Alignment of IL_12697.1 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
5

4
9
5
I

10
6

5
11
6
I

12
7


13
6
I

14
6

6
15
5
I

16
5

7
17
4
I

18
4

8
19
3
I

20
3

9
21
2
I

22
2

10
23
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_12697.1_Instance_1 IL_12697.1,IL_8CRE_392,U37_A469UCAAAUGACAA
IL_12697.1_Sequence_1 IL_12697.18CRE_U37_A469UCAAA*UGACAAtrue100000.00
IL_12697.1_Instance_2 IL_12697.1,IL_8P9A_375,U37_A471UCAAAUGACAA
IL_12697.1_Sequence_2 IL_12697.18P9A_U37_A471UCAAA*UGACAAtrue100000.00

Conserved interactions between motif group positions in IL_12697.1:
1 2 s35 
1 10 cWW 
2 3 s35 
2 9 cWW 
3 7 s33 
3 8 tSH 
4 5 s35 
4 7 tHS 
4 8 s55 
5 6 cWW 
5 7 s55 
6 7 s35 
8 9 s35 
9 10 s35 
4 7 6BR
JAR3D SCFG/MRF model for IL_12697.1:
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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | 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 [0.991950402,0.007999600,0.000049998] | 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 [10] // Basepair U37 - A469 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.011169172,0.014624785,0.014219668,0.030813201,0.000000000],[0.378631746,0.040992595,0.034835247,0.015878615,0.000000000],[0.014561584,0.029380498,0.003590239,0.015185588,0.000000000],[0.038714962,0.014470422,0.328534713,0.014396965,0.000000000],[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 [9] // Basepair C38 - A468 cWW 
BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.023290662,0.219179163,0.001995713,0.008286870,0.000000000],[0.025055138,0.179272748,0.001995713,0.001995713,0.000000000],[0.175997394,0.001995713,0.008578035,0.054988471,0.000000000],[0.164144749,0.129232491,0.001995713,0.001995713,0.000000000],[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 [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Left Index [3] | Right Index [8] // Basepair A39 - C467 tSH 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.112745781,0.113583401,0.154951637,0.125854401,0.000000000],[0.119356604,0.119080223,0.001353438,0.118437346,0.000000000],[0.001353438,0.001353438,0.006616528,0.001353438,0.000000000],[0.006378757,0.001353438,0.114874695,0.001353438,0.000000000],[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 A40 - G465 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009282926,0.022010543,0.009914366,0.223723012,0.000000000],[0.017518170,0.009580259,0.194165974,0.010358839,0.000000000],[0.009895067,0.196683142,0.002041152,0.053213779,0.000000000],[0.196023621,0.011028161,0.023012614,0.011548375,0.000000000],[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 [5] | Right Index [6] // Basepair A41 - U464 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
Sequences of instances from IL_12697.1:
> IL_12697.1  8CRE U   37 A  469
UCAAA*UGACAA
> IL_12697.1  8P9A U   37 A  471
UCAAA*UGACAA