Alignment of IL_71685.1 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
4
I

8
7

4
9
7
I

10
7

5
11
8
I

12
9

6
13
9
I

14
10

7
15
10
I

16
11


17
10
I

18
10

8
19
9
I

20
9

9
21
8
I

22
7

10
23
6
I

24
5

11
25
4
I

26
4

12
27
3
I

28
3

13
29
2
I

30
2

14
31
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_71685.1_Instance_1 IL_71685.1_IL_3U5H_040_G991_U1058GAGGUAAUAAAUAU
IL_71685.1_Sequence_1 IL_71685.1_IL_3U5H_040_G991_U_1058GAGGUAA*UAAAUAUtrue100000.00

Conserved interactions between motif group positions in IL_71685.1:
1 2 s35 
1 14 cWW 
2 3 s35 
2 13 cWW 
3 12 bif 
3 13 s55 
4 5 cSH 
4 9 s33 
5 6 s35 
5 10 tWH 
6 7 s35 
6 9 tHS 
6 10 s55 
7 8 cWW 
8 9 s35 
10 11 s35 
11 12 s35 
12 13 s35 
13 14 s35 
4 10 6BPh
9 4 6BR
6 9 6BR
JAR3D SCFG/MRF model for IL_71685.1:
Character Definition | A,C,G,U,* // Define characters here
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [14] // Initial node G991 - U1058 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.016663800,0.313360908,0.015725272,0.045114411,0.000000000],[0.014618495,0.011663950,0.038590886,0.015584762,0.000000000],[0.015377247,0.044737484,0.003487844,0.358685405,0.000000000],[0.038297587,0.017266078,0.015312095,0.035513776,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [14] // Basepair G991 - U1058 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.435985890,0.018459802,0.277608203,0.018349570,0.000000000],[0.014010176,0.004260849,0.019879497,0.020993817,0.000000000],[0.054529226,0.020209176,0.004260849,0.020356969,0.000000000],[0.018034423,0.043277452,0.015721797,0.014062304,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [13] // Basepair A992 - A1057 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.022972337,0.326477442,0.003861837,0.003861837,0.000000000],[0.018596955,0.015739896,0.003861837,0.003861837,0.000000000],[0.003861837,0.003861837,0.181510317,0.396084684,0.000000000],[0.003861837,0.003861837,0.003861837,0.003861837,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [12] // Basepair G993 - U1056 bif 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [2] | Left Index [4] | Right Index [11] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [10] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [10] | Norm Constant [0.460751978306534] // Cluster node G994:U995 and A1054:A1054
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.026228946,0.005500826,0.026982756,0.005500826,0.000000000],[0.054639536,0.045670107,0.036513624,0.005500826,0.000000000],[0.005500826,0.005500826,0.064376936,0.025659745,0.000000000],[0.559983562,0.005500826,0.067861159,0.059078674,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U995 - A1054 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.055679592,0.057359966,0.003128224,0.002588218,0.000000000],[0.053859163,0.062562107,0.000665346,0.063050334,0.000000000],[0.038079735,0.020824015,0.042566873,0.475642955,0.000000000],[0.004791044,0.055793641,0.000665346,0.062743443,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G994 - U995 cSH 
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.370723561,0.069972932,0.059893903,0.066518667,0.000000000],[0.289240714,0.028663256,0.000721645,0.064026559,0.000000000],[0.003608226,0.000721645,0.006268752,0.000721645,0.000000000],[0.028557666,0.000721645,0.008917540,0.000721645,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair A996 - A1053 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009342473,0.024677534,0.009906945,0.226837217,0.000000000],[0.020281602,0.009395363,0.194134563,0.010378776,0.000000000],[0.009890064,0.195262113,0.002169362,0.028060170,0.000000000],[0.208798271,0.010452176,0.023820256,0.016593115,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [8] // Basepair A997 - U1052 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
Sequences of instances from IL_71685.1:
> IL_71685.1 IL_3U5H_040 G  991 U 1058
GAGGUAA*UAAAUAU