Alignment of IL_66997.2 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
2

2
5
2
I

6
2

3
7
3
I

8
4

4
9
5
I

10
8

5
11
8
I

12
9


13
8
I

14
8

6
15
7
I

16
6

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_66997.2_Instance_1 IL_66997.2,IL_4YAZ_005,G77_C7GAAAUACAC
IL_66997.2_Sequence_1 IL_66997.24YAZ_G77_C7GAAAU*ACACtrue97000.38
IL_66997.2_Instance_2 IL_66997.2,IL_5J7L_013,G203_C214GGACCGGC
IL_66997.2_Sequence_2 IL_66997.25J7L_G203_C214GGACC*GGCtrue100000.00

Conserved interactions between motif group positions in IL_66997.2:
1 2 cSH 
1 8 cWW 
2 3 s35 
3 4 s35 
3 8 cWS 
4 5 s55 
5 6 cWW 
6 7 s35 
7 8 s35 
8 7 7BPh
JAR3D SCFG/MRF model for IL_66997.2:
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 [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [1] | Right Index [8] | Norm Constant [0.150830715907617] // Cluster node 4YAZ|1|R|G|77:4YAZ|1|R|A|79 and 4YAZ|1|R|C|7:4YAZ|1|R|C|7
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.003823887,0.055746509,0.004354386,0.079088977,0.000000000],[0.006716761,0.026247934,0.079759134,0.005218628,0.000000000],[0.004306029,0.594150318,0.000820775,0.010514714,0.000000000],[0.078076789,0.037915021,0.009216620,0.004043518,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4YAZ|1|R|G|77 - 4YAZ|1|R|C|7 cWW 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.072613517,0.661332808,0.072526432,0.071135383,0.000000000],[0.007052045,0.043817479,0.000789426,0.006101741,0.000000000],[0.006592112,0.005525984,0.019547772,0.003493111,0.000000000],[0.002859431,0.021370678,0.002432038,0.002810043,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4YAZ|1|R|A|79 - 4YAZ|1|R|C|7 cWS 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.051095468,0.056684490,0.007186864,0.119586646,0.000000000],[0.051807891,0.110499726,0.001396703,0.086880833,0.000000000],[0.102035962,0.001396703,0.074683770,0.106765195,0.000000000],[0.052960781,0.060245256,0.001396703,0.115377010,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4YAZ|1|R|G|77 - 4YAZ|1|R|A|78 cSH 
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // Initial node 4YAZ|1|R|A|80 - 4YAZ|1|R|A|6 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [4] | Right Index [7] // Fixed node on left for 4YAZ|1|R|C|7
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000] | Position [2] | Left Index [5] | Right Index [7] // Fixed node on right for 4YAZ|1|R|A|79
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Left Index [5] | Right Index [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009285457,0.017323068,0.010436779,0.197555258,0.000000000],[0.021160175,0.009772202,0.212782490,0.012417770,0.000000000],[0.010508004,0.198766713,0.002067002,0.023256875,0.000000000],[0.212699647,0.011830790,0.040032900,0.010104868,0.000000000],[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 [5] | Right Index [6] // Basepair U81 - A4 cWW 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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_66997.2:
> IL_66997.2  4YAZ G   77 C    7
GAAAU*ACAC
> IL_66997.2  5J7L G  203 C  214
GGACC*GGC