Alignment of IL_92446.2 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
6
I

8
9

4
9
9
I

10
10


11
9
I

12
9

5
13
8
I

14
7

6
15
2
I

16
2

7
17
1
I


In
acceptance
region

Cutoff
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Full
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distance
Interior
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Alignment
score
deficit
IL_92446.2_Instance_1 IL_92446.2,IL_1MMS_001,C1076_G1062CAUCGUUG
IL_92446.2_Sequence_1 IL_92446.21MMS_C_1076_G_1062CAUC*GUUGtrue100000.00
IL_92446.2_Instance_2 IL_92446.2,IL_5D8H_002,C1186_G1172CAUCGUUG
IL_92446.2_Sequence_2 IL_92446.25D8H_C_1186_G_1172CAUC*GUUGtrue100000.00
IL_92446.2_Instance_3 IL_92446.2,IL_6PRV_001,C1076_G1062CAUCGUUG
IL_92446.2_Sequence_3 IL_92446.26PRV_C_1076_G_1062CAUC*GUUGtrue100000.00
IL_92446.2_Instance_4 IL_92446.2,IL_4V9F_110,U1180_A1166UACCGUGA
IL_92446.2_Sequence_4 IL_92446.24V9F_U_1180_A_1166UACC*GUGAtrue79002.35
IL_92446.2_Instance_5 IL_92446.2,IL_5J7L_285,C1076_G1062CAUCGUUG
IL_92446.2_Sequence_5 IL_92446.25J7L_C_1076_G_1062CAUC*GUUGtrue100000.00

Conserved interactions between motif group positions in IL_92446.2:
1 2 s35 
1 7 cWW 
2 3 s35 
2 7 s55 
4 5 cWW 
5 6 s33
JAR3D SCFG/MRF model for IL_92446.2:
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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000001230289089] | Pair Probability [[0.009166526,0.016698909,0.010445572,0.192630123,0.000000000],[0.020040483,0.009458332,0.238769746,0.012863164,0.000000000],[0.010545011,0.195597456,0.002021206,0.022714403,0.000000000],[0.205731170,0.012341540,0.031159455,0.009816904,0.000000000],[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 [0.009799118,0.979911808,0.009799118,0.000489956] | Right Letter Distribution [0.071428571,0.071428571,0.214285714,0.642857143,0.000000000] | Left Index [1] | Right Index [7] // Basepair C1076 - G1062 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000] | Position [1] | Left Index [2] | Right Index [6] // Fixed node on left for 1MMS|1|C|U|1060
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 [6] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.214285714,0.071428571,0.642857143,0.000000000] | Position [1] | Left Index [3] | Right Index [6] // Fixed node on left for 1MMS|1|C|U|1061
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 [4] | Right Index [6] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.071428571,0.071428571,0.785714286,0.000000000] | Position [2] | Left Index [4] | Right Index [6] // Fixed node on right for 1MMS|1|C|A|1077
InitialNode  | Left Length Distribution [1.000000000] | 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 [5] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009264105,0.016612765,0.010650229,0.193109658,0.000000000],[0.019697072,0.009435223,0.250623774,0.013396622,0.000000000],[0.010769834,0.197270651,0.002030047,0.022795742,0.000000000],[0.195613131,0.012907388,0.026006356,0.009817401,0.000000000],[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 [4] | Right Index [5] // Basepair C1079 - G1059 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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_92446.2:
> IL_92446.2  1MMS C 1076 G 1062
CAUC*GUUG
> IL_92446.2  5D8H C 1186 G 1172
CAUC*GUUG
> IL_92446.2  6PRV C 1076 G 1062
CAUC*GUUG
> IL_92446.2  4V9F U 1180 A 1166
UACC*GUGA
> IL_92446.2  5J7L C 1076 G 1062
CAUC*GUUG