Alignment of IL_96236.1 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:	1 1 I	2 2 1	3 2 I	4 3 2	5 3 I	6 3 3	7 3 I	8 3 4	9 3 I	10 3 5	11 4 I	12 5	13 4 I	14 3 6	15 3 I	16 3 7	17 3 I	18 3 8	19 2 I	20 2 9	21 1 I	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_96236.1_Instance_1 IL_96236.1,IL_5J7L_399,A844_U934		A		A		U		U		C				G	U	U		A		U
IL_96236.1_Sequence_1 IL_96236.15J7L_A844_U934		A		A		U		U		C		*		G	U	U		A		U		true	100	0	0	0.00

Conserved interactions between motif group positions in IL_96236.1:

1 9 cWW 
2 4 s55 
2 7 tWW 
3 5 cSH 
4 5 s35 
4 8 cWW 
4 9 perp 
5 6 cWW 
5 8 s55 
6 8 s35 
7 8 s53 
7 9 perp 
9 8 7BPh
8 9 2BR

JAR3D SCFG/MRF model for IL_96236.1:

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 [9] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.003460721,0.008205641,0.003696126,0.542567125,0.000000000],[0.006530862,0.003571569,0.072386052,0.027032792,0.000000000],[0.003688931,0.073324465,0.000760952,0.138868552,0.000000000],[0.073078592,0.004111354,0.008579218,0.030137047,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair A844 - U934 cWW 
ClusterNode  | Deletion Probability [0.000000000000000000381350679448848525461538405014458471171802] | Num Left Bases [4] | Num Right Bases [3] | Left Index [2] | Right Index [8] | Norm Constant [0.251730496825129] // Cluster node 5J7L|1|DA|A|845||A:5J7L|1|DA|C|848 and 5J7L|1|DA|G|930:5J7L|1|DA|A|933
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|848 - 5J7L|1|DA|G|930 cWW 
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.017376847,0.042940161,0.003635060,0.373406976,0.000000000],[0.017064104,0.039159201,0.015138258,0.041984236,0.000000000],[0.003635060,0.018018508,0.017398138,0.291185254,0.000000000],[0.041525169,0.034858775,0.017919960,0.024754293,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|845||A - 5J7L|1|DA|U|932 tWW 
Interaction  | Interacting Bases [3,7] | Pair Probability [[0.022793898,0.008853192,0.005000689,0.099064837,0.000000000],[0.055617554,0.004961122,0.099398140,0.005573323,0.000000000],[0.025052211,0.098126034,0.001031541,0.011629929,0.000000000],[0.525671381,0.005235067,0.026892751,0.005098331,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|847||A - 5J7L|1|DA|A|933 cWW 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.091584266,0.098148224,0.008532723,0.093469509,0.000000000],[0.093695846,0.095862018,0.001090000,0.012308576,0.000000000],[0.013771314,0.001090000,0.099428981,0.088695882,0.000000000],[0.093537464,0.118900979,0.001090000,0.088794218,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|846||A - 5J7L|1|DA|C|848 cSH 
Insertion    | Location [5] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 6, position 5 in cluster node
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 [6] | Right Index [5] // New Initial node after Cluster
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_96236.1:> IL_96236.1 5J7L A 844 U 934 AAUUC*GUUAU