Alignment of IL_02555.1 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
3

3
7
4
I

8
5


9
4
I

10
3

4
11
2
I

12
2

5
13
1
I


In
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Cutoff
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Full
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Alignment
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IL_02555.1_Instance_1 IL_02555.1,IL_5J7L_342,C2540_G2523CAAGUG
IL_02555.1_Sequence_1 IL_02555.15J7L_C_2540_G_2523CAAG*UGtrue100000.00
IL_02555.1_Instance_2 IL_02555.1,IL_4WF9_097,C2567_G2550CAAGUG
IL_02555.1_Sequence_2 IL_02555.14WF9_C_2567_G_2550CAAG*UGtrue100000.00
IL_02555.1_Instance_3 IL_02555.1,IL_7A0S_091,C2519_G2502CAAGUG
IL_02555.1_Sequence_3 IL_02555.17A0S_C_2519_G_2502CAAG*UGtrue100000.00
IL_02555.1_Instance_4 IL_02555.1,IL_9DFE_099,C2540_G2523CAAGUG
IL_02555.1_Sequence_4 IL_02555.19DFE_C_2540_G_2523CAAG*UGtrue100000.00
IL_02555.1_Instance_5 IL_02555.1,IL_4V9F_089,C2575_G2558CAAGUG
IL_02555.1_Sequence_5 IL_02555.14V9F_C_2575_G_2558CAAG*UGtrue100000.00
IL_02555.1_Instance_6 IL_02555.1,IL_8P9A_339,U2909_A2892UAAGUA
IL_02555.1_Sequence_6 IL_02555.18P9A_U_2909_A_2892UAAG*UAtrue98000.22
IL_02555.1_Instance_7 IL_02555.1,IL_8CRE_120,U2881_A2864UAAGUA
IL_02555.1_Sequence_7 IL_02555.18CRE_U_2881_A_2864UAAG*UAtrue98000.22
IL_02555.1_Instance_8 IL_02555.1,IL_4KQY_004,C73_G50CAAGCG
IL_02555.1_Sequence_8 IL_02555.14KQY_C73_G50CAAG*CGtrue62003.67
IL_02555.1_Instance_9 IL_02555.1,IL_8DP3_001,C48_G79CUAGCG
IL_02555.1_Sequence_9 IL_02555.18DP3_C48_G79CUAG*CGtrue62003.61

Conserved interactions between motif group positions in IL_02555.1:
1 2 s35 
1 5 cWW 
2 4 tSH 
3 4 cWW 
4 5 s35
JAR3D SCFG/MRF model for IL_02555.1:
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 [5] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008819696,0.016095325,0.010040343,0.185509802,0.000000000],[0.019341809,0.009113711,0.257281078,0.012334023,0.000000000],[0.010133974,0.188240480,0.001946087,0.021872140,0.000000000],[0.207419317,0.011828074,0.030567544,0.009456597,0.000000000],[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 [5] // Basepair C2540 - G2523 cWW 
ClusterNode  | Deletion Probability [0.0000000006231837] | Num Left Bases [2] | Num Right Bases [1] | Left Index [2] | Right Index [4] | Norm Constant [0.291215390086696] // Cluster node 5J7L|1|DA|A|2541:5J7L|1|DA|G|2543 and 5J7L|1|DA|U|2522:5J7L|1|DA|U|2522
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.023039055,0.037604626,0.003778167,0.442036856,0.000000000],[0.018790543,0.015723906,0.003778167,0.003778167,0.000000000],[0.017806511,0.003778167,0.341001612,0.022929794,0.000000000],[0.018585580,0.039812517,0.003778167,0.003778167,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|2541 - 5J7L|1|DA|U|2522 tSH 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.013552813,0.220298406,0.012725731,0.103426658,0.000000000],[0.013543262,0.011293356,0.068735729,0.013246761,0.000000000],[0.012476886,0.092046155,0.002795829,0.305922153,0.000000000],[0.067951837,0.014319241,0.015357955,0.032307228,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|2543 - 5J7L|1|DA|U|2522 cWW 
Insertion    | Location [1] | Length Distribution [0.005492996,0.988739357,0.005492996,0.000274650] | Letter Distribution [0.863636364,0.045454545,0.045454545,0.045454545,0.000000000]// Insertion after nucleotide 2, position 1 in cluster node
InitialNode  | Left Length Distribution [0.992346266,0.007389813,0.000263922] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.992346266,0.007389813,0.000263922] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [3] // New Initial node after Cluster
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_02555.1:
> IL_02555.1  5J7L C 2540 G 2523
CAAG*UG
> IL_02555.1  4WF9 C 2567 G 2550
CAAG*UG
> IL_02555.1  7A0S C 2519 G 2502
CAAG*UG
> IL_02555.1  9DFE C 2540 G 2523
CAAG*UG
> IL_02555.1  4V9F C 2575 G 2558
CAAG*UG
> IL_02555.1  8P9A U 2909 A 2892
UAAG*UA
> IL_02555.1  8CRE U 2881 A 2864
UAAG*UA
> IL_02555.1  4KQY C   73 G   50
CAAG*CG
> IL_02555.1  8DP3 C   48 G   79
CUAG*CG