Alignment of IL_15698.3 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 3 2	6 4 3	7 4 I	8 4 4	10 6	12 4 5	14 3 6	16 2 7	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_15698.3_Instance_1 IL_15698.3,IL_5FJC_003,C44_G58	C	A	A		C		G	U	G
IL_15698.3_Sequence_1 IL_15698.35FJC_C44_G58	C	A	A		C	*	G	U	G	true	100	0	0	0.00
IL_15698.3_Instance_2 IL_15698.3,IL_4OQU_001,C24_G48	C	A	A		C		G	U	G
IL_15698.3_Sequence_2 IL_15698.34OQU_C24_G48	C	A	A		C	*	G	U	G	true	100	0	0	0.00
IL_15698.3_Instance_3 IL_15698.3,IL_4AOB_003,C44_G58	C	A	A		C		G	U	G
IL_15698.3_Sequence_3 IL_15698.34AOB_C44_G58	C	A	A		C	*	G	U	G	true	100	0	0	0.00
IL_15698.3_Instance_4 IL_15698.3,IL_3V7E_003,C44_G90	C	A	A		C		G	U	G
IL_15698.3_Sequence_4 IL_15698.33V7E_C44_G90	C	A	A		C	*	G	U	G	true	100	0	0	0.00
IL_15698.3_Instance_5 IL_15698.3,IL_4KQY_003,C45_G79	C	A	A		C		G	U	G
IL_15698.3_Sequence_5 IL_15698.34KQY_C45_G79	C	A	A		C	*	G	U	G	true	100	0	0	0.00
IL_15698.3_Instance_6 IL_15698.3,IL_8P9A_292,G1618_C1826	G	A	U		A		U	G	C
IL_15698.3_Sequence_6 IL_15698.38P9A_G_1618_C_1826	G	A	U		A	*	U	G	C	true	84	0	0	1.65
IL_15698.3_Instance_7 IL_15698.3,IL_8P9A_389,C270_G285	C	A	U		G		U	G	G
IL_15698.3_Sequence_7 IL_15698.38P9A_C270_G285	C	A	U		G	*	U	G	G	true	70	0	0	3.09
IL_15698.3_Instance_8 IL_15698.3,IL_8CRE_069,G1614_C1822	G	A	U		A		U	G	C
IL_15698.3_Sequence_8 IL_15698.38CRE_G_1614_C_1822	G	A	U		A	*	U	G	C	true	84	0	0	1.65
IL_15698.3_Instance_9 IL_15698.3,IL_5DO4_004,G3_C23	G	A	A	CA	A		U	A	C
IL_15698.3_Sequence_9 IL_15698.35DO4_G3_C23	G	A	A	CA	A	*	U	A	C	true	32	0	0	6.97
IL_15698.3_Instance_10 IL_15698.3,IL_8CRE_406,C268_G283	C	A	U		G		U	G	G
IL_15698.3_Sequence_10 IL_15698.38CRE_C268_G283	C	A	U		G	*	U	G	G	true	70	0	0	3.09

Conserved interactions between motif group positions in IL_15698.3:

1 2 s35 
1 7 cWW 
2 3 s35 
2 6 tSH 
2 7 s55 
3 4 cSH 
4 5 cWW 
4 6 s55 
5 6 s35 
6 7 s35

JAR3D SCFG/MRF model for IL_15698.3:

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
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008897843,0.016739593,0.010199678,0.185036135,0.000000000],[0.017917438,0.008959651,0.255758750,0.012646747,0.000000000],[0.010245353,0.217205367,0.001937640,0.022677285,0.000000000],[0.185992170,0.012459917,0.023903365,0.009423069,0.000000000],[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 [7] // Basepair C44 - G58 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.046967002,0.014536140,0.105980053,0.395526003,0.000000000],[0.017410647,0.014569211,0.003500715,0.003500715,0.000000000],[0.016498878,0.003500715,0.315959935,0.021245930,0.000000000],[0.017220735,0.016581893,0.003500715,0.003500715,0.000000000],[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 [2] | Right Index [6] // Basepair A45 - U57 tSH 
ClusterNode  | Deletion Probability [0.0000000419957704] | Num Left Bases [2] | Num Right Bases [1] | Left Index [3] | Right Index [5] | Norm Constant [0.251944856311106] // Cluster node 5FJC|1|A|A|46:5FJC|1|A|C|47 and 5FJC|1|A|G|56:5FJC|1|A|G|56
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.009941414,0.069110789,0.010496330,0.191906093,0.000000000],[0.016819060,0.009540080,0.203113054,0.011946947,0.000000000],[0.010491161,0.156573618,0.002138385,0.104033421,0.000000000],[0.154674638,0.012146236,0.021483980,0.015584793,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5FJC|1|A|C|47 - 5FJC|1|A|G|56 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.098653659,0.156748817,0.004663545,0.031576760,0.000000000],[0.085523153,0.083479635,0.000966041,0.007634808,0.000000000],[0.008097881,0.000966041,0.086188950,0.079045931,0.000000000],[0.140302093,0.085781856,0.052205711,0.078165119,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5FJC|1|A|A|46 - 5FJC|1|A|C|47 cSH 
Insertion    | Location [1] | Length Distribution [0.894854586,0.004971414,0.099652001,0.000497141,0.000024857] | Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 3, position 1 in cluster node
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 [5] | Right Index [4] // New Initial node after Cluster
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_15698.3:> IL_15698.3 5FJC C 44 G 58 CAAC*GUG > IL_15698.3 4OQU C 24 G 48 CAAC*GUG > IL_15698.3 4AOB C 44 G 58 CAAC*GUG > IL_15698.3 3V7E C 44 G 90 CAAC*GUG > IL_15698.3 4KQY C 45 G 79 CAAC*GUG > IL_15698.3 8P9A G 1618 C 1826 GAUA*UGC > IL_15698.3 8P9A C 270 G 285 CAUG*UGG > IL_15698.3 8CRE G 1614 C 1822 GAUA*UGC > IL_15698.3 5DO4 G 3 C 23 GAACAA*UAC > IL_15698.3 8CRE C 268 G 283 CAUG*UGG