Alignment of IL_38862.4 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 3 2	6 3 3	8 5 4	10 6 5	12 7	14 6 6	16 5 7	18 3 8	20 3 9	22 2 10	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_38862.4_Instance_1 IL_38862.4,IL_9DFE_026,U858_G919	U	G	U	A	G		C	G	A	A	G
IL_38862.4_Sequence_1 IL_38862.49DFE_U858_G919	U	G	U	A	G	*	C	G	A	A	G	true	100	0	0	0.00
IL_38862.4_Instance_2 IL_38862.4,IL_7A0S_111,U871_G931	U	G	U	A	G		C	G	A	A	G
IL_38862.4_Sequence_2 IL_38862.47A0S_U871_G931	U	G	U	A	G	*	C	G	A	A	G	true	100	0	0	0.00
IL_38862.4_Instance_3 IL_38862.4,IL_4V9F_033,G952_C1015	G	G	U	A	G		C	A	A	A	C
IL_38862.4_Sequence_3 IL_38862.44V9F_G952_C_1015	G	G	U	A	G	*	C	A	A	A	C	true	93	0	0	0.80
IL_38862.4_Instance_4 IL_38862.4,IL_5J7L_300,U1474_G1517	U	G	U	A	G		U	G	A	G	G
IL_38862.4_Sequence_4 IL_38862.45J7L_U_1474_G_1517	U	G	U	A	G	*	U	G	A	G	G	true	91	0	0	0.97
IL_38862.4_Instance_5 IL_38862.4,IL_2QWY_007,C16_G50	C	G	U	A	U		A	A	A	A	G
IL_38862.4_Sequence_5 IL_38862.42QWY_C16_G50	C	G	U	A	U	*	A	A	A	A	G	true	92	0	0	0.91

Conserved interactions between motif group positions in IL_38862.4:

1 2 s35 
1 10 cWW 
2 3 cSH 
2 7 s33 
2 9 tSH 
3 4 s35 
3 7 s33 
3 8 tWH 
3 9 s55 
4 5 s35 
4 7 tHS 
4 8 s55 
5 6 cWW 
6 7 s35 
8 9 s35 
9 10 s35 
2 8 6BPh
4 7 6BR

JAR3D SCFG/MRF model for IL_38862.4:

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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.010298836,0.015411731,0.012605324,0.099461441,0.000000000],[0.183597737,0.020032766,0.114256328,0.014605825,0.000000000],[0.012787512,0.111208410,0.002738939,0.018310925,0.000000000],[0.127973890,0.013816041,0.231031993,0.011862304,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair U858 - G919 cWW 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [2] | Num Right Bases [2] | Left Index [2] | Right Index [9] | Norm Constant [0.111475469623490] // Cluster node 9DFE|1|1A|G|859:9DFE|1|1A|U|860 and 9DFE|1|1A|A|917:9DFE|1|1A|A|918
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.018239161,0.004036356,0.018944354,0.004036356,0.000000000],[0.040590873,0.325253122,0.004036356,0.004036356,0.000000000],[0.004036356,0.009675411,0.030696143,0.017952320,0.000000000],[0.451254601,0.004036356,0.023418451,0.039757431,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|U|860 - 9DFE|1|1A|A|917 tWH 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.062361437,0.057705919,0.002268717,0.155865386,0.000000000],[0.059749066,0.057747365,0.002268717,0.002268717,0.000000000],[0.227779157,0.002268717,0.182026226,0.060678325,0.000000000],[0.063644679,0.058830138,0.002268717,0.002268717,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|G|859 - 9DFE|1|1A|A|918 tSH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.028328682,0.028865628,0.001587122,0.028209980,0.000000000],[0.021149212,0.031872234,0.000351416,0.028269118,0.000000000],[0.173255801,0.002459910,0.211342544,0.353133826,0.000000000],[0.028768228,0.028595529,0.000351416,0.033459355,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|G|859 - 9DFE|1|1A|U|860 cSH 
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.153505275,0.132858197,0.164722656,0.135255665,0.000000000],[0.077590391,0.096711001,0.001476291,0.130802101,0.000000000],[0.001476291,0.001476291,0.009828022,0.001476291,0.000000000],[0.007909813,0.001476291,0.081959135,0.001476291,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // Basepair A861 - G916 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010506046,0.072905153,0.011167534,0.171916865,0.000000000],[0.016914358,0.009958243,0.163684434,0.012687218,0.000000000],[0.011039949,0.196202645,0.002245259,0.092635778,0.000000000],[0.172186808,0.013108791,0.026826027,0.016014892,0.000000000],[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 G862 - C915 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_38862.4:> IL_38862.4 9DFE U 858 G 919 UGUAG*CGAAG > IL_38862.4 7A0S U 871 G 931 UGUAG*CGAAG > IL_38862.4 4V9F G 952 C 1015 GGUAG*CAAAC > IL_38862.4 5J7L U 1474 G 1517 UGUAG*UGAGG > IL_38862.4 2QWY C 16 G 50 CGUAU*AAAAG