Alignment of IL_95583.2 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	3 2 I	4 2 2	6 4 3	8 5	10 4 4	12 2 5	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_95583.2_Instance_1 IL_95583.2,IL_5J7L_314,C1837_G1903	C	C	G	G		C	G
IL_95583.2_Sequence_1 IL_95583.25J7L_C_1837_G_1903	C	C	G	G	*	C	G	true	100	0	0	0.00
IL_95583.2_Instance_2 IL_95583.2,IL_9DFE_071,C1837_G1903	C	C	G	G		C	G
IL_95583.2_Sequence_2 IL_95583.29DFE_C_1837_G_1903	C	C	G	G	*	C	G	true	100	0	0	0.00
IL_95583.2_Instance_3 IL_95583.2,IL_1U9S_005,C136_G162	C	A	G	C		G	G
IL_95583.2_Sequence_3 IL_95583.21U9S_C136_G162	C	A	G	C	*	G	G	true	94	0	0	0.60
IL_95583.2_Instance_4 IL_95583.2,IL_4V9F_066,C1893_G1944	C	C	A	G		C	G
IL_95583.2_Sequence_4 IL_95583.24V9F_C_1893_G_1944	C	C	A	G	*	C	G	true	92	0	0	0.76
IL_95583.2_Instance_5 IL_95583.2,IL_8P9A_312,C2196_G2246	C	C	A	G		C	G
IL_95583.2_Sequence_5 IL_95583.28P9A_C_2196_G_2246	C	C	A	G	*	C	G	true	92	0	0	0.76
IL_95583.2_Instance_6 IL_95583.2,IL_8CRE_089,C2174_G2224	C	C	A	G		C	G
IL_95583.2_Sequence_6 IL_95583.28CRE_C_2174_G_2224	C	C	A	G	*	C	G	true	92	0	0	0.76
IL_95583.2_Instance_7 IL_95583.2,IL_7A0S_066,C1829_G1886	C	C	G	G		C	G
IL_95583.2_Sequence_7 IL_95583.27A0S_C_1829_G_1886	C	C	G	G	*	C	G	true	100	0	0	0.00
IL_95583.2_Instance_8 IL_95583.2,IL_9DFE_073,G1846_C1894	G	A	A	G		C	C
IL_95583.2_Sequence_8 IL_95583.29DFE_G_1846_C_1894	G	A	A	G	*	C	C	true	79	0	0	2.03
IL_95583.2_Instance_9 IL_95583.2,IL_4LFB_045,U1199_G1058	U	CA	G	C		G	G
IL_95583.2_Sequence_9 IL_95583.24LFB_U_1199_G_1058	U	CA	G	C	*	G	G	true	67	0	0	3.16
IL_95583.2_Instance_10 IL_95583.2,IL_5J7L_048,U1199_G1058	U	CA	U	C		G	G
IL_95583.2_Sequence_10 IL_95583.25J7L_U_1199_G_1058	U	CA	U	C	*	G	G	true	55	0	0	4.27
IL_95583.2_Instance_11 IL_95583.2,IL_3RW6_003,U38_G21	U	A	A	U		A	G
IL_95583.2_Sequence_11 IL_95583.23RW6_U38_G21	U	A	A	U	*	A	G	true	79	0	0	1.98

Conserved interactions between motif group positions in IL_95583.2:

1 5 cWW 
2 3 s35 
2 5 tHS 
3 4 cWW 
4 5 s35

JAR3D SCFG/MRF model for IL_95583.2:

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 [5] // Initial node
ClusterNode  | Deletion Probability [0.0000000002379439] | Num Left Bases [2] | Num Right Bases [1] | Left Index [1] | Right Index [5] | Norm Constant [0.286073727286833] // Cluster node 5J7L|1|DA|C|1837:5J7L|1|DA|G|1839 and 5J7L|1|DA|G|1903:5J7L|1|DA|G|1903
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.009208251,0.015198363,0.010915184,0.142404866,0.000000000],[0.089105624,0.013481894,0.212839926,0.013192408,0.000000000],[0.011055233,0.154516728,0.002225121,0.019635179,0.000000000],[0.155956237,0.012600390,0.127498609,0.010165989,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|1837 - 5J7L|1|DA|G|1903 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.056538351,0.069848158,0.116893445,0.070360750,0.000000000],[0.051109760,0.047530238,0.002656114,0.055636266,0.000000000],[0.002656114,0.002656114,0.249443178,0.002656114,0.000000000],[0.184506145,0.002656114,0.082197022,0.002656114,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|1839 - 5J7L|1|DA|G|1903 tHS 
Insertion    | Location [1] | Length Distribution [0.003684674,0.811447053,0.183824282,0.001003050,0.000040941] | Letter Distribution [0.366666667,0.566666667,0.033333333,0.033333333,0.000000000]// Insertion after nucleotide 1, 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 [3] | Right Index [4] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008836651,0.017605773,0.010057070,0.183945388,0.000000000],[0.016921107,0.008836984,0.214577919,0.012146841,0.000000000],[0.010017559,0.252374982,0.001916236,0.023457692,0.000000000],[0.192770572,0.012259062,0.024880520,0.009395643,0.000000000],[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 [3] | Right Index [4] // Basepair G1840 - C1902 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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_95583.2:> IL_95583.2 5J7L C 1837 G 1903 CCGG*CG > IL_95583.2 9DFE C 1837 G 1903 CCGG*CG > IL_95583.2 1U9S C 136 G 162 CAGC*GG > IL_95583.2 4V9F C 1893 G 1944 CCAG*CG > IL_95583.2 8P9A C 2196 G 2246 CCAG*CG > IL_95583.2 8CRE C 2174 G 2224 CCAG*CG > IL_95583.2 7A0S C 1829 G 1886 CCGG*CG > IL_95583.2 9DFE G 1846 C 1894 GAAG*CC > IL_95583.2 4LFB U 1199 G 1058 UCAGC*GG > IL_95583.2 5J7L U 1199 G 1058 UCAUC*GG > IL_95583.2 3RW6 U 38 G 21 UAAU*AG