Alignment of IL_31663.1 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
3
I

6
4

3
7
4
I

8
4

4
9
5
I

10
6


11
5
I

12
4

5
13
3
I

14
3

6
15
2
I

16
2

7
17
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_31663.1_Instance_1 IL_31663.1_IL_1S72_072_G2090_C2654GGGGUAC
IL_31663.1_Sequence_1 IL_31663.1_IL_1S72_072_G_2090_C_2654GGGG*UACtrue100000.00
IL_31663.1_Instance_2 IL_31663.1_IL_3U5H_096_G2391_C2988GCGGUAC
IL_31663.1_Sequence_2 IL_31663.1_IL_3U5H_096_G_2391_C_2988GCGG*UACtrue91000.89
IL_31663.1_Instance_3 IL_31663.1_IL_4IOA_061_G1503_C1517GGUCAUAC
IL_31663.1_Sequence_3 IL_31663.1_IL_4IOA_061_G_1503_C_1517GGUCA*UACtrue72002.62
IL_31663.1_Instance_4 IL_31663.1_IL_4A1B_089_G2201_C2232GAAUGCGC
IL_31663.1_Sequence_4 IL_31663.1_IL_4A1B_089_G_2201_C_2232GAAUG*CGCtrue84001.54

Conserved interactions between motif group positions in IL_31663.1:
1 2 s35 
1 7 cWW 
2 3 s35 
2 6 cWW 
3 4 cSH 
4 5 cWW 
4 6 s55 
5 6 s35 
6 7 s35 
JAR3D SCFG/MRF model for IL_31663.1:
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 [7] // Initial node G2090 - C2654 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009999033,0.020370037,0.011577394,0.189754219,0.000000000],[0.016871198,0.008244913,0.204374808,0.013008374,0.000000000],[0.011431659,0.249278495,0.002108170,0.027040831,0.000000000],[0.188658474,0.013655008,0.023325621,0.010301767,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair G2090 - C2654 cWW 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.073099660,0.013566290,0.254261759,0.019747840,0.000000000],[0.109871186,0.008445315,0.022286642,0.033898979,0.000000000],[0.267935052,0.020718493,0.003381916,0.014787046,0.000000000],[0.021584926,0.032759197,0.092206740,0.011448958,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [6] // Basepair G2091 - A2653 cWW 
ClusterNode  | Deletion Probability [0.0000000083639467] | Num Left Bases [2] | Num Right Bases [1] | Left Index [3] | Right Index [5] | Norm Constant [0.304182144042249] // Cluster node G2092:G2093 and U2652:U2652
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.012859560,0.163244755,0.012935470,0.131630069,0.000000000],[0.016240342,0.010006059,0.116966177,0.013339541,0.000000000],[0.012725945,0.131450502,0.002747355,0.202165325,0.000000000],[0.116454854,0.014335429,0.019049889,0.023848728,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2093 - U2652 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.015344910,0.030433764,0.296966426,0.058619023,0.000000000],[0.022451578,0.020314918,0.003176647,0.019513038,0.000000000],[0.020835054,0.023314026,0.321313666,0.024246955,0.000000000],[0.095511653,0.026522551,0.003176647,0.018259145,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2092 - G2093 cSH 
Insertion    | Location [1] | Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000]// Insertion after nucleotide 3, position 1 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 [5] | Right Index [4] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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_31663.1:
> IL_31663.1 IL_1S72_072 G 2090 C 2654
GGGG*UAC
> IL_31663.1 IL_3U5H_096 G 2391 C 2988
GCGG*UAC
> IL_31663.1 IL_4IOA_061 G 1503 C 1517
GGUCA*UAC
> IL_31663.1 IL_4A1B_089 G 2201 C 2232
GAAUG*CGC