Alignment of J4_07491.1 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
11

3
7
12
I

8
13

4
9
14
I

10
15

5
11
15
I

12
16


13
15
I

14
15

6
15
10
I

16
20

7
17
20
I

18
21


19
20
I

20
20

8
21
19
I

22
23

9
23
23
I

24
24


25
23
I

26
23

10
27
8
I

28
7

11
29
6
I

30
5

12
31
2
I

32
2

13
33
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
J4_07491.1_Instance_1 J4_07491.1,J4_4XNR_001,A21_U75AUAAUAGCCGAUU
J4_07491.1_Sequence_1 J4_07491.14XNR_A21_U75AUAAU*AG*CC*GAUUtrue93001.10
J4_07491.1_Instance_2 J4_07491.1,J4_1Y26_001,A21_U75AUAAUAGCCGAUU
J4_07491.1_Sequence_2 J4_07491.11Y26_A21_U75AUAAU*AG*CC*GAUUtrue93001.10
J4_07491.1_Instance_3 J4_07491.1,J4_1Y27_001,A21_U75AUAAUAGCCGACU
J4_07491.1_Sequence_3 J4_07491.11Y27_A21_U75AUAAU*AG*CC*GACUtrue100000.00
J4_07491.1_Instance_4 J4_07491.1,J4_4LX6_001,A21_U75AUAAUAGCCGACU
J4_07491.1_Sequence_4 J4_07491.14LX6_A21_U75AUAAU*AG*CC*GACUtrue100000.00
J4_07491.1_Instance_5 J4_07491.1,J4_3IVN_001,A12_U66AUAACGGCCGACU
J4_07491.1_Sequence_5 J4_07491.13IVN_A12_U66AUAAC*GG*CC*GACUtrue97000.58
J4_07491.1_Instance_6 J4_07491.1,J4_3LA5_001,A21_U75AUAAUAGCCGACU
J4_07491.1_Sequence_6 J4_07491.13LA5_A21_U75AUAAU*AG*CC*GACUtrue100000.00
J4_07491.1_Instance_7 J4_07491.1,J4_3RKF_003,A21_U75AUAACGGCCGACU
J4_07491.1_Sequence_7 J4_07491.13RKF_A21_U75AUAAC*GG*CC*GACUtrue97000.58
J4_07491.1_Instance_8 J4_07491.1,J4_3SKI_001,A30_U81ACAGGUGCCGACU
J4_07491.1_Sequence_8 J4_07491.13SKI_A30_U81ACAGG*UG*CC*GACUtrue79003.43
J4_07491.1_Instance_9 J4_07491.1,J4_3SKL_002,A29_U80ACAGGUGCCGACU
J4_07491.1_Sequence_9 J4_07491.13SKL_A29_U80ACAGG*UG*CC*GACUtrue79003.43

Conserved interactions between motif group positions in J4_07491.1:
1 13 cWW 
2 3 s53 
2 7 s53 
3 5 s55 
3 7 tWS 
4 9 s35 
4 10 s33 
4 11 s55 
5 6 cWW 
5 7 s55 
6 7 s35 
7 8 cWW 
9 10 cWW 
11 12 s35 
12 13 s35 
9 5 7BPh
5 8 7BR
JAR3D SCFG/MRF model for J4_07491.1:
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 [13] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008686775,0.020597022,0.009277664,0.273575663,0.000000000],[0.016393150,0.008965013,0.181696600,0.009693593,0.000000000],[0.009259604,0.184052114,0.001910069,0.049796380,0.000000000],[0.183434948,0.010319930,0.021534740,0.010806737,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [13] // Basepair A21 - U75 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.045454545,0.227272727,0.045454545,0.681818182,0.000000000] | Position [1] | Left Index [2] | Right Index [12] // Fixed node on left for 4XNR|1|X|U|22
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | 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 [3] | Right Index [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.045454545,0.681818182,0.045454545,0.227272727,0.000000000] | Position [2] | Left Index [3] | Right Index [12] // Fixed node on right for 4XNR|1|X|U|74
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [11] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.863636364,0.045454545,0.045454545,0.045454545,0.000000000] | Position [2] | Left Index [3] | Right Index [11] // Fixed node on right for 4XNR|1|X|A|73
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [3] | Right Index [10] // Junction node A23 - G72 ID J2784
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.400000000,0.200000000,0.200000000,0.200000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Initial node 4XNR|1|X|A|23 - 4XNR|1|X|A|45 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.863636364,0.045454545,0.045454545,0.045454545,0.000000000] | Position [1] | Left Index [3] | Right Index [6] // Fixed node on left for 4XNR|1|X|A|23
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | 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 [4] | Right Index [6] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.681818182,0.045454545,0.227272727,0.045454545,0.000000000] | Position [1] | Left Index [4] | Right Index [6] // Fixed node on left for 4XNR|1|X|A|24
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | 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 [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.006470063,0.067760836,0.006512845,0.085744047,0.000000000],[0.018600420,0.010025322,0.180859850,0.012744104,0.000000000],[0.006466371,0.076783527,0.001386385,0.093830482,0.000000000],[0.322977700,0.017263189,0.070620158,0.021954700,0.000000000],[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 U25 - A45 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 [7] | Right Index [10] // Initial node 4XNR|1|X|G|46 - 4XNR|1|X|G|72 from node 
JunctionNode | Branches [2]  | Left Index [7] | Right Index [10] // Junction node G46 - G72 ID J5468
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [8] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009108592,0.018969937,0.010372256,0.188391897,0.000000000],[0.015999490,0.008931890,0.189988229,0.012430900,0.000000000],[0.010257066,0.278079433,0.001955106,0.025046309,0.000000000],[0.185980842,0.012902074,0.021954217,0.009631760,0.000000000],[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 G46 - C53 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 [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [9] | Right Index [10] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.004708455,0.008443390,0.005412948,0.098147429,0.000000000],[0.044777872,0.021449339,0.544064779,0.030454893,0.000000000],[0.005473737,0.100262243,0.001031766,0.011585871,0.000000000],[0.099419812,0.006560143,0.013217656,0.004989666,0.000000000],[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 C54 - G72 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 J4_07491.1:
> J4_07491.1  4XNR A   21 U   75
AUAAU*AG*CC*GAUU
> J4_07491.1  1Y26 A   21 U   75
AUAAU*AG*CC*GAUU
> J4_07491.1  1Y27 A   21 U   75
AUAAU*AG*CC*GACU
> J4_07491.1  4LX6 A   21 U   75
AUAAU*AG*CC*GACU
> J4_07491.1  3IVN A   12 U   66
AUAAC*GG*CC*GACU
> J4_07491.1  3LA5 A   21 U   75
AUAAU*AG*CC*GACU
> J4_07491.1  3RKF A   21 U   75
AUAAC*GG*CC*GACU
> J4_07491.1  3SKI A   30 U   81
ACAGG*UG*CC*GACU
> J4_07491.1  3SKL A   29 U   80
ACAGG*UG*CC*GACU