Alignment of IL_06549.2 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
4


7
3
I

8
3

3
9
2
I

10
2

4
11
1
I


In
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Full
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Interior
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Alignment
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IL_06549.2_Instance_1 IL_06549.2,IL_8P9A_261,G907_C923GGGUAAUC
IL_06549.2_Sequence_1 IL_06549.28P9A_G907_C923GGG*UAAUCtrue99000.09
IL_06549.2_Instance_2 IL_06549.2,IL_8CRE_036,G903_C919GGGUAAUC
IL_06549.2_Sequence_2 IL_06549.28CRE_G903_C919GGG*UAAUCtrue99000.09
IL_06549.2_Instance_3 IL_06549.2,IL_7A0S_021,G788_C804GGAUAACC
IL_06549.2_Sequence_3 IL_06549.27A0S_G788_C804GGA*UAACCtrue95000.51
IL_06549.2_Instance_4 IL_06549.2,IL_5J7L_265,G775_C791GGGCAAUC
IL_06549.2_Sequence_4 IL_06549.25J7L_G775_C791GGG*CAAUCtrue100000.00
IL_06549.2_Instance_5 IL_06549.2,IL_9DFE_021,G775_C791GGAUAACC
IL_06549.2_Sequence_5 IL_06549.29DFE_G775_C791GGA*UAACCtrue95000.51
IL_06549.2_Instance_6 IL_06549.2,IL_4WF9_027,G820_C836GCGCAAUC
IL_06549.2_Sequence_6 IL_06549.24WF9_G820_C836GCG*CAAUCtrue87001.30

Conserved interactions between motif group positions in IL_06549.2:
1 2 s55 
1 3 s53 
1 4 cWW 
2 3 cWW 
3 4 s33
JAR3D SCFG/MRF model for IL_06549.2:
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 [4] // Initial node
BasepairNode | Deletion Probability [0.0000000000000155] | Pair Probability [[0.009366383,0.019506822,0.010665810,0.193723744,0.000000000],[0.016452306,0.009184679,0.195365254,0.012782718,0.000000000],[0.010547361,0.257647718,0.002010439,0.025755166,0.000000000],[0.191244451,0.013267227,0.022575563,0.009904357,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Left Letter Distribution [0.062500000,0.187500000,0.687500000,0.062500000,0.000000000] | Right Length Distribution [0.000000000,0.000000000,0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.625000000,0.125000000,0.025000000,0.225000000,0.000000000] | Left Index [1] | Right Index [4] // Basepair G907 - C923 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.011180369,0.108790153,0.011327798,0.176043740,0.000000000],[0.015504778,0.010236733,0.139087080,0.012204009,0.000000000],[0.011183739,0.162301137,0.002365509,0.148586931,0.000000000],[0.138356324,0.013006699,0.019524802,0.020300198,0.000000000],[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 [2] | Right Index [3] // Basepair G909 - U919 cWW 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | 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_06549.2:
> IL_06549.2  8P9A G  907 C  923
GGG*UAAUC
> IL_06549.2  8CRE G  903 C  919
GGG*UAAUC
> IL_06549.2  7A0S G  788 C  804
GGA*UAACC
> IL_06549.2  5J7L G  775 C  791
GGG*CAAUC
> IL_06549.2  9DFE G  775 C  791
GGA*UAACC
> IL_06549.2  4WF9 G  820 C  836
GCG*CAAUC