Alignment of IL_43124.2 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
3
I

4
4

2
5
4
I

6
5

3
7
5
I

8
6


9
5
I

10
5

4
11
4
I

12
4

5
13
3
I

14
2

6
15
2
I

16
2

7
17
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_43124.2_Instance_1 IL_43124.2_IL_3GX5_003_G56_C47GUGCAAC
IL_43124.2_Sequence_1 IL_43124.2_IL_3GX5_003_G56_C47GUG*CAACtrue100000.00
IL_43124.2_Instance_2 IL_43124.2_IL_4AOB_003_G56_C47GUGCAAC
IL_43124.2_Sequence_2 IL_43124.2_IL_4AOB_003_G56_C47GUG*CAACtrue100000.00
IL_43124.2_Instance_3 IL_43124.2_IL_3V7E_007_G288_C247GUGCAAC
IL_43124.2_Sequence_3 IL_43124.2_IL_3V7E_007_G288_C247GUG*CAACtrue100000.00
IL_43124.2_Instance_4 IL_43124.2_IL_4KQY_003_G77_C48GUGCAAC
IL_43124.2_Sequence_4 IL_43124.2_IL_4KQY_003_G77_C48GUG*CAACtrue100000.00
IL_43124.2_Instance_5 IL_43124.2_IL_4B5R_003_G56_C47GUGCAAC
IL_43124.2_Sequence_5 IL_43124.2_IL_4B5R_003_G56_C47GUG*CAACtrue100000.00
IL_43124.2_Instance_6 IL_43124.2_IL_1J2B_003_C926_G947CGCGAGG
IL_43124.2_Sequence_6 IL_43124.2_IL_1J2B_003_C926_G947CGC*GAGGtrue78002.12
IL_43124.2_Instance_7 IL_43124.2_IL_4A1B_093_U2974_G2389UACGCGG
IL_43124.2_Sequence_7 IL_43124.2_IL_4A1B_093_U_2974_G_2389UAC*GCGGtrue69002.91
IL_43124.2_Instance_8 IL_43124.2_IL_3U5H_071_U1824_A1621UGCGAUA
IL_43124.2_Sequence_8 IL_43124.2_IL_3U5H_071_U_1824_A_1621UGC*GAUAtrue71002.75
IL_43124.2_Instance_9 IL_43124.2_IL_3U5H_012_U177_G241UUCGAGUG
IL_43124.2_Sequence_9 IL_43124.2_IL_3U5H_012_U177_G241UUC*GAGUGtrue61003.70
IL_43124.2_Instance_10 IL_43124.2_IL_1X8W_009_C316_G405CUCGUUG
IL_43124.2_Sequence_10 IL_43124.2_IL_1X8W_009_C316_G405CUC*GUUGtrue53004.50
IL_43124.2_Instance_11 IL_43124.2_IL_3Q1Q_006_A179_U201AGCGGCU
IL_43124.2_Sequence_11 IL_43124.2_IL_3Q1Q_006_A179_U201AGC*GGCUtrue92000.73

Conserved interactions between motif group positions in IL_43124.2:
1 2 s35 
1 7 cWW 
2 3 s35 
2 5 tHS 
2 7 s55 
3 4 cWW 
3 5 s55 
4 5 s35 
5 6 s35 
6 7 cSH 
JAR3D SCFG/MRF model for IL_43124.2:
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 [7] // Initial node G56 - C47 from junction 
ClusterNode  | Deletion Probability [0.0000000752256015] | Num Left Bases [1] | Num Right Bases [2] | Left Index [1] | Right Index [7] | Norm Constant [0.249241205320160] // Cluster node G56:G56 and A46:C47
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.009643656,0.017743843,0.011116974,0.163701052,0.000000000],[0.067339819,0.009199884,0.180791773,0.012510100,0.000000000],[0.011138561,0.208425677,0.002205865,0.022375070,0.000000000],[0.164574954,0.012391145,0.095803274,0.011038354,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G56 - C47 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.070820127,0.131469830,0.074440085,0.009251830,0.000000000],[0.075385232,0.070175051,0.001590324,0.093328000,0.000000000],[0.009938947,0.010256490,0.130627801,0.073632882,0.000000000],[0.076767980,0.080806256,0.022773670,0.068735496,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A46 - C47 cSH 
Insertion    | Location [2] | Length Distribution [0.904811823,0.094550986,0.000616637,0.000020555] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 6, position 2 in cluster node
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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [5] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.026190392,0.046162582,0.015757625,0.016835666,0.000000000],[0.015373566,0.014150407,0.003309124,0.016092581,0.000000000],[0.053502174,0.003309124,0.333812897,0.003309124,0.000000000],[0.401053931,0.003309124,0.019426036,0.028405649,0.000000000],[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 [5] // Basepair U57 - A45 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009286118,0.017299080,0.010773992,0.177247259,0.000000000],[0.017597460,0.007805594,0.248854464,0.012519905,0.000000000],[0.010786420,0.239296072,0.001975440,0.023439283,0.000000000],[0.177340704,0.012464760,0.023756114,0.009557335,0.000000000],[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 G58 - C44 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_43124.2:
> IL_43124.2 IL_3GX5_003 G   56 C   47
GUG*CAAC
> IL_43124.2 IL_4AOB_003 G   56 C   47
GUG*CAAC
> IL_43124.2 IL_3V7E_007 G  288 C  247
GUG*CAAC
> IL_43124.2 IL_4KQY_003 G   77 C   48
GUG*CAAC
> IL_43124.2 IL_4B5R_003 G   56 C   47
GUG*CAAC
> IL_43124.2 IL_1J2B_003 C  926 G  947
CGC*GAGG
> IL_43124.2 IL_4A1B_093 U 2974 G 2389
UAC*GCGG
> IL_43124.2 IL_3U5H_071 U 1824 A 1621
UGC*GAUA
> IL_43124.2 IL_3U5H_012 U  177 G  241
UUC*GAGUG
> IL_43124.2 IL_1X8W_009 C  316 G  405
CUC*GUUG
> IL_43124.2 IL_3Q1Q_006 A  179 U  201
AGC*GGCU