Alignment of J3_90256.1 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
2

2
5
2
I

6
2

3
7
2
I

8
2

4
9
2
I

10
2

5
11
3
I

12
10

6
13
10
I

14
13

7
15
13
I

16
14


17
13
I

18
13

8
19
12
I

20
11

9
21
10
I

22
10

10
23
9
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
5
I

34
4

15
35
3
I

36
2

16
37
2
I

38
2

17
39
1
I


In
acceptance
region

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Full
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distance
Interior
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Alignment
score
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J3_90256.1_Instance_1 J3_90256.1,J3_6JQ6_001,G69_C68GUUAAAACCGUGGGCAGAC
J3_90256.1_Sequence_1 J3_90256.16JQ6_G69_C68GUUAAAACC*GUGGG*CAGACtrue100000.00
J3_90256.1_Instance_2 J3_90256.1,J3_6JQ6_002,G69_C68GUUAAAACCGUGGGCAGAC
J3_90256.1_Sequence_2 J3_90256.16JQ6_G69_C68GUUAAAACC*GUGGG*CAGACtrue100000.00

Conserved interactions between motif group positions in J3_90256.1:
1 2 s35 
1 17 cWW 
2 16 cWW 
3 4 s35 
4 5 s35 
4 17 cWS 
5 16 cWS 
6 10 tHS 
6 11 s53 
7 8 cWW 
8 9 s35 
9 10 s35 
12 13 cWW 
12 14 s55 
14 15 s35 
15 16 s35 
16 17 s35 
11 10 2BR
5 16 2BR
JAR3D SCFG/MRF model for J3_90256.1:
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
ClusterNode  | Deletion Probability [0.000000000000000000385733987058166880422626915436200828665941] | Num Left Bases [5] | Num Right Bases [2] | Left Index [1] | Right Index [17] | Norm Constant [0.062827108509975] // Cluster node 6JQ6|1|U|G|69:6JQ6|1|U|A|74||A and 6JQ6|1|U|A|67||||11_555:6JQ6|1|U|C|68||||11_555
Interaction  | Interacting Bases [2,6] | 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]] // Cluster Interaction 6JQ6|1|U|U|70 - 6JQ6|1|U|A|67||||11_555 cWW 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.239509115,0.202271002,0.213757220,0.206617428,0.000000000],[0.016161407,0.013181506,0.002199013,0.013377455,0.000000000],[0.021852929,0.002199013,0.028008345,0.010460203,0.000000000],[0.007850573,0.008281367,0.006553550,0.007719875,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6JQ6|1|U|A|74||A - 6JQ6|1|U|A|67||||11_555 cWS 
Interaction  | Interacting Bases [1,7] | 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 6JQ6|1|U|G|69 - 6JQ6|1|U|C|68||||11_555 cWW 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.199412271,0.236401213,0.199173117,0.195352999,0.000000000],[0.019366427,0.017190312,0.002167934,0.016756688,0.000000000],[0.018103352,0.002167934,0.053682368,0.009592831,0.000000000],[0.007852611,0.008384066,0.006678898,0.007716981,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6JQ6|1|U|A|73 - 6JQ6|1|U|C|68||||11_555 cWS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 6JQ6|1|U|A|72
Insertion    | Location [2] | 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 2, position 2 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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [15] // Initial node 6JQ6|1|U|A|75 - 6JQ6|1|U|G|66||||11_555 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Position [2] | Left Index [6] | Right Index [15] // Fixed node on right for 6JQ6|1|U|A|73
InitialNode  | Left Length Distribution [1.000000000] | 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 [14] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [6] | Right Index [14] // Fixed node on right for 6JQ6|1|U|A|72
InitialNode  | Left Length Distribution [1.000000000] | 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] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [6] | Right Index [13] // Junction node A75 - C64 ID J2435
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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.112745781,0.113583401,0.154951637,0.125854401,0.000000000],[0.119356604,0.119080223,0.001353438,0.118437346,0.000000000],[0.001353438,0.001353438,0.006616528,0.001353438,0.000000000],[0.006378757,0.001353438,0.114874695,0.001353438,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | 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 [10] // Basepair A75 - G29 tHS 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Position [2] | Left Index [7] | Right Index [9] // Fixed node on right for 6JQ6|1|U|A|67||||11_555
InitialNode  | Left Length Distribution [1.000000000] | 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 [8] // New Initial node after Fixed node
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 [7] | Right Index [8] // Basepair C77 - G27 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 [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | 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 6JQ6|1|U|G|30||||11_555 - 6JQ6|1|U|C|64||||11_555 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.041666667,0.041666667,0.875000000,0.041666667,0.000000000] | Position [1] | Left Index [11] | Right Index [13] // Fixed node on left for 6JQ6|1|U|G|69
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 G31 - C64 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_90256.1:
> J3_90256.1  6JQ6 G   69 C   68
GUUAAAACC*GUGGG*CAGAC
> J3_90256.1  6JQ6 G   69 C   68
GUUAAAACC*GUGGG*CAGAC