Alignment of IL_81522.2 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	3 2 I	4 2 2	5 2 I	6 2 3	8 4 4	10 5	12 4 5	13 3 I	14 2 6	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_81522.2_Instance_1 IL_81522.2,IL_4M6D_014,G28_C39	G	U	U		A	C		G	UU	C
IL_81522.2_Sequence_1 IL_81522.24M6D_G28_C39	G	U	U		A	C	*	G	UU	C	true	100	0	0	0.00
IL_81522.2_Instance_2 IL_81522.2,IL_4M4O_005,G28_C39	G	U	U		A	C		G	UU	C
IL_81522.2_Sequence_2 IL_81522.24M4O_G28_C39	G	U	U		A	C	*	G	UU	C	true	100	0	0	0.00
IL_81522.2_Instance_3 IL_81522.2,IL_6XJQ_003,U42_G17	U		A	G	G	C		G		G
IL_81522.2_Sequence_3 IL_81522.26XJQ_U42_G17	U		A	G	G	C	*	G		G	true	67	0	0	3.16

Conserved interactions between motif group positions in IL_81522.2:

1 6 cWW 
3 4 s35 
3 6 cWS 
4 5 cWW 
5 6 s35

JAR3D SCFG/MRF model for IL_81522.2:

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 [6] // Initial node
ClusterNode  | Deletion Probability [0.0000000000027123] | Num Left Bases [3] | Num Right Bases [1] | Left Index [1] | Right Index [6] | Norm Constant [0.253560107387286] // Cluster node 4M6D|1|H|G|28:4M6D|1|H|A|31 and 4M6D|1|H|C|39:4M6D|1|H|C|39
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.010138447,0.017999390,0.012030637,0.145215023,0.000000000],[0.111154629,0.015527922,0.148017973,0.014062841,0.000000000],[0.012052549,0.169605488,0.002470680,0.022513399,0.000000000],[0.159661783,0.013947978,0.134332446,0.011268815,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4M6D|1|H|G|28 - 4M6D|1|H|C|39 cWW 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.188072600,0.223882790,0.187847045,0.184244160,0.000000000],[0.018265146,0.016212777,0.002044653,0.015803811,0.000000000],[0.017073896,0.002044653,0.106570518,0.009047330,0.000000000],[0.007406068,0.007907302,0.006299099,0.007278151,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4M6D|1|H|A|31 - 4M6D|1|H|C|39 cWS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4M6D|1|H|U|30
Insertion    | Location [1] | Length Distribution [0.334863624,0.653524170,0.011072104,0.000540103] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion after nucleotide 1, position 1 in cluster node
Insertion    | Location [2] | Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000]// Insertion after nucleotide 2, position 2 in cluster node
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.324061572,0.016203079,0.648393195,0.010802052,0.000540103] | Right Letter Distribution [0.083333333,0.083333333,0.083333333,0.750000000,0.000000000] | Left Index [4] | Right Index [5] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009443990,0.016935343,0.010857030,0.196859360,0.000000000],[0.020079540,0.009618431,0.236072779,0.013656751,0.000000000],[0.010978957,0.201101150,0.002069466,0.023238378,0.000000000],[0.199411444,0.013158017,0.026511334,0.010008030,0.000000000],[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 C32 - G36 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_81522.2:> IL_81522.2 4M6D G 28 C 39 GUUAC*GUUC > IL_81522.2 4M4O G 28 C 39 GUUAC*GUUC > IL_81522.2 6XJQ U 42 G 17 UAGGC*GG