Alignment of IL_57188.5 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
3
I

8
3

4
9
4
I

10
5

5
11
5
I

12
5

6
13
5
I

14
5

7
15
6
I

16
7


17
6
I

18
5

8
19
4
I

20
3

9
21
3
I

22
3

10
23
2
I

24
2

11
25
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_57188.5_Instance_1 IL_57188.5,IL_9DFE_038,C1018_G1144CUAAGUGCUUAAG
IL_57188.5_Sequence_1 IL_57188.59DFE_C_1018_G_1144CUAAGUG*CUUAAGtrue95000.86
IL_57188.5_Instance_2 IL_57188.5,IL_4V9F_040,U1115_A1248UUAAGUGCUCAAA
IL_57188.5_Sequence_2 IL_57188.54V9F_U_1115_A_1248UUAAGUG*CUCAAAtrue98000.30
IL_57188.5_Instance_3 IL_57188.5,IL_5J7L_280,U1018_A1144UUAAGUGCUAAA
IL_57188.5_Sequence_3 IL_57188.55J7L_U_1018_A_1144UUAAGUG*CUAAAtrue100000.00
IL_57188.5_Instance_4 IL_57188.5,IL_4WF9_039,U1062_A1188UUAAGUGCUAAA
IL_57188.5_Sequence_4 IL_57188.54WF9_U_1062_A_1188UUAAGUG*CUAAAtrue100000.00
IL_57188.5_Instance_5 IL_57188.5,IL_7A0S_036,C1029_G1155CUCAGUGCUCAAG
IL_57188.5_Sequence_5 IL_57188.57A0S_C_1029_G_1155CUCAGUG*CUCAAGtrue92001.44

Conserved interactions between motif group positions in IL_57188.5:
1 2 s35 
1 11 cWW 
2 3 s35 
2 4 cSH 
2 10 tWW 
2 11 s55 
3 4 s53 
3 9 s53 
4 6 s55 
4 9 tWW 
5 6 cSH 
5 7 s35 
5 8 s33 
5 9 s55 
6 7 s35 
7 8 cWW 
8 10 perp 
10 11 s55 
7 11 2BR
JAR3D SCFG/MRF model for IL_57188.5:
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 [11] // Initial node
BasepairNode | Deletion Probability [0.0000001230289089] | Pair Probability [[0.008971369,0.016871195,0.010036256,0.191671055,0.000000000],[0.020727304,0.009504551,0.215061691,0.011796248,0.000000000],[0.010095364,0.192251066,0.002003525,0.022551723,0.000000000],[0.225967248,0.011209843,0.041465653,0.009815909,0.000000000],[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 [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000] | Left Index [1] | Right Index [11] // Basepair C1018 - G1144 cWW 
ClusterNode  | Deletion Probability [0.0000000000001252] | Num Left Bases [3] | Num Right Bases [2] | Left Index [2] | Right Index [10] | Norm Constant [0.107967099456197] // Cluster node 9DFE|1|1A|U|1019:9DFE|1|1A|A|1021 and 9DFE|1|1A|U|1141:9DFE|1|1A|A|1142|||A
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.015670192,0.038722823,0.003278045,0.434947362,0.000000000],[0.015388165,0.035313208,0.013651465,0.037860784,0.000000000],[0.003278045,0.016248833,0.015689392,0.262586703,0.000000000],[0.037446804,0.031435146,0.016159964,0.022323068,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|A|1021 - 9DFE|1|1A|U|1141 tWW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.015560842,0.015299030,0.003259057,0.037229894,0.000000000],[0.038498522,0.033098522,0.016154712,0.031253058,0.000000000],[0.003259057,0.013572389,0.016620668,0.016066358,0.000000000],[0.433048562,0.037641476,0.261065675,0.028372175,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|U|1019 - 9DFE|1|1A|A|1142|||A tWW 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.102154859,0.096752380,0.004944901,0.013796476,0.000000000],[0.099777216,0.093373493,0.001061587,0.008888900,0.000000000],[0.009061197,0.001061587,0.089431332,0.086905524,0.000000000],[0.213301508,0.091099193,0.001061587,0.087328260,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|U|1019 - 9DFE|1|1A|A|1021 cSH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.642857143,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 9DFE|1|1A|A|1020
Insertion    | Location [4] | Length Distribution [0.399409739,0.594195770,0.006099361,0.000295130] | Letter Distribution [0.100000000,0.500000000,0.100000000,0.300000000,0.000000000]// Insertion after nucleotide 9, position 4 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 [5] | Right Index [8] // Initial node 9DFE|1|1A|G|1022 - 9DFE|1|1A|C|1140 from node 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [5] | Right Index [8] | Norm Constant [1.000000000000000] // Cluster node 9DFE|1|1A|G|1022:9DFE|1|1A|G|1024 and 9DFE|1|1A|C|1140:9DFE|1|1A|C|1140
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.004692894,0.009773618,0.005343954,0.097062545,0.000000000],[0.008243196,0.004601854,0.097885001,0.006404600,0.000000000],[0.026423031,0.551270192,0.005036511,0.064521312,0.000000000],[0.095820331,0.006647357,0.011311167,0.004962438,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|G|1024 - 9DFE|1|1A|C|1140 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.077031253,0.078491313,0.004315696,0.076708478,0.000000000],[0.057508863,0.086666866,0.000955568,0.076869287,0.000000000],[0.067302366,0.000955568,0.082097414,0.143175873,0.000000000],[0.078226465,0.077756860,0.000955568,0.090982561,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|G|1022 - 9DFE|1|1A|U|1023 cSH 
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 [8] | Right Index [7] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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_57188.5:
> IL_57188.5  9DFE C 1018 G 1144
CUAAGUG*CUUAAG
> IL_57188.5  4V9F U 1115 A 1248
UUAAGUG*CUCAAA
> IL_57188.5  5J7L U 1018 A 1144
UUAAGUG*CUAAA
> IL_57188.5  4WF9 U 1062 A 1188
UUAAGUG*CUAAA
> IL_57188.5  7A0S C 1029 G 1155
CUCAGUG*CUCAAG