Alignment of IL_07300.2 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
2
I

4
3

2
5
3
I

6
3

3
7
3
I

8
3

4
9
3
I

10
3

5
11
4
I

12
5

6
13
5
I

14
6


15
5
I

16
5

7
17
4
I

18
3

8
19
2
I

20
2

9
21
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_07300.2_Instance_1 IL_07300.2_IL_4BPP_048_G963_C994GGGAUCGUC
IL_07300.2_Sequence_1 IL_07300.2_IL_4BPP_048_G963_C994GGGAUC*GUCtrue100000.00
IL_07300.2_Instance_2 IL_07300.2_IL_3U5F_052_G985_C1016GGGAUCGUC
IL_07300.2_Sequence_2 IL_07300.2_IL_3U5F_052_G985_C_1016GGGAUC*GUCtrue100000.00
IL_07300.2_Instance_3 IL_07300.2_IL_3U5F_025_C443_G461CCAAUCGGAG
IL_07300.2_Sequence_3 IL_07300.2_IL_3U5F_025_C443_G461CCAAUC*GGAGtrue57006.06

Conserved interactions between motif group positions in IL_07300.2:
1 2 s35 
1 9 cWW 
2 3 s35 
2 4 cSH 
2 9 s55 
4 5 s35 
5 6 s35 
5 8 cWW 
6 7 cWW 
7 8 s35 
8 9 s35 
9 8 7BPh
JAR3D SCFG/MRF model for IL_07300.2:
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 [9] // Initial node G963 - C994 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.005920700,0.042892868,0.006869810,0.113031849,0.000000000],[0.011260389,0.017890463,0.134015667,0.007991732,0.000000000],[0.006880836,0.473352674,0.001259882,0.014909433,0.000000000],[0.113114749,0.029325018,0.015190513,0.006093416,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair G963 - C994 cWW 
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [2] | Right Index [8] | Norm Constant [1.000000000000000] // Cluster node G964:U967 and U993:U993
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.013748369,0.119816711,0.013578679,0.093317534,0.000000000],[0.021353163,0.016649569,0.079603771,0.014822702,0.000000000],[0.013384072,0.079523629,0.003964907,0.040938747,0.000000000],[0.101704498,0.015772974,0.022441654,0.349379021,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U967 - U993 cWW 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.056782158,0.057669685,0.019735388,0.016478813,0.000000000],[0.071586160,0.068179769,0.004118188,0.059337231,0.000000000],[0.389215811,0.015449748,0.031090124,0.065799650,0.000000000],[0.021391896,0.055519563,0.004118188,0.063527626,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G964 - A966 cSH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion G965
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Right Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Left Index [6] | Right Index [7] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009933419,0.017038443,0.011544982,0.190528657,0.000000000],[0.020571967,0.008484264,0.242033011,0.013790371,0.000000000],[0.011692161,0.206400787,0.002129068,0.023556849,0.000000000],[0.191635263,0.013137326,0.027308888,0.010214543,0.000000000],[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 C968 - G992 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_07300.2:
> IL_07300.2 IL_4BPP_048 G  963 C  994
GGGAUC*GUC
> IL_07300.2 IL_3U5F_052 G  985 C 1016
GGGAUC*GUC
> IL_07300.2 IL_3U5F_025 C  443 G  461
CCAAUC*GGAG