Alignment of IL_26222.2 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
2
I

8
2

4
9
2
I

10
2

5
11
3
I

12
4


13
3
I

14
2

6
15
2
I

16
2

7
17
2
I

18
2

8
19
2
I

20
2

9
21
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_26222.2_Instance_1 IL_26222.2,IL_4WF9_033,G909_C957GCACUAAAC
IL_26222.2_Sequence_1 IL_26222.24WF9_G909_C957GCACU*AAACtrue100000.00
IL_26222.2_Instance_2 IL_26222.2,IL_7A0S_029,G877_C924GCACUAAAC
IL_26222.2_Sequence_2 IL_26222.27A0S_G877_C924GCACU*AAACtrue100000.00
IL_26222.2_Instance_3 IL_26222.2,IL_9DFE_028,G864_C912GCACUAAAC
IL_26222.2_Sequence_3 IL_26222.29DFE_G864_C912GCACU*AAACtrue100000.00
IL_26222.2_Instance_4 IL_26222.2,IL_5J7L_272,G864_C912GCACUAAAC
IL_26222.2_Sequence_4 IL_26222.25J7L_G864_C912GCACU*AAACtrue100000.00
IL_26222.2_Instance_5 IL_26222.2,IL_8P9A_268,G999_C1049GCGAAUAAAC
IL_26222.2_Sequence_5 IL_26222.28P9A_G999_C_1049GCGAAU*AAACtrue89001.67
IL_26222.2_Instance_6 IL_26222.2,IL_8CRE_043,G995_C1045GCGAAUAAAC
IL_26222.2_Sequence_6 IL_26222.28CRE_G995_C_1045GCGAAU*AAACtrue89001.67

Conserved interactions between motif group positions in IL_26222.2:
1 2 s35 
1 3 tSW 
1 9 cWW 
2 3 s53 
2 4 cSH 
2 6 tWH 
3 4 s35 
4 5 s35 
4 9 cWS 
5 6 cWW 
6 9 s35 
7 8 s35 
9 7 7BPh
JAR3D SCFG/MRF model for IL_26222.2:
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 [9] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000000319870323534092682713332759317165949125] | Num Left Bases [5] | Num Right Bases [4] | Left Index [1] | Right Index [9] | Norm Constant [0.004461019866877] // Cluster node 4WF9|1|X|G|909:4WF9|1|X|U|913 and 4WF9|1|X|A|954:4WF9|1|X|C|957
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.029558166,0.003453297,0.098788114,0.003453297,0.000000000],[0.401933476,0.025159497,0.003453297,0.003453297,0.000000000],[0.003453297,0.012056445,0.031053956,0.031831792,0.000000000],[0.034727452,0.003453297,0.015526095,0.298645225,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|C|910 - 4WF9|1|X|A|954 tWH 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.008693416,0.016882694,0.009536121,0.188912817,0.000000000],[0.021212105,0.009460668,0.189548413,0.010628111,0.000000000],[0.009554720,0.187122556,0.001967108,0.022177826,0.000000000],[0.253314615,0.009983070,0.051283436,0.009722321,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|U|913 - 4WF9|1|X|A|954 cWW 
Interaction  | Interacting Bases [1,9] | Pair Probability [[0.003679589,0.053642867,0.004190070,0.076104487,0.000000000],[0.006463298,0.025257446,0.076749356,0.005021698,0.000000000],[0.004143537,0.609465400,0.000789802,0.010117932,0.000000000],[0.075130495,0.036484266,0.008868823,0.003890933,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|G|909 - 4WF9|1|X|C|957 cWW 
Interaction  | Interacting Bases [4,9] | Pair Probability [[0.029105501,0.246113907,0.028691084,0.029298906,0.000000000],[0.057189470,0.460197441,0.000859964,0.058134750,0.000000000],[0.007437840,0.006019749,0.013027246,0.003560805,0.000000000],[0.004581468,0.047962116,0.003577953,0.004241800,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|C|912 - 4WF9|1|X|C|957 cWS 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.144299127,0.143607793,0.001793530,0.008672475,0.000000000],[0.167834763,0.007908239,0.001793530,0.007170510,0.000000000],[0.321720112,0.001793530,0.001793530,0.005881590,0.000000000],[0.155211804,0.007794610,0.014112197,0.008612658,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|G|909 - 4WF9|1|X|A|911 tSW 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.074081710,0.074659521,0.004122880,0.073037140,0.000000000],[0.138620443,0.123994722,0.000862589,0.060014733,0.000000000],[0.063494280,0.000862589,0.075730924,0.078233932,0.000000000],[0.075870334,0.075861931,0.000862589,0.079689684,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|C|910 - 4WF9|1|X|C|912 cSH 
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.812500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 4WF9|1|X|A|955
Interaction  | Interacting Bases [8,8] | Pair Probability [[0.812500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 4WF9|1|X|A|956
Insertion    | Location [2] | Length Distribution [0.661815186,0.335026775,0.003020733,0.000137306] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000]// Insertion after nucleotide 2, position 2 in cluster node
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [5] // New Initial node after Cluster
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_26222.2:
> IL_26222.2  4WF9 G  909 C  957
GCACU*AAAC
> IL_26222.2  7A0S G  877 C  924
GCACU*AAAC
> IL_26222.2  9DFE G  864 C  912
GCACU*AAAC
> IL_26222.2  5J7L G  864 C  912
GCACU*AAAC
> IL_26222.2  8P9A G  999 C 1049
GCGAAU*AAAC
> IL_26222.2  8CRE G  995 C 1045
GCGAAU*AAAC