Alignment of J4_34476.1 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
5

2
5
5
I

6
8

3
7
8
I

8
9

4
9
9
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10
10

5
11
10
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12
11


13
10
I

14
10

6
15
9
I

16
9

7
17
8
I

18
8

8
19
7
I

20
15

9
21
15
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22
16

10
23
16
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24
17


25
16
I

26
16

11
27
15
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28
15

12
29
14
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30
19

13
31
19
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32
20

14
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21
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34
24

15
35
24
I

36
25


37
24
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38
24

16
39
23
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40
22

17
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19
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42
19

18
43
5
I

44
5

19
45
4
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46
3

20
47
2
I

48
2

21
49
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
J4_34476.1_Instance_1 J4_34476.1,J4_4V9F_007,G1828_C2020GACUGCAUAGUGAAUAUUAAC
J4_34476.1_Sequence_1 J4_34476.14V9F_G_1828_C_2020GACUG*CAUAG*UGAAU*AUUAACtrue100000.00
J4_34476.1_Instance_2 J4_34476.1,J4_5TBW_006,G2130_C2322GACUGCAUAGUGAUUAUUAAC
J4_34476.1_Sequence_2 J4_34476.15TBW_G_2130_C_2322GACUG*CAUAG*UGAUU*AUUAACtrue100000.00

Conserved interactions between motif group positions in J4_34476.1:
1 21 cWW 
2 3 s35 
2 9 tHS 
2 13 s55 
2 19 tSW 
3 4 s35 
3 8 tHS 
4 5 s35 
4 7 tHS 
5 6 cWW 
5 7 s55 
6 7 s35 
7 8 s35 
8 9 s35 
8 12 s33 
9 10 s35 
9 12 tHS 
10 11 cWW 
11 12 s35 
13 14 s35 
13 18 tHS 
13 19 s55 
14 15 s35 
15 16 cWW 
16 17 s35 
17 18 s35 
19 20 s35 
20 21 s35 
12 8 6BPh
10 13 2BPh
20 2 6BR
20 3 2BR
9 12 6BR
10 12 6BR
JAR3D SCFG/MRF model for J4_34476.1:
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 [21] // 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 [21] // Basepair G1828 - C2020 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.971153846,0.009615385,0.009615385,0.009615385,0.000000000] | Position [2] | Left Index [2] | Right Index [20] // Fixed node on right for 4V9F|1|0|A|2019
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 [2] | Right Index [19] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.262686918,0.016863115,0.002430791,0.012821247,0.000000000],[0.201859823,0.020003976,0.002430791,0.010908028,0.000000000],[0.195570129,0.002430791,0.002430791,0.008757493,0.000000000],[0.215903894,0.014549871,0.016750946,0.013601395,0.000000000],[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 [19] // Basepair A1829 - A2018 tSW 
JunctionNode | Branches [2]  | Left Index [3] | Right Index [18] // Junction node C1830 - U2017 ID J971
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 [8] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.131981958,0.134240277,0.128533182,0.135762660,0.000000000],[0.095112703,0.125867935,0.001468808,0.166488612,0.000000000],[0.001468808,0.001468808,0.007622310,0.001468808,0.000000000],[0.006957326,0.001468808,0.058620191,0.001468808,0.000000000],[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 [3] | Right Index [8] // Basepair C1830 - U1846 tHS 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.025323600,0.020653807,0.019572199,0.020428519,0.000000000],[0.017243852,0.017283083,0.004152808,0.019670677,0.000000000],[0.004152808,0.004152808,0.374815217,0.004152808,0.000000000],[0.434888690,0.004152808,0.025203505,0.004152808,0.000000000],[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 [4] | Right Index [7] // Basepair U1831 - A1845 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 [5] | Right Index [6] // Basepair G1832 - C1844 cWW 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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 [9] | Right Index [18] // Initial node 4V9F|1|0|A|1847 - 4V9F|1|0|U|2017 from node 
JunctionNode | Branches [2]  | Left Index [9] | Right Index [18] // Junction node A1847 - U2017 ID J8234
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 [9] | Right Index [12] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.043697995,0.044022640,0.386803555,0.048778633,0.000000000],[0.046260217,0.046153098,0.003671957,0.045903932,0.000000000],[0.000524565,0.000524565,0.017951032,0.000524565,0.000000000],[0.002472278,0.000524565,0.311661837,0.000524565,0.000000000],[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 [9] | Right Index [12] // Basepair A1847 - G1884 tHS 
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.001108349,0.020773868,0.001001838,0.005918454,0.000000000],[0.000960213,0.000894904,0.002549219,0.001007948,0.000000000],[0.034313136,0.101789007,0.007945615,0.814169340,0.000000000],[0.002559471,0.001100988,0.001007458,0.002900192,0.000000000],[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 [10] | Right Index [11] // Basepair G1848 - U1883 cWW 
HairpinNode  | Num Bases [1] | Left Index [11] | Right Index [11] | 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 [13] | Right Index [18] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.120391741,0.120856821,0.124325641,0.153307608,0.000000000],[0.109966274,0.113714611,0.001336998,0.123579390,0.000000000],[0.001336998,0.001336998,0.008263305,0.001336998,0.000000000],[0.006576967,0.001336998,0.110995656,0.001336998,0.000000000],[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 [13] | Right Index [18] // Basepair A1885 - U2017 tHS 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Position [1] | Left Index [14] | Right Index [17] // Fixed node on left for 4V9F|1|0|A|1886
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 [15] | Right Index [17] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Position [2] | Left Index [15] | Right Index [17] // Fixed node on right for 4V9F|1|0|U|2016
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 [15] | Right Index [16] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000224863733088] | 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 [0.990049834,0.009900498,0.000049502,0.000000165] | 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 [15] | Right Index [16] // Basepair U1887 - A2015 cWW 
HairpinNode  | Num Bases [1] | Left Index [16] | Right Index [16] | 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_34476.1:
> J4_34476.1  4V9F G 1828 C 2020
GACUG*CAUAG*UGAAU*AUUAAC
> J4_34476.1  5TBW G 2130 C 2322
GACUG*CAUAG*UGAUU*AUUAAC