Alignment of IL_46174.3 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
2
I

12
2

6
13
3
I

14
4

7
15
4
I

16
5


17
4
I

18
4

8
19
3
I

20
2

9
21
2
I

22
2

10
23
2
I

24
2

11
25
2
I

26
2

12
27
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_46174.3_Instance_1 IL_46174.3,IL_8CRE_408,U346_A314UUUCAACGUAUCAA
IL_46174.3_Sequence_1 IL_46174.38CRE_U346_A314UUUCAACG*UAUCAAtrue100000.08
IL_46174.3_Instance_2 IL_46174.3,IL_8P9A_391,U348_A316UUUCAACGUAUCAA
IL_46174.3_Sequence_2 IL_46174.38P9A_U348_A316UUUCAACG*UAUCAAtrue100000.08
IL_46174.3_Instance_3 IL_46174.3,IL_5J7L_014,C277_G247CGACGAUCGAUUAG
IL_46174.3_Sequence_3 IL_46174.35J7L_C277_G247CGACGAUC*GAUUAGtrue93001.42
IL_46174.3_Instance_4 IL_46174.3,IL_4LFB_011,C277_G247CGACGACGCAUCAG
IL_46174.3_Sequence_4 IL_46174.34LFB_C277_G247CGACGACG*CAUCAGtrue100000.00
IL_46174.3_Instance_5 IL_46174.3,IL_3RW6_002,C43_G18CAAUGACGUAAGACAG
IL_46174.3_Sequence_5 IL_46174.33RW6_C43_G18CAAUGACG*UAAGACAGtrue74005.11

Conserved interactions between motif group positions in IL_46174.3:
1 2 s35 
1 12 cWW 
2 11 tSS 
2 12 s55 
3 4 s55 
3 11 s53 
4 9 s33 
4 11 tSH 
5 6 s35 
5 9 tHW 
5 11 s55 
5 12 tSS 
6 7 s35 
6 9 s55 
6 10 cWW 
7 8 cWW 
7 10 s55 
8 10 s35 
9 10 s53 
9 11 s35 
6 5 7BPh
9 11 2BPh
11 2 6BR
11 4 6BR
5 11 6BR
9 11 2BR
JAR3D SCFG/MRF model for IL_46174.3:
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 [12] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000000000000029021405463065428485660525039999] | Num Left Bases [6] | Num Right Bases [4] | Left Index [1] | Right Index [12] | Norm Constant [0.117008820568612] // Cluster node 8CRE|1|CM|U|346:8CRE|1|CM|C|352 and 8CRE|1|CM|A|310:8CRE|1|CM|A|314
Interaction  | Interacting Bases [5,7] | Pair Probability [[0.803231417,0.018844492,0.002201613,0.009948471,0.000000000],[0.001511225,0.001868573,0.001090739,0.000440323,0.000000000],[0.133317176,0.000440323,0.016185120,0.002110466,0.000000000],[0.001511225,0.000440323,0.004713074,0.002145443,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|A|351 - 8CRE|1|CM|A|310 tHW 
Interaction  | Interacting Bases [6,8] | Pair Probability [[0.002258967,0.017330000,0.003007505,0.005237479,0.000000000],[0.069815701,0.643098415,0.029091658,0.021683181,0.000000000],[0.003084620,0.004976126,0.001072788,0.006082084,0.000000000],[0.011408774,0.008425958,0.013315724,0.160111018,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|C|352 - 8CRE|1|CM|C|312 cWW 
Interaction  | Interacting Bases [2,9] | Pair Probability [[0.260468194,0.048672574,0.049381382,0.047608366,0.000000000],[0.094585337,0.018917067,0.021849086,0.018917067,0.000000000],[0.184654794,0.018917067,0.021299188,0.044345720,0.000000000],[0.113632956,0.018917067,0.018917067,0.018917067,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|U|347 - 8CRE|1|CM|A|313 tSS 
Interaction  | Interacting Bases [4,9] | Pair Probability [[0.222551838,0.025457994,0.000451073,0.002385117,0.000000000],[0.201478893,0.030653792,0.000451073,0.000451073,0.000000000],[0.238483019,0.000451073,0.002916006,0.026484733,0.000000000],[0.206969977,0.039912193,0.000451073,0.000451073,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|A|350 - 8CRE|1|CM|A|313 tSH 
Interaction  | Interacting Bases [1,10] | Pair Probability [[0.009068947,0.016785052,0.010240914,0.192150589,0.000000000],[0.020383894,0.009481442,0.226915719,0.012329706,0.000000000],[0.010320187,0.193924261,0.002012365,0.022633063,0.000000000],[0.215849209,0.011775691,0.036312554,0.009816407,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|U|346 - 8CRE|1|CM|A|314 cWW 
Interaction  | Interacting Bases [5,10] | Pair Probability [[0.290766161,0.211686976,0.246332931,0.200749936,0.000000000],[0.000435523,0.000435523,0.004512991,0.000435523,0.000000000],[0.003414902,0.000435523,0.003556849,0.035495069,0.000000000],[0.000435523,0.000435523,0.000435523,0.000435523,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|A|351 - 8CRE|1|CM|A|314 tSS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.357142857,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8CRE|1|CM|U|348
Insertion    | Location [3] | Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Letter Distribution [0.071428571,0.642857143,0.071428571,0.214285714,0.000000000]// Insertion after nucleotide 3, position 3 in cluster node
Insertion    | Location [7] | Length Distribution [0.007839294,0.783929446,0.009799118,0.196374326,0.001959824,0.000097991] | Letter Distribution [0.277777778,0.055555556,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 9, position 7 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 [7] | Right Index [8] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.012976294,0.180303759,0.012628659,0.127035366,0.000000000],[0.015259622,0.011195867,0.110804474,0.013656246,0.000000000],[0.012449884,0.113794944,0.002702943,0.227432330,0.000000000],[0.099055733,0.014431233,0.018151332,0.028121313,0.000000000],[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 [7] | Right Index [8] // Basepair G353 - U309 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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_46174.3:
> IL_46174.3  8CRE U  346 A  314
UUUCAACG*UAUCAA
> IL_46174.3  8P9A U  348 A  316
UUUCAACG*UAUCAA
> IL_46174.3  5J7L C  277 G  247
CGACGAUC*GAUUAG
> IL_46174.3  4LFB C  277 G  247
CGACGACG*CAUCAG
> IL_46174.3  3RW6 C   43 G   18
CAAUGACG*UAAGACAG