Alignment of IL_67767.4 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 3 3	8 3 4	10 5 5	12 6	14 5 6	16 3 7	18 3 8	20 2 9	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_67767.4_Instance_1 IL_67767.4,IL_5VCI_006,C8_G5	C	U	A	A	G		U	A	U	G
IL_67767.4_Sequence_1 IL_67767.45VCI_C8_G5	C	U	A	A	G	*	U	A	U	G	true	100	0	0	0.00
IL_67767.4_Instance_2 IL_67767.4,IL_4PCJ_005,C8_G28	C	U	A	A	G		U	A	U	G
IL_67767.4_Sequence_2 IL_67767.44PCJ_C8_G28	C	U	A	A	G	*	U	A	U	G	true	100	0	0	0.00
IL_67767.4_Instance_3 IL_67767.4,IL_1U6B_013,C147_G163	C	U	A	A	G		U	A	U	G
IL_67767.4_Sequence_3 IL_67767.41U6B_C147_G163	C	U	A	A	G	*	U	A	U	G	true	100	0	0	0.00
IL_67767.4_Instance_4 IL_67767.4,IL_5DCV_010,C45_G6	C	U	A	A	G		U	A	U	G
IL_67767.4_Sequence_4 IL_67767.45DCV_C45_G6	C	U	A	A	G	*	U	A	U	G	true	100	0	0	0.00
IL_67767.4_Instance_5 IL_67767.4,IL_3IGI_012,C346_G335	C	U	A	A	G		U	A	U	G
IL_67767.4_Sequence_5 IL_67767.43IGI_C346_G335	C	U	A	A	G	*	U	A	U	G	true	100	0	0	0.00
IL_67767.4_Instance_6 IL_67767.4,IL_5XTM_008,C41_G6	C	U	A	A	G		U	A	U	G
IL_67767.4_Sequence_6 IL_67767.45XTM_C41_G6	C	U	A	A	G	*	U	A	U	G	true	100	0	0	0.00
IL_67767.4_Instance_7 IL_67767.4,IL_1U6B_003,C61_G83	C	U	A	A	G		U	A	U	G
IL_67767.4_Sequence_7 IL_67767.41U6B_C61_G83	C	U	A	A	G	*	U	A	U	G	true	100	0	0	0.00

Conserved interactions between motif group positions in IL_67767.4:

1 2 s35 
1 9 cWW 
2 3 s35 
2 7 tWH 
2 9 s55 
3 4 cSH 
3 6 s33 
3 7 s55 
4 5 s35 
4 7 s55 
4 8 cWW 
5 6 cWW 
7 9 s35 
3 7 6BPh

JAR3D SCFG/MRF model for IL_67767.4:

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 [0.0000244705618206] | Pair Probability [[0.009090944,0.016302246,0.010451159,0.189500131,0.000000000],[0.019328903,0.009258863,0.264630806,0.013146218,0.000000000],[0.010568529,0.193583350,0.001992102,0.022369654,0.000000000],[0.191956811,0.012666128,0.025520256,0.009633898,0.000000000],[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 [9] // Basepair C8 - G5 cWW 
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [3] | Num Right Bases [2] | Left Index [2] | Right Index [8] | Norm Constant [0.259819701056345] // Cluster node 5VCI|1|A|U|9:5VCI|1|A|A|11 and 5VCI|1|B|A|3:5VCI|1|B|U|4
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.017898242,0.003960910,0.018590254,0.003960910,0.000000000],[0.039832166,0.319173624,0.003960910,0.003960910,0.000000000],[0.003960910,0.009494562,0.030122383,0.017616762,0.000000000],[0.461511524,0.003960910,0.022980723,0.039014302,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5VCI|1|A|U|9 - 5VCI|1|B|A|3 tWH 
Interaction  | Interacting Bases [3,5] | Pair Probability [[0.008849144,0.020982013,0.009451078,0.259997638,0.000000000],[0.016699564,0.009132583,0.185092798,0.009874781,0.000000000],[0.009432681,0.187492341,0.001945771,0.050727154,0.000000000],[0.186863639,0.010512826,0.021937258,0.011008732,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5VCI|1|A|A|11 - 5VCI|1|B|U|4 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.352852925,0.261010701,0.013075308,0.032881623,0.000000000],[0.050465493,0.047159357,0.000549112,0.003878037,0.000000000],[0.003890669,0.000549112,0.045624754,0.044265555,0.000000000],[0.052840181,0.046137608,0.000549112,0.044270456,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5VCI|1|A|A|10 - 5VCI|1|A|A|11 cSH 
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 [6] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.015099647,0.283013738,0.013648585,0.080630330,0.000000000],[0.013081510,0.012191763,0.034729394,0.013731825,0.000000000],[0.013356188,0.039620776,0.003092784,0.374698981,0.000000000],[0.034869064,0.014999364,0.013725146,0.039510904,0.000000000],[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 G12 - U2 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_67767.4:> IL_67767.4 5VCI C 8 G 5 CUAAG*UAUG > IL_67767.4 4PCJ C 8 G 28 CUAAG*UAUG > IL_67767.4 1U6B C 147 G 163 CUAAG*UAUG > IL_67767.4 5DCV C 45 G 6 CUAAG*UAUG > IL_67767.4 3IGI C 346 G 335 CUAAG*UAUG > IL_67767.4 5XTM C 41 G 6 CUAAG*UAUG > IL_67767.4 1U6B C 61 G 83 CUAAG*UAUG