9F|1|0|A|247
InitialNode  | Left Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [10] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000000000001983] | Num Left Bases [2] | Num Right Bases [3] | Left Index [4] | Right Index [10] | Norm Constant [0.015370993125333] // Cluster node 4V9F|1|0|G|264:4V9F|1|0|U|265 and 4V9F|1|0|G|246:4V9F|1|0|A|248
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.048446242,0.028101215,0.188399177,0.184275804,0.000000000],[0.061159861,0.027631920,0.002219693,0.088588075,0.000000000],[0.002219693,0.002219693,0.015904433,0.101150175,0.000000000],[0.013471378,0.002219693,0.231773254,0.002219693,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|U|265 - 4V9F|1|0|G|246 tHS 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.102496164,0.108506004,0.001230398,0.104729351,0.000000000],[0.103257637,0.108254748,0.001230398,0.001230398,0.000000000],[0.132843734,0.001230398,0.006015026,0.104431541,0.000000000],[0.114413092,0.107670315,0.001230398,0.001230398,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|G|264 - 4V9F|1|0|A|247 tSH 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.013682284,0.029344389,0.005205454,0.098625107,0.000000000],[0.031746660,0.014209080,0.099210224,0.006030729,0.000000000],[0.015102610,0.315644458,0.001025231,0.012349286,0.000000000],[0.314104624,0.019568793,0.019092147,0.005058924,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|U|265 - 4V9F|1|0|A|248 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.072088071,0.073454437,0.102969234,0.071786009,0.000000000],[0.053818455,0.081105356,0.000894248,0.071936499,0.000000000],[0.062983498,0.000894248,0.076829131,0.099228758,0.000000000],[0.073206585,0.072767115,0.000894248,0.085144108,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|G|264 - 4V9F|1|0|U|265 cSH 
Insertion    | Location [1] | Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 4, position 1 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 [6] | Right Index [7] // New Initial node after Cluster
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 G266 - C245 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_33886.1:> IL_33886.1 4V9F C 260 G 249 CAAUGUG*CGAAG > IL_33886.1 1NTA A 105 U 19 ACCACGG*CUUCU