Alignment of J3_83516.1 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
4
I

6
5

3
7
6
I

8
7

4
9
8
I

10
9

5
11
10
I

12
11

6
13
12
I

14
13

7
15
14
I

16
15

8
17
16
I

18
21

9
19
21
I

20
22


21
21
I

22
21

10
23
20
I

24
24

11
25
25
I

26
26

12
27
27
I

28
28

13
29
29
I

30
30

14
31
31
I

32
32


33
31
I

34
30

15
35
30
I

36
30

16
37
30
I

38
30

17
39
30
I

40
30

18
41
30
I

42
30

19
43
30
I

44
30

20
45
18
I

46
17

21
47
2
I

48
2

22
49
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
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Alignment
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J3_83516.1_Instance_1 J3_83516.1,J3_4LFB_004,G973_C962GAAGAACCUUACGGCGAUUUAAUUC
J3_83516.1_Sequence_1 J3_83516.14LFB_G973_C962GAAGAACCUUAC*GGCGA*UUUAAUUCtrue100000.00
J3_83516.1_Instance_2 J3_83516.1,J3_5J7L_006,G973_C962GAAGAACCUUACGGCUAUUUAAUUC
J3_83516.1_Sequence_2 J3_83516.15J7L_G973_C962GAAGAACCUUAC*GGCUA*UUUAAUUCtrue100000.00
J3_83516.1_Instance_3 J3_83516.1,J3_4V88_037,G1198_U1187GGGGAAACUCACGGCCGCUUAAUUU
J3_83516.1_Sequence_3 J3_83516.14V88_G_1198_U_1187GGGGAAACUCAC*GGCCG*CUUAAUUUtrue94001.49

