Alignment of IL_47444.3 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

6
13
7
I

14
8


15
7
I

16
7

7
17
6
I

18
6

8
19
5
I

20
5

9
21
4
I

22
4

10
23
3
I

24
3

11
25
2
I

26
2

12
27
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_47444.3_Instance_1 IL_47444.3_IL_1DUH_002_U45_G64UCAGGUAAGCAG
IL_47444.3_Sequence_1 IL_47444.3_IL_1DUH_002_U45_G64UCAGGU*AAGCAGtrue100000.00
IL_47444.3_Instance_2 IL_47444.3_IL_1DUH_004_U45_G64UCAGGUAAGCAG
IL_47444.3_Sequence_2 IL_47444.3_IL_1DUH_004_U45_G64UCAGGU*AAGCAGtrue100000.00
IL_47444.3_Instance_3 IL_47444.3_IL_2PXV_002_U146_G165UCAGGUAAGCAG
IL_47444.3_Sequence_3 IL_47444.3_IL_2PXV_002_U146_G165UCAGGU*AAGCAGtrue100000.00
IL_47444.3_Instance_4 IL_47444.3_IL_1LNT_002_U4_G21UCAGGUAAGCAG
IL_47444.3_Sequence_4 IL_47444.3_IL_1LNT_002_U4_G21UCAGGU*AAGCAGtrue100000.00
IL_47444.3_Instance_5 IL_47444.3_IL_1MFQ_007_C190_G209CCAGGUGAGCAG
IL_47444.3_Sequence_5 IL_47444.3_IL_1MFQ_007_C190_G209CCAGGU*GAGCAGtrue90001.77
IL_47444.3_Instance_6 IL_47444.3_IL_2XXA_015_U40_G59UCAGAGCAGCAG
IL_47444.3_Sequence_6 IL_47444.3_IL_2XXA_015_U40_G59UCAGAG*CAGCAGtrue93001.34
IL_47444.3_Instance_7 IL_47444.3_IL_3U5H_127_C3161_G3289CCACACGCGUGG
IL_47444.3_Sequence_7 IL_47444.3_IL_3U5H_127_C_3161_G_3289CCACAC*GCGUGGtrue440010.01
IL_47444.3_Instance_8 IL_47444.3_IL_4FAW_007_U214_A163UACAGAUAGGUA
IL_47444.3_Sequence_8 IL_47444.3_IL_4FAW_007_U214_A163UACAGA*UAGGUAtrue54008.21
IL_47444.3_Instance_9 IL_47444.3_IL_1D4R_002_G12_C17GGGAGCGGGAGC
IL_47444.3_Sequence_9 IL_47444.3_IL_1D4R_002_G12_C17GGGAGC*GGGAGCtrue51008.91

Conserved interactions between motif group positions in IL_47444.3:
1 2 s35 
1 12 cWW 
2 9 s33 
2 11 tSH 
3 4 s35 
3 10 tHW 
3 11 s55 
4 5 s35 
4 9 tHS 
4 10 s55 
5 6 s35 
5 8 cWW 
5 9 s55 
6 7 cWW 
7 8 s35 
8 9 s35 
9 10 s35 
10 11 s35 
11 12 s35 
9 3 6BPh
2 10 6BPh
JAR3D SCFG/MRF model for IL_47444.3:
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 [12] // Initial node U45 - G64 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.010861630,0.015518619,0.012759211,0.101819593,0.000000000],[0.173445935,0.011997144,0.128406679,0.014433747,0.000000000],[0.012959429,0.115200367,0.002728704,0.018324658,0.000000000],[0.115535013,0.013473421,0.240394114,0.012141736,0.000000000],[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 [12] // Basepair U45 - G64 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.050489329,0.042183614,0.000520707,0.027051559,0.000000000],[0.419540607,0.255029502,0.027381659,0.003644947,0.000000000],[0.043601253,0.000520707,0.027349873,0.006066193,0.000000000],[0.048627321,0.046951315,0.000520707,0.000520707,0.000000000],[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 [2] | Right Index [11] // Basepair C46 - A63 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.017695077,0.279180118,0.002241342,0.045999899,0.000000000],[0.002241342,0.010605986,0.025978054,0.002241342,0.000000000],[0.149311367,0.207805235,0.015309849,0.010728810,0.000000000],[0.002241342,0.002241342,0.023148360,0.203030532,0.000000000],[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 [3] | Right Index [10] // Basepair A47 - C62 tHW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008241149,0.006583009,0.079647297,0.005438157,0.000000000],[0.004483626,0.004166170,0.030377634,0.004738347,0.000000000],[0.000948703,0.000948703,0.719138102,0.000948703,0.000000000],[0.088506880,0.000948703,0.043936112,0.000948703,0.000000000],[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 [4] | Right Index [9] // Basepair G48 - G61 tHS 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.095476982,0.063682634,0.259729097,0.017796169,0.000000000],[0.012936191,0.005797560,0.018701505,0.032815706,0.000000000],[0.307844781,0.019297171,0.025207837,0.051425081,0.000000000],[0.016902877,0.034170536,0.014254373,0.023961499,0.000000000],[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 [5] | Right Index [8] // Basepair G49 - A60 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009252775,0.018190197,0.010372744,0.181878762,0.000000000],[0.051344320,0.009257883,0.190042721,0.011475298,0.000000000],[0.010430036,0.179189206,0.002156526,0.022148569,0.000000000],[0.212757301,0.011207133,0.068104341,0.012192189,0.000000000],[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 [6] | Right Index [7] // Basepair U50 - A59 cWW 
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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_47444.3:
> IL_47444.3 IL_1DUH_002 U   45 G   64
UCAGGU*AAGCAG
> IL_47444.3 IL_1DUH_004 U   45 G   64
UCAGGU*AAGCAG
> IL_47444.3 IL_2PXV_002 U  146 G  165
UCAGGU*AAGCAG
> IL_47444.3 IL_1LNT_002 U    4 G   21
UCAGGU*AAGCAG
> IL_47444.3 IL_1MFQ_007 C  190 G  209
CCAGGU*GAGCAG
> IL_47444.3 IL_2XXA_015 U   40 G   59
UCAGAG*CAGCAG
> IL_47444.3 IL_3U5H_127 C 3161 G 3289
CCACAC*GCGUGG
> IL_47444.3 IL_4FAW_007 U  214 A  163
UACAGA*UAGGUA
> IL_47444.3 IL_1D4R_002 G   12 C   17
GGGAGC*GGGAGC