Alignment of IL_83150.2 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 2 2	6 2 3	8 2 4	10 2 5	12 4	14 2 6	15 2 I	16 2 7	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_83150.2_Instance_1 IL_83150.2,IL_4WF9_050,G1356_C1370	G	G	A	A	G		C	G	C
IL_83150.2_Sequence_1 IL_83150.24WF9_G_1356_C_1370	G	G	A	A	G	*	C	G	C	true	100	0	0	0.00
IL_83150.2_Instance_2 IL_83150.2,IL_7A0S_047,G1332_C1346	G	G	A	A	G		C	G	C
IL_83150.2_Sequence_2 IL_83150.27A0S_G_1332_C_1346	G	G	A	A	G	*	C	G	C	true	100	0	0	0.00
IL_83150.2_Instance_3 IL_83150.2,IL_8P9A_345,U3047_A3094	U	A	A	U	U		A	CC	A
IL_83150.2_Sequence_3 IL_83150.28P9A_U_3047_A_3094	U	A	A	U	U	*	A	CC	A	true	97	0	0	0.31
IL_83150.2_Instance_4 IL_83150.2,IL_8CRE_126,U3019_A3066	U	A	A	U	U		A	CC	A
IL_83150.2_Sequence_4 IL_83150.28CRE_U_3019_A_3066	U	A	A	U	U	*	A	CC	A	true	97	0	0	0.31

Conserved interactions between motif group positions in IL_83150.2:

1 2 s33 
1 7 cWW 
2 6 tHH 
3 4 s35 
4 5 s35 
4 7 cWS 
5 6 cWW 
5 7 s55 
6 7 s35 
4 7 6BR

JAR3D SCFG/MRF model for IL_83150.2:

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 [7] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000027443570427925820176520957936016555856547] | Num Left Bases [5] | Num Right Bases [2] | Left Index [1] | Right Index [7] | Norm Constant [0.063637507107939] // Cluster node 4WF9|1|X|G|1356:4WF9|1|X|G|1360 and 4WF9|1|X|C|1368:4WF9|1|X|C|1370
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.191467916,0.148237255,0.008456450,0.008784229,0.000000000],[0.156026810,0.001823930,0.161255026,0.017110886,0.000000000],[0.008653821,0.213908124,0.004461081,0.001823930,0.000000000],[0.010983560,0.063359124,0.001823930,0.001823930,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|G|1357 - 4WF9|1|X|C|1368 tHH 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.009203552,0.018544658,0.010295215,0.194997478,0.000000000],[0.019194364,0.009501956,0.196157927,0.011930519,0.000000000],[0.010244330,0.217046390,0.002027020,0.024427390,0.000000000],[0.216938755,0.011848709,0.037639682,0.010002057,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|G|1360 - 4WF9|1|X|C|1368 cWW 
Interaction  | Interacting Bases [1,7] | Pair Probability [[0.009203552,0.018544658,0.010295215,0.194997478,0.000000000],[0.019194364,0.009501956,0.196157927,0.011930519,0.000000000],[0.010244330,0.217046390,0.002027020,0.024427390,0.000000000],[0.216938755,0.011848709,0.037639682,0.010002057,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|G|1356 - 4WF9|1|X|C|1370 cWW 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.128816013,0.159083246,0.128591472,0.126381572,0.000000000],[0.017038636,0.015415878,0.002401666,0.015499352,0.000000000],[0.014867564,0.002110425,0.037081679,0.008721315,0.000000000],[0.129082442,0.071931339,0.065521870,0.077455532,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|A|1359 - 4WF9|1|X|C|1370 cWS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.750000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4WF9|1|X|A|1358
Insertion    | Location [6] | Length Distribution [0.006093845,0.493601463,0.493601463,0.006398537,0.000304692] | Letter Distribution [0.062500000,0.562500000,0.312500000,0.062500000,0.000000000]// Insertion after nucleotide 6, position 6 in cluster node
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [5] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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_83150.2:> IL_83150.2 4WF9 G 1356 C 1370 GGAAG*CGC > IL_83150.2 7A0S G 1332 C 1346 GGAAG*CGC > IL_83150.2 8P9A U 3047 A 3094 UAAUU*ACCA > IL_83150.2 8CRE U 3019 A 3066 UAAUU*ACCA