Alignment of IL_90459.3 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_90459.3
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
4

3
7
4
I

8
5


9
4
I

10
4

4
11
3
I

12
3

5
13
2
I

14
2

6
15
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_90459.3_Instance_1 IL_90459.3_IL_4IOA_037_C1132_G1045CGCGAUG
IL_90459.3_Sequence_1 IL_90459.3_IL_4IOA_037_C_1132_G_1045CGC*GAUGtrue98000.17
IL_90459.3_Instance_2 IL_90459.3_IL_2QBG_040_C1121_G1034CGCGAUG
IL_90459.3_Sequence_2 IL_90459.3_IL_2QBG_040_C_1121_G_1034CGC*GAUGtrue98000.17
IL_90459.3_Instance_3 IL_90459.3_IL_3V2F_041_C1121_G1034CGCGAUG
IL_90459.3_Sequence_3 IL_90459.3_IL_3V2F_041_C_1121_G_1034CGC*GAUGtrue98000.17
IL_90459.3_Instance_4 IL_90459.3_IL_4A1C_001_C67_G97CAAUCAG
IL_90459.3_Sequence_4 IL_90459.3_IL_4A1C_001_C67_G97CAA*UCAGtrue100000.00
IL_90459.3_Instance_5 IL_90459.3_IL_3U5H_138_G3328_C3378GUAUUAAGC
IL_90459.3_Sequence_5 IL_90459.3_IL_3U5H_138_G_3328_C_3378GUA*UUAAGCtrue76002.31
IL_90459.3_Instance_6 IL_90459.3_IL_4A1B_129_G3286_C3334GUAUUCAGC
IL_90459.3_Sequence_6 IL_90459.3_IL_4A1B_129_G_3286_C_3334GUA*UUCAGCtrue62003.61
IL_90459.3_Instance_7 IL_90459.3_IL_2Y9B_001_U825_G804UUGCCG
IL_90459.3_Sequence_7 IL_90459.3_IL_2Y9B_001_U825_G804UUG*CCGtrue90000.98
IL_90459.3_Instance_8 IL_90459.3_IL_1S72_085_U2545_G2613UUCGUGAG
IL_90459.3_Sequence_8 IL_90459.3_IL_1S72_085_U_2545_G_2613UUC*GUGAGtrue73002.52
IL_90459.3_Instance_9 IL_90459.3_IL_3U5F_074_G1352_C1373GUGUUAUC
IL_90459.3_Sequence_9 IL_90459.3_IL_3U5F_074_G_1352_C_1373GUG*UUAUCtrue67003.14

Conserved interactions between motif group positions in IL_90459.3:
1 2 s35 
1 6 cWW 
2 3 s35 
2 5 cWW 
2 6 s55 
3 4 cWW 
3 5 s55 
4 5 s35 
JAR3D SCFG/MRF model for IL_90459.3:
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 [6] // Initial node C1132 - G1045 from junction 
BasepairNode | Deletion Probability [0.0000000207694325] | Pair Probability [[0.010059085,0.016709368,0.011765394,0.148424081,0.000000000],[0.079921576,0.009525552,0.200524308,0.013560844,0.000000000],[0.011854065,0.189373536,0.002298327,0.021714464,0.000000000],[0.149974270,0.013138568,0.110603748,0.010552815,0.000000000],[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 [0.222432705,0.441810016,0.113721776,0.220721684,0.001252712,0.000061108] | Right Letter Distribution [0.392857143,0.107142857,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair C1132 - G1045 cWW 
BasepairNode | Deletion Probability [0.0000073600808576] | Pair Probability [[0.026386433,0.120956510,0.119329082,0.026512032,0.000000000],[0.015806411,0.012345035,0.021065763,0.054224136,0.000000000],[0.150766680,0.021860238,0.003890100,0.058563719,0.000000000],[0.023298207,0.069910175,0.016516457,0.258569024,0.000000000],[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 [0.883191757,0.005519948,0.110644301,0.000613328,0.000030666] | Right Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Left Index [2] | Right Index [5] // Basepair G1133 - A1043 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009833110,0.049199864,0.010754983,0.199307317,0.000000000],[0.018197807,0.008540104,0.211715629,0.011980972,0.000000000],[0.010760300,0.183124357,0.002146804,0.066510832,0.000000000],[0.168917576,0.011971032,0.022875826,0.014163487,0.000000000],[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 C1134 - G1042 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_90459.3:
> IL_90459.3 IL_4IOA_037 C 1132 G 1045
CGC*GAUG
> IL_90459.3 IL_2QBG_040 C 1121 G 1034
CGC*GAUG
> IL_90459.3 IL_3V2F_041 C 1121 G 1034
CGC*GAUG
> IL_90459.3 IL_4A1C_001 C   67 G   97
CAA*UCAG
> IL_90459.3 IL_3U5H_138 G 3328 C 3378
GUA*UUAAGC
> IL_90459.3 IL_4A1B_129 G 3286 C 3334
GUA*UUCAGC
> IL_90459.3 IL_2Y9B_001 U  825 G  804
UUG*CCG
> IL_90459.3 IL_1S72_085 U 2545 G 2613
UUC*GUGAG
> IL_90459.3 IL_3U5F_074 G 1352 C 1373
GUG*UUAUC