Alignment of IL_88367.1 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
6

3
7
6
I

8
6

4
9
7
I

10
8

5
11
8
I

12
9

6
13
10
I

14
13

7
15
14
I

16
15


17
14
I

18
13

8
19
13
I

20
13

9
21
12
I

22
11

10
23
8
I

24
8

11
25
7
I

26
6

12
27
5
I

28
4

13
29
3
I

30
3

14
31
2
I

32
2

15
33
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_88367.1_Instance_1 IL_88367.1_IL_4A1B_045_A1018_U1083AGGUAAAUUUAAAUU
IL_88367.1_Sequence_1 IL_88367.1_IL_4A1B_045_A_1018_U_1083AGGUAAA*UUUAAAUUtrue100000.00

Conserved interactions between motif group positions in IL_88367.1:
1 2 s35 
1 15 cWW 
2 14 bif 
3 4 cSH 
3 11 s33 
4 5 s35 
4 12 tWH 
5 6 s35 
5 11 tHS 
5 12 s55 
6 7 s35 
7 8 cWW 
7 9 tSH 
9 10 s35 
10 11 s35 
12 13 s35 
13 14 s35 
14 15 s35 
11 3 6BR
5 11 6BR
JAR3D SCFG/MRF model for IL_88367.1:
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 [15] // Initial node A1018 - U1083 from junction 
BasepairNode | Deletion Probability [0.0000224390099112] | 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 [0.989901010,0.009999000,0.000099990] | 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 [15] // Basepair A1018 - U1083 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 [2] | Right Index [14] // Basepair G1019 - U1082 bif 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [2] | Left Index [3] | Right Index [13] // 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 [3] | Right Index [12] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [3] | Right Index [12] | Norm Constant [0.339207964837216] // Cluster node G1020:U1021 and A1080:A1080
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 U1021 - A1080 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.109399626,0.112701236,0.006146356,0.005085348,0.000000000],[0.105822836,0.122922437,0.001307276,0.123881708,0.000000000],[0.010688473,0.005845023,0.011947953,0.140628542,0.000000000],[0.009413474,0.109623711,0.001307276,0.123278727,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1020 - U1021 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 [5] | Right Index [11] // 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 [5] | Right Index [11] // Basepair A1022 - A1079 tHS 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [6] | Right Index [10] // Fixed node on left
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [2] | Left Index [7] | Right Index [10] // 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 [7] | Right Index [9] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [7] | Right Index [9] | Norm Constant [0.253218861320121] // Cluster node A1024:A1024 and U1076:U1077
Interaction  | Interacting Bases [1,2] | 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]] // Cluster Interaction A1024 - U1076 cWW 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.032237520,0.018923185,0.004073171,0.417218066,0.000000000],[0.025930022,0.017417610,0.004073171,0.004073171,0.000000000],[0.019395920,0.004073171,0.379996231,0.023911335,0.000000000],[0.020722872,0.019808215,0.004073171,0.004073171,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1024 - U1077 tSH 
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 [8] | Right Index [7] // New Initial node after Cluster
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_88367.1:
> IL_88367.1 IL_4A1B_045 A 1018 U 1083
AGGUAAA*UUUAAAUU