Alignment of J3_11279.1 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:		1
1
I

2
2

1
3
2
I

4
3

2
5
3
I

6
4

3
7
5
I

8
6

4
9
6
I

10
6

5
11
7
I

12
8

6
13
9
I

14
12

7
15
12
I

16
13

8
17
13
I

18
14


19
13
I

20
13

9
21
12
I

22
12

10
23
11
I

24
16

11
25
17
I

26
18

12
27
18
I

28
19


29
18
I

30
18

13
31
7
I

32
6

14
33
6
I

34
6

15
35
5
I

36
4

16
37
4
I

38
4

17
39
3
I

40
3

18
41
2
I

42
2

19
43
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
J3_11279.1_Instance_1 J3_11279.1,J3_4V88_035,U1609_A1587UGAUUACGCCAGCUAGUAA
J3_11279.1_Sequence_1 J3_11279.14V88_U_1609_A_1587UGAUUACG*CCAG*CUAGUAAtrue100000.00
J3_11279.1_Instance_2 J3_11279.1,J3_4LFB_002,U1372_A1350UGAAUACGCAAGCUAGUAA
J3_11279.1_Sequence_2 J3_11279.14LFB_U_1372_A_1350UGAAUACG*CAAG*CUAGUAAtrue98000.42

Conserved interactions between motif group positions in J3_11279.1:
1 2 s35 
1 19 cWW 
2 16 s33 
2 17 s33 
2 18 tSH 
2 19 s55 
3 4 s35 
3 15 s35 
3 17 tHW 
3 18 s55 
4 5 s35 
4 12 cSS 
4 15 tHH 
5 6 s35 
5 11 cSS 
5 14 tWW 
5 15 tHH 
6 7 s55 
6 14 s53 
7 8 s35 
7 10 tHS 
8 9 cWW 
8 10 s55 
9 10 s35 
10 11 s35 
11 12 s35 
12 13 cWW 
15 17 s55 
16 17 cSH 
17 18 s35 
18 19 s35 
16 3 6BPh
15 4 6BPh
2 17 6BPh
18 2 6BR
2 16 6BR
JAR3D SCFG/MRF model for J3_11279.1:
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 [19] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009034335,0.017544761,0.009910087,0.196321162,0.000000000],[0.022043953,0.009831675,0.196981684,0.011044900,0.000000000],[0.009929415,0.194460696,0.002044250,0.023047545,0.000000000],[0.224032836,0.010374563,0.053294552,0.010103588,0.000000000],[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 [19] // Basepair U1609 - A1587 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.043697995,0.046260217,0.000524565,0.002472278,0.000000000],[0.044022640,0.046153098,0.000524565,0.000524565,0.000000000],[0.386803555,0.003671957,0.017951032,0.311661837,0.000000000],[0.048778633,0.045903932,0.000524565,0.000524565,0.000000000],[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 [18] // Basepair G1610 - A1586 tSH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [3] | Right Index [17] | Norm Constant [0.262628314674858] // Cluster node 4V88|1|A6|A|1611:4V88|1|A6|A|1611 and 4V88|1|A6|G|1584:4V88|1|A6|U|1585
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.018775607,0.041784723,0.004155072,0.435115030,0.000000000],[0.004155072,0.334819390,0.009959982,0.004155072,0.000000000],[0.019501541,0.004155072,0.031598971,0.024107229,0.000000000],[0.004155072,0.004155072,0.018480329,0.040926768,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V88|1|A6|A|1611 - 4V88|1|A6|U|1585 tHW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.031106004,0.031695591,0.001742722,0.030975664,0.000000000],[0.023222664,0.034996963,0.000385868,0.031040601,0.000000000],[0.190241664,0.002701077,0.232062401,0.289715574,0.000000000],[0.031588643,0.031399012,0.000385868,0.036739684,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V88|1|A6|G|1584 - 4V88|1|A6|U|1585 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 [4] | Right Index [15] // New Initial node after Cluster
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [2] | Num Right Bases [2] | Left Index [4] | Right Index [15] | Norm Constant [0.347593404916940] // Cluster node 4V88|1|A6|U|1612:4V88|1|A6|U|1613 and 4V88|1|A6|U|1582:4V88|1|A6|A|1583
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.024978059,0.030331969,0.005356900,0.036479807,0.000000000],[0.047086784,0.030567281,0.018993974,0.027347187,0.000000000],[0.005356900,0.018115093,0.025662695,0.038984076,0.000000000],[0.046635242,0.029148575,0.059657587,0.555297871,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V88|1|A6|U|1613 - 4V88|1|A6|U|1582 tWW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.224222066,0.024347699,0.002906192,0.002830298,0.000000000],[0.198197600,0.000605666,0.025755761,0.004120569,0.000000000],[0.199854173,0.025421475,0.001300419,0.000605666,0.000000000],[0.248148423,0.040472658,0.000605666,0.000605666,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V88|1|A6|U|1612 - 4V88|1|A6|A|1583 tHH 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.027763291,0.002712953,0.002803976,0.002615796,0.000000000],[0.041811329,0.000583943,0.002731151,0.002576815,0.000000000],[0.345318523,0.002686920,0.001073297,0.000583943,0.000000000],[0.517494779,0.048075397,0.000583943,0.000583943,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V88|1|A6|U|1613 - 4V88|1|A6|A|1583 tHH 
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 [6] | Right Index [13] // Initial node 4V88|1|A6|A|1614 - 4V88|1|A6|C|1581 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [6] | Right Index [13] // Fixed node on left for 4V88|1|A6|U|1582
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 [7] | Right Index [13] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [7] | Right Index [13] // Junction node C1615 - C1581 ID J9575
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 [7] | Right Index [10] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.021173329,0.022777398,0.159997631,0.149222499,0.000000000],[0.191232394,0.261905707,0.001814285,0.117484082,0.000000000],[0.001814285,0.001814285,0.007798213,0.001814285,0.000000000],[0.007533518,0.001814285,0.049989519,0.001814285,0.000000000],[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 [7] | Right Index [10] // Basepair C1615 - C1162 tHS 
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 [8] | Right Index [9] // Basepair G1616 - C1161 cWW 
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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 [11] | Right Index [13] // Initial node 4V88|1|A6|A|1163 - 4V88|1|A6|C|1581 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [11] | Right Index [13] // Fixed node on left for 4V88|1|A6|A|1587
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 [12] | Right Index [13] // 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 [12] | Right Index [13] // Basepair G1164 - C1581 cWW 
HairpinNode  | Num Bases [1] | Left Index [13] | Right Index [13] | 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_11279.1:
> J3_11279.1  4V88 U 1609 A 1587
UGAUUACG*CCAG*CUAGUAA
> J3_11279.1  4LFB U 1372 A 1350
UGAAUACG*CAAG*CUAGUAA