Alignment of J3_32601.2 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for J3_32601.2
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 3 5	12 3 6	14 7 7	16 8	18 7 8	19 6 I	20 10 9	22 11	24 10 10	26 3 11	28 2 12	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
J3_32601.2_Instance_1 J3_32601.2,J3_4Y4O_026,A2561_U2547	A	U	U	A	A	A	G		C	AU	C		G	U	U
J3_32601.2_Sequence_1 J3_32601.24Y4O_A_2561_U_2547	A	U	U	A	A	A	G	*	C	AU	C	*	G	U	U	true	100	0	0	0.00
J3_32601.2_Instance_2 J3_32601.2,J3_5J7L_046,U2561_A2547	U	U	U	A	A	A	G		C	AU	C		G	U	A
J3_32601.2_Sequence_2 J3_32601.25J7L_U_2561_A_2547	U	U	U	A	A	A	G	*	C	AU	C	*	G	U	A	true	94	0	0	1.21
J3_32601.2_Instance_3 J3_32601.2,J3_4WF9_009,A2588_U2574	A	U	U	A	A	A	G		C	AU	C		G	U	U
J3_32601.2_Sequence_3 J3_32601.24WF9_A_2588_U_2574	A	U	U	A	A	A	G	*	C	AU	C	*	G	U	U	true	100	0	0	0.00
J3_32601.2_Instance_4 J3_32601.2,J3_7A0S_011,A2540_U2526	A	U	U	A	A	A	G		C	AU	C		G	U	U
J3_32601.2_Sequence_4 J3_32601.27A0S_A_2540_U_2526	A	U	U	A	A	A	G	*	C	AU	C	*	G	U	U	true	100	0	0	0.00

Conserved interactions between motif group positions in J3_32601.2:

1 2 s35 
1 12 cWW 
2 3 s35 
2 6 tWH 
3 5 tSH 
3 6 s55 
4 5 s35 
5 6 s35 
5 9 cSS 
5 10 tSS 
6 12 s35 
7 8 cWW 
7 9 s55 
7 11 cHW 
9 10 cWW 
10 11 s35 
3 6 6BPh
12 6 7BR

JAR3D SCFG/MRF model for J3_32601.2:

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 [12] // Initial node
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.005407015,0.011870004,0.005838859,0.427900096,0.000000000],[0.011428502,0.005704753,0.115060937,0.020517178,0.000000000],[0.005836962,0.115308319,0.001203069,0.097136915,0.000000000],[0.127140102,0.006335715,0.020980132,0.022331442,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair A2561 - U2547 cWW 
ClusterNode  | Deletion Probability [0.000000000000015625000000000002841172490091166211760239940914] | Num Left Bases [5] | Num Right Bases [1] | Left Index [2] | Right Index [11] | Norm Constant [1.000000000000000] // Cluster node 4Y4O|1|2A|U|2562:4Y4O|1|2A|A|2566 and 4Y4O|1|2A|U|2546:4Y4O|1|2A|U|2546
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.045573318,0.041626842,0.000506110,0.002489657,0.000000000],[0.045749370,0.043045745,0.000506110,0.000506110,0.000000000],[0.047062464,0.000506110,0.003128007,0.042016506,0.000000000],[0.392738279,0.327459838,0.003542767,0.003542767,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4Y4O|1|2A|U|2563 - 4Y4O|1|2A|A|2565 tSH 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.018414538,0.004075167,0.019126511,0.004075167,0.000000000],[0.040981170,0.328380556,0.004075167,0.004075167,0.000000000],[0.004075167,0.009768444,0.030991298,0.018124938,0.000000000],[0.445978203,0.004075167,0.023643628,0.040139714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4Y4O|1|2A|U|2562 - 4Y4O|1|2A|A|2566 tWH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.750000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4Y4O|1|2A|A|2564
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.750000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 4Y4O|1|2A|U|2546
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // Initial node 4Y4O|1|2A|G|2567 - 4Y4O|1|2A|G|2545 from node 
JunctionNode | Branches [2]  | Left Index [7] | Right Index [10] // Junction node G2567 - G2545 ID J9339
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.000000000,0.012187690,0.975015235,0.012187690,0.000609385] | Right Letter Distribution [0.450000000,0.050000000,0.050000000,0.450000000,0.000000000] | Left Index [7] | Right Index [8] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009546506,0.019881954,0.010870922,0.197449200,0.000000000],[0.016768697,0.009361308,0.199122279,0.013028540,0.000000000],[0.010750195,0.243371713,0.002049102,0.026250458,0.000000000],[0.194922229,0.013522366,0.023009709,0.010094826,0.000000000],[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 [7] | Right Index [8] // Basepair G2567 - C2517 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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 [0.450000000,0.050000000,0.050000000,0.450000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [9] | Right Index [10] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009353183,0.016772504,0.010752635,0.194966481,0.000000000],[0.019886467,0.009525946,0.243418233,0.013525436,0.000000000],[0.010873390,0.199167485,0.002049567,0.023014932,0.000000000],[0.197494026,0.013031497,0.026256418,0.009911799,0.000000000],[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 C2520 - G2545 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_32601.2:> J3_32601.2 4Y4O A 2561 U 2547 AUUAAAG*CAUC*GUU > J3_32601.2 5J7L U 2561 A 2547 UUUAAAG*CAUC*GUA > J3_32601.2 4WF9 A 2588 U 2574 AUUAAAG*CAUC*GUU > J3_32601.2 7A0S A 2540 U 2526 AUUAAAG*CAUC*GUU