Alignment of IL_31737.3 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
4
I

6
5

3
7
5
I

8
6


9
5
I

10
5

4
11
2
I

12
2

5
13
1
I


In
acceptance
region

Cutoff
score
Full
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distance
Interior
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distance
Alignment
score
deficit
IL_31737.3_Instance_1 IL_31737.3,IL_2ET8_001,G41_C6GUCGUC
IL_31737.3_Sequence_1 IL_31737.32ET8_G41_C6GUC*GUCtrue80001.89
IL_31737.3_Instance_2 IL_31737.3,IL_2O3X_001,G42_C7GUCGUC
IL_31737.3_Sequence_2 IL_31737.32O3X_G42_C7GUC*GUCtrue80001.89
IL_31737.3_Instance_3 IL_31737.3,IL_2GUN_002,A14_U4AAGCU
IL_31737.3_Sequence_3 IL_31737.32GUN_A14_U4AAG*CUtrue85001.47
IL_31737.3_Instance_4 IL_31737.3,IL_7A0S_044,G1241_C1234GAGUAC
IL_31737.3_Sequence_4 IL_31737.37A0S_G_1241_C_1234GAG*UACtrue86001.31
IL_31737.3_Instance_5 IL_31737.3,IL_8VFS_003,C14_G16CCGCCG
IL_31737.3_Sequence_5 IL_31737.38VFS_C14_G16CCG*CCGtrue71002.78
IL_31737.3_Instance_6 IL_31737.3,IL_2O3X_003,C30_G19CACGAAG
IL_31737.3_Sequence_6 IL_31737.32O3X_C30_G19CAC*GAAGtrue85001.44
IL_31737.3_Instance_7 IL_31737.3,IL_4WF9_047,G1266_U1259GACGAU
IL_31737.3_Sequence_7 IL_31737.34WF9_G_1266_U_1259GAC*GAUtrue87001.22
IL_31737.3_Instance_8 IL_31737.3,IL_4M4O_004,G26_C41GAGCAC
IL_31737.3_Sequence_8 IL_31737.34M4O_G26_C41GAG*CACtrue100000.00
IL_31737.3_Instance_9 IL_31737.3,IL_4M6D_013,G26_C41GAGCAC
IL_31737.3_Sequence_9 IL_31737.34M6D_G26_C41GAG*CACtrue100000.00
IL_31737.3_Instance_10 IL_31737.3,IL_8UO6_002,C41_G63CGCGACG
IL_31737.3_Sequence_10 IL_31737.38UO6_C41_G63CGC*GACGtrue56004.18
IL_31737.3_Instance_11 IL_31737.3,IL_3C3Z_002,C15_G10CACGAAG
IL_31737.3_Sequence_11 IL_31737.33C3Z_C15_G10CAC*GAAGtrue85001.44
IL_31737.3_Instance_12 IL_31737.3,IL_8CRE_477,U1030_G1014UAAUCUUG
IL_31737.3_Sequence_12 IL_31737.38CRE_U_1030_G_1014UAA*UCUUGtrue24007.19

Conserved interactions between motif group positions in IL_31737.3:
1 2 s35 
1 5 cWW 
2 3 s35 
2 5 s55 
3 4 cWW
JAR3D SCFG/MRF model for IL_31737.3:
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 [5] // Initial node
BasepairNode | Deletion Probability [0.0000000210112506] | Pair Probability [[0.009348761,0.038147238,0.010456812,0.170408364,0.000000000],[0.037974672,0.010389401,0.196909720,0.012323520,0.000000000],[0.010446456,0.206469380,0.002079245,0.055983327,0.000000000],[0.160739688,0.012410573,0.053888617,0.012024225,0.000000000],[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 [0.085066814,0.579969693,0.250740460,0.083809753,0.000396060,0.000017220] | Right Letter Distribution [0.527777778,0.194444444,0.027777778,0.250000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair G41 - C6 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.607142857,0.107142857,0.107142857,0.178571429,0.000000000] | Position [1] | Left Index [2] | Right Index [4] // Fixed node on left for 2ET8|1|A|U|5
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 [4] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009204057,0.038143215,0.010196140,0.182474066,0.000000000],[0.016794277,0.009018005,0.227863705,0.012191705,0.000000000],[0.010190093,0.209690660,0.001986965,0.056400376,0.000000000],[0.169679553,0.012266937,0.022151727,0.011748520,0.000000000],[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 [3] | Right Index [4] // Basepair C43 - G4 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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_31737.3:
> IL_31737.3  2ET8 G   41 C    6
GUC*GUC
> IL_31737.3  2O3X G   42 C    7
GUC*GUC
> IL_31737.3  2GUN A   14 U    4
AAG*CU
> IL_31737.3  7A0S G 1241 C 1234
GAG*UAC
> IL_31737.3  8VFS C   14 G   16
CCG*CCG
> IL_31737.3  2O3X C   30 G   19
CAC*GAAG
> IL_31737.3  4WF9 G 1266 U 1259
GAC*GAU
> IL_31737.3  4M4O G   26 C   41
GAG*CAC
> IL_31737.3  4M6D G   26 C   41
GAG*CAC
> IL_31737.3  8UO6 C   41 G   63
CGC*GACG
> IL_31737.3  3C3Z C   15 G   10
CAC*GAAG
> IL_31737.3  8CRE U 1030 G 1014
UAA*UCUUG