Conserved interactions between motif group positions in J3_83516.1:
1 2 s33 
1 22 cWW 
3 7 perp 
3 12 s53 
3 13 s55 
4 5 s35 
5 6 s35 
6 7 s33 
7 8 s53 
8 21 s55 
9 10 cWW 
9 11 s55 
10 11 s35 
10 19 tSS 
11 12 s35 
12 21 perp 
14 15 cWW 
14 16 s55 
14 20 s55 
15 16 s35 
16 17 s35 
16 20 tWW 
17 19 tSH 
17 20 s53 
18 19 s35 
19 20 s33 
21 22 s35 
5 4 7BPh
6 5 7BPh
3 13 7BPh
17 20 6BPh
11 21 2BPh
5 3 7BR
6 3 6BR
21 12 7BR
JAR3D SCFG/MRF model for J3_83516.1:
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 [22] // Initial node
BasepairNode | Deletion Probability [0.0000038011627649] | Pair Probability [[0.011654807,0.111384843,0.012043853,0.160831324,0.000000000],[0.015817510,0.010523206,0.146063039,0.013525053,0.000000000],[0.011861335,0.171070354,0.002450295,0.134475360,0.000000000],[0.143284186,0.014296389,0.020241456,0.020476992,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Left Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [22] // Basepair G973 - C962 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000] | Position [1] | Left Index [2] | Right Index [21] // Fixed node on left for 4LFB|1|A|U|956
InitialNode  | Left Length Distribution [0.005372012,0.333064733,0.650013430,0.011012624,0.000537201] | Left Letter Distribution [0.357142857,0.071428571,0.500000000,0.071428571,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [21] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.934782609,0.021739130,0.021739130,0.021739130,0.000000000] | Position [1] | Left Index [3] | Right Index [21] // Fixed node on left for 4LFB|1|A|U|957
InitialNode  | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [21] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.500000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [4] | Right Index [21] // Fixed node on left for 4LFB|1|A|A|958
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [21] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.021739130,0.934782609,0.021739130,0.021739130,0.000000000] | Position [1] | Left Index [5] | Right Index [21] // Fixed node on left for 4LFB|1|A|A|959
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [6] | Right Index [21] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.004672897,0.004672897,0.004672897,0.985981308,0.000000000] | Position [1] | Left Index [6] | Right Index [21] // Fixed node on left for 4LFB|1|A|U|960
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [21] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.300000000,0.100000000,0.500000000,0.000000000] | Position [1] | Left Index [7] | Right Index [21] // Fixed node on left for 4LFB|1|A|U|961
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [8] | Right Index [21] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [8] | Right Index [21] // Fixed node on left for 4LFB|1|A|C|962
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [21] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.029411765,0.029411765,0.029411765,0.911764706,0.000000000] | Position [2] | Left Index [9] | Right Index [21] // Fixed node on right for 4LFB|1|A|G|1221
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [20] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [9] | Right Index [20] // Junction node C984 - U960 ID J9592
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [10] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009443990,0.016935343,0.010857030,0.196859360,0.000000000],[0.020079540,0.009618431,0.236072779,0.013656751,0.000000000],[0.010978957,0.201101150,0.002069466,0.023238378,0.000000000],[0.199411444,0.013158017,0.026511334,0.010008030,0.000000000],[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 C984 - G1221 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
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 [20] // Initial node 4LFB|1|A|G|1222 - 4LFB|1|A|U|960 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.021739130,0.021739130,0.934782609,0.021739130,0.000000000] | Position [1] | Left Index [11] | Right Index [20] // Fixed node on left for 4LFB|1|A|A|975
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [20] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.700000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [12] | Right Index [20] // Fixed node on left for 4LFB|1|A|G|976
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [20] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.300000000,0.300000000,0.300000000,0.000000000] | Position [1] | Left Index [13] | Right Index [20] // Fixed node on left for 4LFB|1|A|A|977
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [20] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000000078125000000000012233710187403301545271878291] | Num Left Bases [1] | Num Right Bases [6] | Left Index [14] | Right Index [20] | Norm Constant [1.000000000000000] // Cluster node 4LFB|1|A|A|1225:4LFB|1|A|A|1225 and 4LFB|1|A|U|955:4LFB|1|A|U|960
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.009341597,0.021222893,0.010204228,0.220628516,0.000000000],[0.017209227,0.009475562,0.195205747,0.011223855,0.000000000],[0.010150854,0.208524333,0.002037222,0.043966533,0.000000000],[0.195018545,0.011831944,0.022937162,0.011021781,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|A|1225 - 4LFB|1|A|U|955 cWW 
Interaction  | Interacting Bases [4,6] | Pair Probability [[0.046015777,0.042030986,0.000511023,0.002513829,0.000000000],[0.046193539,0.043463665,0.000511023,0.000511023,0.000000000],[0.047519381,0.000511023,0.003158376,0.042424434,0.000000000],[0.386842534,0.330639059,0.003577163,0.003577163,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|U|957 - 4LFB|1|A|A|959 tSH 
Interaction  | Interacting Bases [3,7] | Pair Probability [[0.024735553,0.030037484,0.005304892,0.036125634,0.000000000],[0.046629630,0.030270511,0.018809566,0.027081681,0.000000000],[0.005304892,0.017939218,0.025413542,0.038605590,0.000000000],[0.046182473,0.028865579,0.059078387,0.559615368,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|U|956 - 4LFB|1|A|U|960 tWW 
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 4LFB|1|A|A|958
InitialNode  | Left Length Distribution [0.952380952,0.047619048] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.952380952,0.047619048] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [15] | Right Index [14] // New Initial node after Cluster
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 J3_83516.1:
> J3_83516.1  4LFB G  973 C  962
GAAGAACCUUAC*GGCGA*UUUAAUUC
> J3_83516.1  5J7L G  973 C  962
GAAGAACCUUAC*GGCUA*UUUAAUUC
> J3_83516.1  4V88 G 1198 U 1187
GGGGAAACUCAC*GGCCG*CUUAAUUU