Alignment of IL_78800.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_78800.1
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 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_78800.1_Instance_1 IL_78800.1,IL_8CRE_481,U1363_A1333	U	U	C	U		A	AU	A
IL_78800.1_Sequence_1 IL_78800.18CRE_U_1363_A_1333	U	U	C	U	*	A	AU	A	true	100	0	0	0.00
IL_78800.1_Instance_2 IL_78800.1,IL_8P9A_445,U1377_A1348	U	U	C	U		A	AU	A
IL_78800.1_Sequence_2 IL_78800.18P9A_U_1377_A_1348	U	U	C	U	*	A	AU	A	true	100	0	0	0.00

Conserved interactions between motif group positions in IL_78800.1:

1 2 cSH 
1 3 cSH 
1 5 s33 
1 6 cWW 
2 3 s35 
3 4 perp 
4 5 cWW 
5 6 s35 
4 3 7BPh

JAR3D SCFG/MRF model for IL_78800.1:

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 [6] // Initial node
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [1] | Right Index [6] | Norm Constant [0.066624459375454] // Cluster node 8CRE|1|CM|U|1363:8CRE|1|CM|C|1365 and 8CRE|1|CM|A|1333:8CRE|1|CM|A|1333
Interaction  | Interacting Bases [1,4] | 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 8CRE|1|CM|U|1363 - 8CRE|1|CM|A|1333 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.069668957,0.069985942,0.003916025,0.070855926,0.000000000],[0.069330701,0.079833341,0.000864144,0.071667035,0.000000000],[0.070563039,0.000864144,0.072678473,0.082277753,0.000000000],[0.071086215,0.070395388,0.000864144,0.195148774,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|U|1363 - 8CRE|1|CM|U|1364 cSH 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.090686381,0.097185987,0.008449069,0.092553141,0.000000000],[0.092777259,0.094922194,0.001079314,0.012187904,0.000000000],[0.013636301,0.001079314,0.098454187,0.087826315,0.000000000],[0.092620430,0.127539205,0.001079314,0.087923686,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|U|1363 - 8CRE|1|CM|C|1365 cSH 
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 [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.416666667,0.083333333,0.083333333,0.416666667,0.000000000] | Left Index [4] | Right Index [5] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003342868,0.006491880,0.003666912,0.072642400,0.000000000],[0.008156663,0.003637899,0.072886805,0.004086814,0.000000000],[0.003674064,0.071953993,0.000756410,0.008528011,0.000000000],[0.549094592,0.026871438,0.138039672,0.026169580,0.000000000],[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 U1366 - A1330 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_78800.1:> IL_78800.1 8CRE U 1363 A 1333 UUCU*AAUA > IL_78800.1 8P9A U 1377 A 1348 UUCU*AAUA