Alignment of IL_47078.3 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 4 5	12 5	14 4 6	15 3 I	16 2 7	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_47078.3_Instance_1 IL_47078.3,IL_5J7L_041,U1380_A935	U	U	C	C	C		G	C	A
IL_47078.3_Sequence_1 IL_47078.35J7L_U_1380_A935	U	U	C	C	C	*	G	C	A	true	96	0	0	0.34
IL_47078.3_Instance_2 IL_47078.3,IL_4LFB_037,U1380_A935	U	U	C	C	C		G	C	A
IL_47078.3_Sequence_2 IL_47078.34LFB_U_1380_A935	U	U	C	C	C	*	G	C	A	true	96	0	0	0.34
IL_47078.3_Instance_3 IL_47078.3,IL_5J7L_043,G993_C1045	G	A	C	A	U		A		C
IL_47078.3_Sequence_3 IL_47078.35J7L_G993_C_1045	G	A	C	A	U	*	A		C	true	100	0	0	0.00
IL_47078.3_Instance_4 IL_47078.3,IL_4LFB_039,G993_C1045	G	A	C	A	U		A		C
IL_47078.3_Sequence_4 IL_47078.34LFB_G993_C_1045	G	A	C	A	U	*	A		C	true	100	0	0	0.00

Conserved interactions between motif group positions in IL_47078.3:

1 7 cWW 
2 3 s35 
4 5 s35 
4 7 cWS 
5 6 cWW 
6 7 s35 
2 1 7BR

JAR3D SCFG/MRF model for IL_47078.3:

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 [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [1] | Right Index [7] | Norm Constant [0.250792367330097] // Cluster node 5J7L|1|AA|U|1380:5J7L|1|AA|C|1383 and 5J7L|1|AA|A|935:5J7L|1|AA|A|935
Interaction  | Interacting Bases [1,5] | 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 5J7L|1|AA|U|1380 - 5J7L|1|AA|A|935 cWW 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.107170601,0.136946515,0.105968530,0.107198193,0.000000000],[0.156383098,0.128528656,0.002339675,0.129920131,0.000000000],[0.023155686,0.002339675,0.040695929,0.010128882,0.000000000],[0.012119336,0.016512008,0.009212388,0.011380697,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|AA|C|1383 - 5J7L|1|AA|A|935 cWS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.477272727,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.022727273,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.022727273,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.477272727,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|AA|U|1381
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.750000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|AA|C|1382
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 [0.496627836,0.496627836,0.006437768,0.000306560] | Right Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Left Index [5] | Right Index [6] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009106890,0.016989933,0.010236072,0.193756118,0.000000000],[0.020753249,0.009584275,0.218305904,0.012178967,0.000000000],[0.010305927,0.194944276,0.002027252,0.022809627,0.000000000],[0.218224654,0.011603275,0.039263037,0.009910544,0.000000000],[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 [5] | Right Index [6] // Basepair C1384 - G933 cWW 
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_47078.3:> IL_47078.3 5J7L U 1380 A 935 UUCCC*GCA > IL_47078.3 4LFB U 1380 A 935 UUCCC*GCA > IL_47078.3 5J7L G 993 C 1045 GACAU*AC > IL_47078.3 4LFB G 993 C 1045 GACAU*AC