Alignment of IL_98591.3 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
2

2
5
2
I

6
2

3
7
2
I

8
2

4
9
3
I

10
4

5
11
4
I

12
5

6
13
5
I

14
6


15
5
I

16
5

7
17
4
I

18
4

8
19
3
I

20
2

9
21
2
I

22
2

10
23
2
I

24
2

11
25
2
I

26
2

12
27
2
I

28
2

13
29
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_98591.3_Instance_1 IL_98591.3_IL_3V2F_067_U1798_A1821UGCGAACGGAGGUAUA
IL_98591.3_Sequence_1 IL_98591.3_IL_3V2F_067_U_1798_A_1821UGCGAAC*GGAGGUAUAtrue94001.36
IL_98591.3_Instance_2 IL_98591.3_IL_4IOA_065_U1789_A1813UGCCAACGGACGUAUA
IL_98591.3_Sequence_2 IL_98591.3_IL_4IOA_065_U_1789_A_1813UGCCAAC*GGACGUAUAtrue98000.51
IL_98591.3_Instance_3 IL_98591.3_IL_2QBG_071_U1798_A1821UGCAAACGGACGUAUA
IL_98591.3_Sequence_3 IL_98591.3_IL_2QBG_071_U_1798_A_1821UGCAAAC*GGACGUAUAtrue100000.00
IL_98591.3_Instance_4 IL_98591.3_IL_1S72_065_C1854_G1877CGCAAAUACUCGUACG
IL_98591.3_Sequence_4 IL_98591.3_IL_1S72_065_C_1854_G_1877CGCAAAU*ACUCGUACGtrue80004.37

Conserved interactions between motif group positions in IL_98591.3:
1 4 cSS 
1 12 s35 
1 13 cWW 
2 3 s53 
2 11 tSS 
2 12 s53 
3 4 s55 
3 10 tWW 
3 12 tHH 
4 5 s35 
4 8 s33 
4 9 tHH 
5 6 s35 
5 8 tHS 
6 7 cWW 
6 8 s55 
7 8 s35 
8 9 s33 
9 10 s55 
10 11 s35 
12 13 s55 
12 2 6BPh
8 4 6BPh
9 4 6BPh
2 12 6BPh
11 3 6BR
5 8 6BR
JAR3D SCFG/MRF model for IL_98591.3:
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 [13] // Initial node U1798 - A1821 from junction 
ClusterNode  | Deletion Probability [0.000000000000000000000000000239456582305914910000000000000000] | Num Left Bases [4] | Num Right Bases [5] | Left Index [1] | Right Index [13] | Norm Constant [0.038961326718714] // Cluster node U1798:A1802 and A1815:A1821
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.441749542,0.015205919,0.075103199,0.098489209,0.000000000],[0.056325096,0.001443277,0.053941313,0.088214880,0.000000000],[0.029154810,0.052792421,0.002289604,0.001443277,0.000000000],[0.028991690,0.051969210,0.001443277,0.001443277,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1802 - A1815 tHH 
Interaction  | Interacting Bases [3,6] | Pair Probability [[0.019014290,0.019018870,0.006250487,0.026309014,0.000000000],[0.024244124,0.028687159,0.663510195,0.029548129,0.000000000],[0.006250487,0.025586574,0.020400031,0.018196760,0.000000000],[0.035814972,0.030755175,0.024764652,0.021649081,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1800 - G1817 tWW 
Interaction  | Interacting Bases [2,7] | Pair Probability [[0.001549151,0.002727414,0.015998825,0.013617496,0.000000000],[0.000211773,0.000211773,0.000211773,0.001058865,0.000000000],[0.016473642,0.046369184,0.120208586,0.779667332,0.000000000],[0.000211773,0.000211773,0.000211773,0.001058865,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1799 - U1818 tSS 
Interaction  | Interacting Bases [3,8] | Pair Probability [[0.079674918,0.078577819,0.003724751,0.003645748,0.000000000],[0.655402229,0.000881344,0.041046967,0.005187295,0.000000000],[0.025118855,0.072642517,0.002497325,0.000881344,0.000000000],[0.024567540,0.004388660,0.000881344,0.000881344,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1800 - A1819 tHH 
Interaction  | Interacting Bases [1,9] | Pair Probability [[0.009165038,0.019030160,0.010081135,0.199658022,0.000000000],[0.023115364,0.009112997,0.204928790,0.011047591,0.000000000],[0.010129904,0.192879101,0.002111419,0.023228345,0.000000000],[0.234721258,0.010832296,0.027253714,0.012704867,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1798 - A1821 cWW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.069564796,0.064432445,0.066759450,0.067283927,0.000000000],[0.080157187,0.061605000,0.064605906,0.031370144,0.000000000],[0.067351560,0.005632734,0.058859672,0.059614966,0.000000000],[0.100984120,0.065911246,0.066185624,0.069681223,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1798 - A1802 cSS 
Insertion    | Location [3] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.416666667,0.250000000,0.250000000,0.083333333,0.000000000]// Insertion after nucleotide 3, position 3 in cluster node
Insertion    | Location [5] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.083333333,0.583333333,0.250000000,0.083333333,0.000000000]// Insertion after nucleotide 9, position 5 in cluster node
Insertion    | Location [8] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.083333333,0.250000000,0.083333333,0.583333333,0.000000000]// Insertion after nucleotide 12, position 8 in cluster node
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.041492445,0.082494358,0.378797887,0.045100819,0.000000000],[0.048364757,0.043877065,0.003499517,0.043448887,0.000000000],[0.000499931,0.000499931,0.016954426,0.000499931,0.000000000],[0.002380608,0.000499931,0.291089576,0.000499931,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair A1803 - G1814 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009613617,0.017593128,0.010983027,0.192350441,0.000000000],[0.021287894,0.008639455,0.234523700,0.012787711,0.000000000],[0.011096459,0.200570476,0.002109537,0.023296342,0.000000000],[0.204768830,0.012284769,0.027115440,0.010979173,0.000000000],[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 C1804 - G1813 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_98591.3:
> IL_98591.3 IL_3V2F_067 U 1798 A 1821
UGCGAAC*GGAGGUAUA
> IL_98591.3 IL_4IOA_065 U 1789 A 1813
UGCCAAC*GGACGUAUA
> IL_98591.3 IL_2QBG_071 U 1798 A 1821
UGCAAAC*GGACGUAUA
> IL_98591.3 IL_1S72_065 C 1854 G 1877
CGCAAAU*ACUCGUACG