Alignment of J4_36568.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for J4_36568.1
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 6 3	8 7	10 6 4	12 11 5	14 12 6	16 13 7	18 13 8	20 13 9	22 15	24 13 10	26 12 11	28 11 12	30 17 13	32 19 14	34 20	36 19 15	38 3 16	40 2 17	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
J4_36568.1_Instance_1 J4_36568.1,J4_6CZR_012,G137_C217	G	A	G		C	A	U	G	U	G		C	A	A	A	G		C	G	C
J4_36568.1_Sequence_1 J4_36568.16CZR_G137_C217	G	A	G	*	C	A	U	G	U	G	*	C	A	A	A	G	*	C	G	C	true	100	0	0	0.00
J4_36568.1_Instance_2 J4_36568.1,J4_4LFB_002,G142_C221	G	A	G		C	A	U	G	U	G		C	A	A	A	G		C	G	C
J4_36568.1_Sequence_2 J4_36568.14LFB_G142_C221	G	A	G	*	C	A	U	G	U	G	*	C	A	A	A	G	*	C	G	C	true	100	0	0	0.00

Conserved interactions between motif group positions in J4_36568.1:

1 2 s35 
1 12 tSS 
1 17 cWW 
2 16 cWW 
3 4 cWW 
3 5 s55 
4 5 s35 
5 6 s35 
5 12 tWH 
6 7 perp 
6 11 tWH 
7 8 cSH 
7 9 s35 
7 10 s33 
7 11 s55 
8 9 s35 
8 11 s55 
9 10 cWW 
11 12 s35 
12 17 cSS 
13 14 perp 
13 16 tSS 
14 15 cWW 
14 16 s55 
15 16 s35 
16 17 s35 
7 11 6BR
2 13 2BR

JAR3D SCFG/MRF model for J4_36568.1:

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 [17] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | 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 [0.991950402,0.007999600,0.000049998] | 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 [17] // Basepair G137 - C217 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.054751622,0.026819613,0.680860227,0.032118623,0.000000000],[0.005237974,0.003567420,0.006938252,0.015590870,0.000000000],[0.127060878,0.007016170,0.001322505,0.005836269,0.000000000],[0.006411220,0.016473031,0.005711236,0.004284091,0.000000000],[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 [2] | Right Index [16] // Basepair A138 - G216 cWW 
JunctionNode | Branches [2]  | Left Index [3] | Right Index [15] // Junction node G139 - C215 ID J7655
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 [3] | Right Index [4] // 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 [3] | Right Index [4] // Basepair G139 - C173 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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 [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [15] // Initial node 6CZR|1|1a|A|174 - 6CZR|1|1a|C|215 from node 
JunctionNode | Branches [2]  | Left Index [5] | Right Index [15] // Junction node A174 - C215 ID J7951
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 [5] | Right Index [12] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.381184813,0.003615770,0.318975856,0.003615770,0.000000000],[0.030948835,0.015344049,0.003615770,0.003615770,0.000000000],[0.003615770,0.008956754,0.132906372,0.038702064,0.000000000],[0.016338652,0.003615770,0.017330382,0.017617604,0.000000000],[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 [5] | Right Index [12] // Basepair A174 - A203 tWH 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.018775607,0.004155072,0.019501541,0.004155072,0.000000000],[0.041784723,0.334819390,0.004155072,0.004155072,0.000000000],[0.004155072,0.009959982,0.031598971,0.018480329,0.000000000],[0.435115030,0.004155072,0.024107229,0.040926768,0.000000000],[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 [6] | Right Index [11] // Basepair U175 - A202 tWH 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [7] | Right Index [10] | Norm Constant [1.000000000000000] // Cluster node 6CZR|1|1a|G|176:6CZR|1|1a|G|178 and 6CZR|1|1a|C|201:6CZR|1|1a|C|201
Interaction  | Interacting Bases [3,4] | 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]] // Cluster Interaction 6CZR|1|1a|G|178 - 6CZR|1|1a|C|201 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.039008099,0.039747463,0.002185439,0.038844648,0.000000000],[0.029122095,0.043887507,0.000483893,0.038926081,0.000000000],[0.170407287,0.002419466,0.207867842,0.261554453,0.000000000],[0.039613346,0.039375542,0.000483893,0.046072946,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6CZR|1|1a|G|176 - 6CZR|1|1a|U|177 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 [10] | Right Index [9] // New Initial node after Cluster
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
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 [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [13] | Right Index [15] // Initial node 6CZR|1|1a|A|204 - 6CZR|1|1a|C|215 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [13] | Right Index [15] // Fixed node on left for 6CZR|1|1a|A|204
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [14] | Right Index [15] // New Initial node after Fixed 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 [14] | Right Index [15] // Basepair G205 - C215 cWW 
HairpinNode  | Num Bases [1] | Left Index [15] | Right Index [15] | 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 J4_36568.1:> J4_36568.1 6CZR G 137 C 217 GAG*CAUGUG*CAAAG*CGC > J4_36568.1 4LFB G 142 C 221 GAG*CAUGUG*CAAAG*CGC