Alignment of IL_42032.1 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 2 2	6 4 3	8 4 4	10 4 5	12 4 6	14 4 7	16 6	18 4 8	20 2 9	22 2 10	24 2 11	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_42032.1_Instance_1 IL_42032.1,IL_4LFB_050,G1175_C1161	G	A	G	G	A	A	G		C	U	G	C
IL_42032.1_Sequence_1 IL_42032.14LFB_G_1175_C_1161	G	A	G	G	A	A	G	*	C	U	G	C	true	100	0	0	0.00
IL_42032.1_Instance_2 IL_42032.1,IL_5J7L_053,G1175_C1161	G	A	G	G	A	A	G		C	U	G	C
IL_42032.1_Sequence_2 IL_42032.15J7L_G_1175_C_1161	G	A	G	G	A	A	G	*	C	U	G	C	true	100	0	0	0.00

Conserved interactions between motif group positions in IL_42032.1:

1 2 s35 
1 11 cWW 
2 3 s35 
2 10 cWW 
3 4 s35 
3 7 tWH 
5 6 s35 
7 8 cWW 
8 10 s55 
9 11 cSH 
10 11 s35 
4 7 6BPh
6 4 7BR

JAR3D SCFG/MRF model for IL_42032.1:

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
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [2] | Num Right Bases [3] | Left Index [1] | Right Index [11] | Norm Constant [0.252538986476388] // Cluster node 4LFB|1|A|G|1175:4LFB|1|A|A|1176 and 4LFB|1|A|U|1159:4LFB|1|A|C|1161
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.029784876,0.014589866,0.379329069,0.017472527,0.000000000],[0.014247286,0.009703380,0.018872041,0.042407159,0.000000000],[0.345605520,0.019083979,0.003597212,0.015874647,0.000000000],[0.017438516,0.044806635,0.015534560,0.011652725,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|A|1176 - 4LFB|1|A|G|1160 cWW 
Interaction  | Interacting Bases [1,5] | 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]] // Cluster Interaction 4LFB|1|A|G|1175 - 4LFB|1|A|C|1161 cWW 
Interaction  | Interacting Bases [3,5] | 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 4LFB|1|A|U|1159 - 4LFB|1|A|C|1161 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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [8] // Initial node 4LFB|1|A|G|1177 - 4LFB|1|A|C|1158 from node 
ClusterNode  | Deletion Probability [0.000000000000015625000000000002841172490091166211760239940914] | Num Left Bases [5] | Num Right Bases [1] | Left Index [3] | Right Index [8] | Norm Constant [0.258737969315878] // Cluster node 4LFB|1|A|G|1177:4LFB|1|A|G|1181 and 4LFB|1|A|C|1158:4LFB|1|A|C|1158
Interaction  | Interacting Bases [5,6] | 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]] // Cluster Interaction 4LFB|1|A|G|1181 - 4LFB|1|A|C|1158 cWW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.171179440,0.004657003,0.089394853,0.004657003,0.000000000],[0.041878349,0.028575103,0.004657003,0.004657003,0.000000000],[0.004657003,0.007217804,0.485308187,0.046899153,0.000000000],[0.035416118,0.004657003,0.036240855,0.029948118,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|G|1177 - 4LFB|1|A|G|1181 tWH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.031250000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.031250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.906250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.031250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4LFB|1|A|G|1178
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4LFB|1|A|A|1179
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.875000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.041666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.041666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4LFB|1|A|A|1180
InitialNode  | Left Length Distribution [0.952380952,0.047619048] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.952380952,0.047619048] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [7] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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_42032.1:> IL_42032.1 4LFB G 1175 C 1161 GAGGAAG*CUGC > IL_42032.1 5J7L G 1175 C 1161 GAGGAAG*CUGC