Alignment of IL_25872.4 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
4

3
7
4
I

8
5

4
9
5
I

10
6


11
5
I

12
5

5
13
4
I

14
4

6
15
3
I

16
3

7
17
2
I

18
2

8
19
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_25872.4_Instance_1 IL_25872.4,IL_1CSL_001,G46_C74GGGCGGUAC
IL_25872.4_Sequence_1 IL_25872.41CSL_G46_C74GGGC*GGUACtrue99000.08
IL_25872.4_Instance_2 IL_25872.4,IL_1DUQ_001,G104_C127GGGCGGUAC
IL_25872.4_Sequence_2 IL_25872.41DUQ_G104_C127GGGC*GGUACtrue99000.08
IL_25872.4_Instance_3 IL_25872.4,IL_7R9F_001,C5_G8CGGGCGGG
IL_25872.4_Sequence_3 IL_25872.47R9F_C5_G8CGGG*CGGGtrue85001.41
IL_25872.4_Instance_4 IL_25872.4,IL_7WIE_001,G49_U13GAGAUGGU
IL_25872.4_Sequence_4 IL_25872.47WIE_G49_U13GAGA*UGGUtrue100000.00
IL_25872.4_Instance_5 IL_25872.4,IL_6DTD_001,A31_U8AAACGCAU
IL_25872.4_Sequence_5 IL_25872.46DTD_A31_U8AAAC*GCAUtrue72002.70

Conserved interactions between motif group positions in IL_25872.4:
1 2 s35 
1 8 cWW 
2 3 s35 
2 7 cWW 
2 8 s55 
3 4 s35 
3 6 cWH 
3 7 s55 
4 5 cWW 
5 6 s33 
6 7 s55 
7 8 s35 
6 6 2BPh
JAR3D SCFG/MRF model for IL_25872.4:
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 [8] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.010516047,0.073156823,0.011144933,0.182463124,0.000000000],[0.016652679,0.009942010,0.173816961,0.012652359,0.000000000],[0.011057680,0.185973025,0.002244750,0.097855704,0.000000000],[0.161540193,0.013138537,0.021585836,0.016259337,0.000000000],[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 [8] // Basepair G46 - C74 cWW 
BasepairNode | Deletion Probability [0.0000028285212255] | Pair Probability [[0.168581226,0.016814302,0.271366766,0.018880194,0.000000000],[0.014728695,0.009560698,0.020019046,0.037657959,0.000000000],[0.281532577,0.020102734,0.036732860,0.018064858,0.000000000],[0.018707015,0.037867995,0.016056939,0.013326134,0.000000000],[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 [0.595367176,0.400197141,0.004238541,0.000197141] | Right Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair G47 - A73 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.001007928,0.040293642,0.072561915,0.008539002,0.000000000],[0.001007928,0.010683622,0.007055495,0.003635228,0.000000000],[0.041909512,0.001007928,0.773406635,0.001007928,0.000000000],[0.003483624,0.001007928,0.022071213,0.011320473,0.000000000],[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 [3] | Right Index [6] // Basepair G48 - G71 cWH 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009253120,0.018182514,0.010469835,0.204160012,0.000000000],[0.018543573,0.009376871,0.227543114,0.012631439,0.000000000],[0.010513933,0.206690655,0.002020512,0.029216213,0.000000000],[0.194065633,0.012565763,0.024632950,0.010133862,0.000000000],[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 [4] | Right Index [5] // Basepair C49 - G70 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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_25872.4:
> IL_25872.4  1CSL G   46 C   74
GGGC*GGUAC
> IL_25872.4  1DUQ G  104 C  127
GGGC*GGUAC
> IL_25872.4  7R9F C    5 G    8
CGGG*CGGG
> IL_25872.4  7WIE G   49 U   13
GAGA*UGGU
> IL_25872.4  6DTD A   31 U    8
AAAC*GCAU