Alignment of IL_22564.1 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
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
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distance
Alignment
score
deficit
IL_22564.1_Instance_1 IL_22564.1,IL_8CRE_463,G1474_C1505GUAUAAGCGAAAUC
IL_22564.1_Sequence_1 IL_22564.18CRE_G_1474_C_1505GUAUAAGC*GAAAUCtrue91001.56
IL_22564.1_Instance_2 IL_22564.1,IL_8P9A_449,G1488_C1518GUCUAACGUAAUC
IL_22564.1_Sequence_2 IL_22564.18P9A_G_1488_C_1518GUCUAAC*GUAAUCtrue100000.00

Conserved interactions between motif group positions in IL_22564.1:
1 6 tSS 
1 8 s33 
1 9 cWW 
2 3 perp 
2 5 s35 
2 6 s33 
2 7 s53 
3 4 s35 
4 5 cSH 
5 6 cWW 
6 8 cSS 
8 2 6BPh
JAR3D SCFG/MRF model for IL_22564.1:
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 [0.000000000000000000000000000000075522783116710514280331600352] | Num Left Bases [5] | Num Right Bases [4] | Left Index [1] | Right Index [9] | Norm Constant [0.004618463055059] // Cluster node 8CRE|1|CM|G|1474:8CRE|1|CM|C|1481 and 8CRE|1|CM|G|1500:8CRE|1|CM|C|1505
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.020814325,0.017422103,0.019901827,0.012513985,0.000000000],[0.002436905,0.002436905,0.214331865,0.002436905,0.000000000],[0.236896108,0.002436905,0.263298345,0.195326202,0.000000000],[0.002436905,0.002436905,0.002436905,0.002436905,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|G|1474 - 8CRE|1|CM|G|1500 tSS 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|C|1481 - 8CRE|1|CM|G|1500 cWW 
Interaction  | Interacting Bases [1,9] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|G|1474 - 8CRE|1|CM|C|1505 cWW 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.082210046,0.097234592,0.033420247,0.052352316,0.000000000],[0.080415734,0.079793580,0.031205189,0.035250447,0.000000000],[0.035590367,0.041009111,0.082216806,0.077287923,0.000000000],[0.082398445,0.081776461,0.031205189,0.076633547,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|G|1480 - 8CRE|1|CM|C|1481 cSH 
Interaction  | Interacting Bases [6,8] | Pair Probability [[0.186693611,0.024987054,0.025580639,0.023621300,0.000000000],[0.193995912,0.027238031,0.001093673,0.003725525,0.000000000],[0.221428767,0.001117795,0.002478354,0.019882187,0.000000000],[0.190424981,0.025084591,0.025283684,0.027363897,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|G|1500 - 8CRE|1|CM|A|1502 cSS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8CRE|1|CM|U|1475
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8CRE|1|CM|A|1478
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 8CRE|1|CM|A|1501
Insertion    | Location [2] | Length Distribution [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.250000000,0.250000000,0.083333333,0.416666667,0.000000000]// Insertion after nucleotide 2, position 2 in cluster node
Insertion    | Location [3] | Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 3, position 3 in cluster node
Insertion    | Location [8] | Length Distribution [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.416666667,0.083333333,0.083333333,0.416666667,0.000000000]// Insertion after nucleotide 8, position 8 in cluster node
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 [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_22564.1:
> IL_22564.1  8CRE G 1474 C 1505
GUAUAAGC*GAAAUC
> IL_22564.1  8P9A G 1488 C 1518
GUCUAAC*GUAAUC