Alignment of IL_51265.3 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 3 3	7 3 I	8 3 4	10 5 5	12 6 6	14 7	16 6 7	18 5 8	20 3 9	22 2 10	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_51265.3_Instance_1 IL_51265.3,IL_3SIV_001,C33_G50	C	A	A	U	G	A	G		U	G	A	G
IL_51265.3_Sequence_1 IL_51265.33SIV_C33_G50	C	A	A	U	G	A	G	*	U	G	A	G	true	100	0	0	0.00
IL_51265.3_Instance_2 IL_51265.3,IL_3SIU_002,C33_G50	C	A	A	U	G	A	G		U	G	A	G
IL_51265.3_Sequence_2 IL_51265.33SIU_C33_G50	C	A	A	U	G	A	G	*	U	G	A	G	true	100	0	0	0.00
IL_51265.3_Instance_3 IL_51265.3,IL_3SIV_003,C33_G50	C	A	A	U	G	A	G		U	G	A	G
IL_51265.3_Sequence_3 IL_51265.33SIV_C33_G50	C	A	A	U	G	A	G	*	U	G	A	G	true	100	0	0	0.00
IL_51265.3_Instance_4 IL_51265.3,IL_4LCK_006,C6_G97	C	G	A	U	G	A	G		C	G	A	G
IL_51265.3_Sequence_4 IL_51265.34LCK_C6_G97	C	G	A	U	G	A	G	*	C	G	A	G	true	93	0	0	1.10
IL_51265.3_Instance_5 IL_51265.3,IL_2OZB_002,C28_G45	C	A	A	U	G	A	G		C	G	A	G
IL_51265.3_Sequence_5 IL_51265.32OZB_C28_G45	C	A	A	U	G	A	G	*	C	G	A	G	true	98	0	0	0.28
IL_51265.3_Instance_6 IL_51265.3,IL_1E7K_001,C28_G45	C	A	A	U	G	A	G		C	G	A	G
IL_51265.3_Sequence_6 IL_51265.31E7K_C28_G45	C	A	A	U	G	A	G	*	C	G	A	G	true	98	0	0	0.28

Conserved interactions between motif group positions in IL_51265.3:

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

JAR3D SCFG/MRF model for IL_51265.3:

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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.004553963,0.008166350,0.026176706,0.094927059,0.000000000],[0.009682505,0.004638079,0.555559699,0.006585388,0.000000000],[0.005294135,0.096972482,0.004989559,0.011205720,0.000000000],[0.096157693,0.006344894,0.063919821,0.004825947,0.000000000],[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 [10] // Basepair C33 - G50 cWW 
ClusterNode  | Deletion Probability [0.0000000000031115] | Num Left Bases [3] | Num Right Bases [1] | Left Index [2] | Right Index [9] | Norm Constant [0.365714344673504] // Cluster node 3SIV|1|C|A|34:3SIV|1|C|G|37 and 3SIV|1|F|A|49:3SIV|1|F|A|49
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.386660257,0.089930574,0.092289748,0.086312922,0.000000000],[0.004202078,0.001199031,0.033347911,0.001199031,0.000000000],[0.169868484,0.001199031,0.034534058,0.091457706,0.000000000],[0.004202078,0.001199031,0.001199031,0.001199031,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3SIV|1|C|A|34 - 3SIV|1|F|A|49 tSS 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.071386868,0.075572621,0.000856952,0.004038816,0.000000000],[0.071917221,0.075397625,0.000856952,0.000856952,0.000000000],[0.311431012,0.002548272,0.012457694,0.216287725,0.000000000],[0.079686809,0.074990577,0.000856952,0.000856952,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3SIV|1|C|G|37 - 3SIV|1|F|A|49 tSH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.953125000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.015625000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.015625000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.015625000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3SIV|1|C|A|35
Insertion    | Location [2] | Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Letter Distribution [0.062500000,0.062500000,0.062500000,0.812500000,0.000000000]// Insertion after nucleotide 3, position 2 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 [5] | Right Index [8] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.052834690,0.053227214,0.373726391,0.058977624,0.000000000],[0.055932640,0.055803123,0.003171226,0.055501860,0.000000000],[0.000634245,0.000634245,0.015503117,0.000634245,0.000000000],[0.002989200,0.000634245,0.269161687,0.000634245,0.000000000],[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 [5] | Right Index [8] // Basepair A38 - G48 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.012304240,0.152595251,0.012221578,0.137557369,0.000000000],[0.014828613,0.010745729,0.115211142,0.013322044,0.000000000],[0.012014775,0.148821138,0.002566200,0.197277540,0.000000000],[0.113221234,0.014204047,0.018215096,0.024894003,0.000000000],[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 [6] | Right Index [7] // Basepair G39 - U47 cWW 
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_51265.3:> IL_51265.3 3SIV C 33 G 50 CAAUGAG*UGAG > IL_51265.3 3SIU C 33 G 50 CAAUGAG*UGAG > IL_51265.3 3SIV C 33 G 50 CAAUGAG*UGAG > IL_51265.3 4LCK C 6 G 97 CGAUGAG*CGAG > IL_51265.3 2OZB C 28 G 45 CAAUGAG*CGAG > IL_51265.3 1E7K C 28 G 45 CAAUGAG*CGAG