Alignment of J3_13944.1 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:	2 2 1	4 3 2	6 3 3	8 3 4	9 3 I	10 3 5	12 7 6	14 8	16 7 7	18 10 8	20 11 9	22 12	24 11 10	26 10 11	27 4 I	28 3 12	30 2 13	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
J3_13944.1_Instance_1 J3_13944.1,J3_7A0S_014,C12_G113	C	C	C	A	U	A	G		C	G	C		G	U	C	A	G
J3_13944.1_Sequence_1 J3_13944.17A0S_C12_G113	C	C	C	A	U	A	G	*	C	G	C	*	G	U	C	A	G	true	94	0	0	1.30
J3_13944.1_Instance_2 J3_13944.1,J3_5J7L_049,G10_C110	G	C	C	G	U	A	G		C	G	C		G	G	A	A	C
J3_13944.1_Sequence_2 J3_13944.15J7L_G10_C110	G	C	C	G	U	A	G	*	C	G	C	*	G	G	A	A	C	true	100	0	0	0.00

Conserved interactions between motif group positions in J3_13944.1:

1 2 s35 
1 13 cWW 
2 3 s35 
2 5 tSS 
2 12 cWW 
4 6 perp 
4 8 tSS 
5 12 s35 
6 7 cWW 
6 8 s55 
7 8 s35 
8 9 s35 
8 11 tHS 
9 10 cWW 
10 11 s35 
12 13 s35

JAR3D SCFG/MRF model for J3_13944.1:

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 [13] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009635135,0.018686586,0.011023774,0.200055053,0.000000000],[0.018686946,0.009628796,0.215804967,0.013537321,0.000000000],[0.011023788,0.215804297,0.002089517,0.025115689,0.000000000],[0.200055346,0.013537264,0.025116064,0.010199456,0.000000000],[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 [13] // Basepair C12 - G113 cWW 
ClusterNode  | Deletion Probability [0.000000000000015429359482326747228196069233951473250875292831] | Num Left Bases [4] | Num Right Bases [1] | Left Index [2] | Right Index [12] | Norm Constant [0.279194021038105] // Cluster node 7A0S|1|Y|C|13:7A0S|1|Y|A|17 and 7A0S|1|Y|A|112:7A0S|1|Y|A|112
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.010153793,0.013295259,0.012926971,0.028012001,0.000000000],[0.435119769,0.037265996,0.031668407,0.014435104,0.000000000],[0.013237803,0.026709543,0.003263854,0.013805080,0.000000000],[0.035195420,0.013154930,0.298667921,0.013088150,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|Y|C|13 - 7A0S|1|Y|A|112 cWW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.055704100,0.055704100,0.055704100,0.055704100,0.000000000],[0.164438503,0.055704100,0.055704100,0.055704100,0.000000000],[0.055704100,0.055704100,0.055704100,0.055704100,0.000000000],[0.055704100,0.055704100,0.055704100,0.055704100,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|Y|C|13 - 7A0S|1|Y|A|17 tSS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.625000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 7A0S|1|Y|C|14
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 7A0S|1|Y|A|15
Insertion    | Location [3] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion after nucleotide 4, position 3 in cluster node
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 [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000] | Left Index [6] | Right Index [11] // Initial node 7A0S|1|Y|G|18 - 7A0S|1|Y|U|110 from node 
JunctionNode | Branches [2]  | Left Index [6] | Right Index [11] // Junction node G18 - U110 ID J1576
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [7] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | 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 [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [7] // Basepair G18 - C70 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
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [8] | Right Index [11] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.031730993,0.025346635,0.017857393,0.022576124,0.000000000],[0.015700587,0.016041052,0.003652803,0.018956052,0.000000000],[0.003652803,0.003652803,0.375084203,0.102583284,0.000000000],[0.329686787,0.003652803,0.026172876,0.003652803,0.000000000],[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 [8] | Right Index [11] // Basepair G71 - U110 tHS 
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [10] // Basepair C72 - G109 cWW 
HairpinNode  | Num Bases [1] | Left Index [10] | Right Index [10] | 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 J3_13944.1:> J3_13944.1 7A0S C 12 G 113 CCCAUAG*CGC*GUCAG > J3_13944.1 5J7L G 10 C 110 GCCGUAG*CGC*GGAAC