Alignment of IL_67887.1 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
3

2
5
4
I

6
5


7
4
I

8
3

3
9
3
I

10
3

4
11
2
I

12
2

5
13
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_67887.1_Instance_1 IL_67887.1_IL_3RW6_003_A20_U41AGUAAU
IL_67887.1_Sequence_1 IL_67887.1_IL_3RW6_003_A20_U41AG*UAAUtrue94000.54
IL_67887.1_Instance_2 IL_67887.1_IL_4FAW_005_G128_U238GGUUGAU
IL_67887.1_Sequence_2 IL_67887.1_IL_4FAW_005_G128_U238GG*UUGAUtrue100000.00

Conserved interactions between motif group positions in IL_67887.1:
1 2 s35 
1 5 cWW 
2 3 cWW 
2 4 tSH 
2 5 s55 
3 5 s35 
4 5 s35 
JAR3D SCFG/MRF model for IL_67887.1:
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 [5] // Initial node A20 - U41 from junction 
BasepairNode | Deletion Probability [0.0000015195492620] | Pair Probability [[0.012875655,0.167362170,0.012690460,0.139544678,0.000000000],[0.017278970,0.010426425,0.115221913,0.012854497,0.000000000],[0.012509796,0.118823330,0.002800872,0.196378937,0.000000000],[0.122336675,0.013723253,0.019374350,0.025798019,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [1] | Right Index [5] // Basepair A20 - U41 cWW 
ClusterNode  | Deletion Probability [0.0000000006171744] | Num Left Bases [1] | Num Right Bases [2] | Left Index [2] | Right Index [4] | Norm Constant [0.316951872077325] // Cluster node G21:G21 and U38:A40
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.016500430,0.310288742,0.015571103,0.044672112,0.000000000],[0.014475176,0.011549597,0.038212544,0.015431970,0.000000000],[0.015226490,0.044298882,0.003453650,0.364972803,0.000000000],[0.037922120,0.017096803,0.015161977,0.035165601,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G21 - U38 cWW 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.073244666,0.074626455,0.002664993,0.188942478,0.000000000],[0.070262839,0.067908836,0.002664993,0.002664993,0.000000000],[0.086862504,0.002664993,0.212156020,0.069245779,0.000000000],[0.072228285,0.068532177,0.002664993,0.002664993,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G21 - A40 tSH 
Insertion    | Location [2] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000]// Insertion after nucleotide 3, position 2 in cluster node
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 [3] | Right Index [2] // New Initial node after Cluster
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_67887.1:
> IL_67887.1 IL_3RW6_003 A   20 U   41
AG*UAAU
> IL_67887.1 IL_4FAW_005 G  128 U  238
GG*UUGAU