Alignment of IL_69543.3 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	8 5 4	10 5 5	11 5 I	12 5 6	14 7	16 5 7	18 5 8	19 5 I	20 5 9	22 4 10	24 3 11	26 2 12	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_69543.3_Instance_1 IL_69543.3,IL_8P9A_301,C1711_G1733	C	G	G	A	A	U	U		G	G	A	G	A	U	G
IL_69543.3_Sequence_1 IL_69543.38P9A_C_1711_G_1733	C	G	G	A	A	U	U	*	G	G	A	G	A	U	G	true	100	0	0	0.00
IL_69543.3_Instance_2 IL_69543.3,IL_8CRE_078,U1707_G1729	U	G	G	A	A	U	U		G	G	A	G	A	U	G
IL_69543.3_Sequence_2 IL_69543.38CRE_U_1707_G_1729	U	G	G	A	A	U	U	*	G	G	A	G	A	U	G	true	99	0	0	0.23
IL_69543.3_Instance_3 IL_69543.3,IL_9L6X_002,C6_G31	C	A	G	A	G	A	A		U	G	U	G	A	G	G
IL_69543.3_Sequence_3 IL_69543.39L6X_C6_G31	C	A	G	A	G	A	A	*	U	G	U	G	A	G	G	true	80	0	0	3.93

Conserved interactions between motif group positions in IL_69543.3:

1 2 s35 
1 12 cWW 
2 3 s35 
2 11 tSH 
2 12 s55 
3 4 s35 
3 9 s33 
3 10 tSH 
4 7 tSS 
4 8 s33 
4 9 tHS 
4 10 s55 
5 6 s35 
6 7 cWW 
10 11 s35 
11 12 s35 
8 8 2BPh
3 10 6BPh
9 3 6BR
4 7 6BR
3 9 6BR
4 9 6BR

JAR3D SCFG/MRF model for IL_69543.3:

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 [12] // Initial node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.010008314,0.015906297,0.011951013,0.143543808,0.000000000],[0.113253323,0.015638746,0.171362823,0.014397321,0.000000000],[0.012135476,0.146322383,0.002470993,0.020335440,0.000000000],[0.161392960,0.013617556,0.136517933,0.011145613,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair C1711 - G1733 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.050260457,0.063450175,0.058243639,0.013975854,0.000000000],[0.029153549,0.028666679,0.002302816,0.002302816,0.000000000],[0.195454347,0.002302816,0.016500022,0.249699113,0.000000000],[0.191176562,0.091905521,0.002302816,0.002302816,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [11] // Basepair G1712 - U1732 tSH 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.043273743,0.045811089,0.000519472,0.002448275,0.000000000],[0.043595236,0.045705009,0.000519472,0.000519472,0.000000000],[0.392756919,0.003636307,0.017776750,0.308635994,0.000000000],[0.048305054,0.045458262,0.000519472,0.000519472,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // Basepair G1713 - A1731 tSH 
ClusterNode  | Deletion Probability [0.000000000000000000384010711367214351577654699383264706497383] | Num Left Bases [3] | Num Right Bases [3] | Left Index [4] | Right Index [9] | Norm Constant [0.201969868463057] // Cluster node 8P9A|1|AR|A|1714:8P9A|1|AR|U|1717 and 8P9A|1|AR|G|1727:8P9A|1|AR|G|1730
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.229900085,0.231041542,0.253649052,0.238080083,0.000000000],[0.000481407,0.000481407,0.004368547,0.000481407,0.000000000],[0.003300261,0.000481407,0.003429267,0.032379908,0.000000000],[0.000481407,0.000481407,0.000481407,0.000481407,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|A|1714 - 8P9A|1|AR|G|1727 tSS 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.010488908,0.016497752,0.012698690,0.101695031,0.000000000],[0.205516623,0.021615334,0.092055563,0.014005064,0.000000000],[0.012898676,0.089434432,0.002856478,0.027252089,0.000000000],[0.121610822,0.013331452,0.245283817,0.012759270,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|U|1717 - 8P9A|1|AR|G|1727 cWW 
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.121788976,0.122693781,0.461195057,0.135949022,0.000000000],[0.025786009,0.025726299,0.000864138,0.025587411,0.000000000],[0.000292399,0.000292399,0.004224495,0.000292399,0.000000000],[0.001378078,0.000292399,0.073344740,0.000292399,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|A|1714 - 8P9A|1|AR|G|1730 tHS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8P9A|1|AR|A|1715
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.021739130,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.021739130,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.934782609,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.021739130,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 8P9A|1|AR|G|1728
Insertion    | Location [2] | Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.300000000,0.100000000,0.100000000,0.500000000,0.000000000]// Insertion after nucleotide 5, position 2 in cluster node
Insertion    | Location [5] | Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.500000000,0.100000000,0.100000000,0.300000000,0.000000000]// Insertion after nucleotide 8, position 5 in cluster node
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [6] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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_69543.3:> IL_69543.3 8P9A C 1711 G 1733 CGGAAUU*GGAGAUG > IL_69543.3 8CRE U 1707 G 1729 UGGAAUU*GGAGAUG > IL_69543.3 9L6X C 6 G 31 CAGAGAA*UGUGAGG