Alignment of IL_26728.3 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 5 2	6 5 3	8 5 4	10 7 5	12 8	14 7 6	16 5 7	18 3 8	20 2 9	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_26728.3_Instance_1 IL_26728.3,IL_7EOG_002,U40_G10	U	G	U	C	G		C	U	G	G
IL_26728.3_Sequence_1 IL_26728.37EOG_U40_G10	U	G	U	C	G	*	C	U	G	G	true	100	0	0	0.00
IL_26728.3_Instance_2 IL_26728.3,IL_7SZU_002,U21_G55	U	G	U	C	G		C	U	G	G
IL_26728.3_Sequence_2 IL_26728.37SZU_U21_G55	U	G	U	C	G	*	C	U	G	G	true	100	0	0	0.00

Conserved interactions between motif group positions in IL_26728.3:

1 9 cWW 
2 3 cSH 
3 4 cSH 
3 7 cWW 
4 5 s35 
5 6 cWW 
6 7 s35 
7 8 s35 
7 6 7BPh
3 2 7BR

JAR3D SCFG/MRF model for IL_26728.3:

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 [9] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.011246147,0.013983971,0.014277598,0.037274594,0.000000000],[0.302538153,0.027950744,0.042354115,0.016034133,0.000000000],[0.014590167,0.037125289,0.003306148,0.014672010,0.000000000],[0.086192816,0.014679149,0.350222612,0.013552354,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair U40 - G10 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Position [2] | Left Index [2] | Right Index [8] // Fixed node on right for 7EOG|1|A|C|43
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [2] | Right Index [7] | Norm Constant [0.237975038274496] // Cluster node 7EOG|1|A|G|41:7EOG|1|A|C|43 and 7EOG|1|A|U|8:7EOG|1|A|U|8
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.000932617,0.017105332,0.000832670,0.010180168,0.000000000],[0.001030763,0.001111418,0.001243087,0.006398552,0.000000000],[0.000815278,0.001266329,0.000257046,0.022986703,0.000000000],[0.006352182,0.004949734,0.005268340,0.919269779,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7EOG|1|A|U|42 - 7EOG|1|A|U|8 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.079296878,0.080799881,0.004442628,0.078964610,0.000000000],[0.059200300,0.089215891,0.000983673,0.079130149,0.000000000],[0.069281848,0.000983673,0.084512044,0.117975163,0.000000000],[0.080527243,0.080043827,0.000983673,0.093658519,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7EOG|1|A|G|41 - 7EOG|1|A|U|42 cSH 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.041572873,0.044552452,0.003873262,0.042428642,0.000000000],[0.042531383,0.043514674,0.000494784,0.005587236,0.000000000],[0.006251217,0.000494784,0.045133827,0.040261748,0.000000000],[0.212297444,0.266999829,0.002473920,0.201531927,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7EOG|1|A|U|42 - 7EOG|1|A|C|43 cSH 
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[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 G44 - C7 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_26728.3:> IL_26728.3 7EOG U 40 G 10 UGUCG*CUGG > IL_26728.3 7SZU U 21 G 55 UGUCG*CUGG