Alignment of IL_25573.1 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
2
I

10
2

5
11
3
I

12
4

6
13
4
I

14
5


15
4
I

16
4

7
17
3
I

18
2

8
19
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_25573.1_Instance_1 IL_25573.1,IL_1F1T_003,G23_C10GGUAACGAC
IL_25573.1_Sequence_1 IL_25573.11F1T_G23_C10GGUAAC*GACtrue100000.00

Conserved interactions between motif group positions in IL_25573.1:
1 5 tSW 
1 7 s33 
1 8 cWW 
4 5 s35 
5 6 s35 
6 7 cWW 
7 8 s35 
3 6 6BPh
6 1 7BR
5 3 7BR
8 7 7BR
JAR3D SCFG/MRF model for IL_25573.1:
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
ClusterNode  | Deletion Probability [0.000000000000015625000000000002841172490091166211760239940914] | Num Left Bases [5] | Num Right Bases [1] | Left Index [1] | Right Index [8] | Norm Constant [0.258204492640432] // Cluster node 1F1T|1|A|G|23:1F1T|1|A|A|27 and 1F1T|1|A|C|10:1F1T|1|A|C|10
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.004841606,0.050416664,0.005513298,0.100138349,0.000000000],[0.008504413,0.023738407,0.100986868,0.006607555,0.000000000],[0.005452069,0.529512277,0.001039223,0.013313184,0.000000000],[0.098856770,0.034290020,0.011669605,0.005119692,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1F1T|1|A|G|23 - 1F1T|1|A|C|10 cWW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.207393546,0.041279986,0.000515549,0.002492898,0.000000000],[0.241220078,0.002273219,0.000515549,0.002061159,0.000000000],[0.267675690,0.000515549,0.000515549,0.001690660,0.000000000],[0.223077762,0.002240557,0.004056544,0.002475704,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1F1T|1|A|G|23 - 1F1T|1|A|A|27 tSW 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 1F1T|1|A|G|24
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.833333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 1F1T|1|A|5BU|25
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 1F1T|1|A|A|26
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [6] | Right Index [7] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.004741436,0.008502533,0.005450864,0.098834917,0.000000000],[0.050405519,0.024145075,0.529397411,0.034282440,0.000000000],[0.005512079,0.100964543,0.001038993,0.011667026,0.000000000],[0.100116212,0.006606094,0.013310241,0.005024617,0.000000000],[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 C28 - G8 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_25573.1:
> IL_25573.1  1F1T G   23 C   10
GGUAAC*GAC