Alignment of IL_39585.1 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
3

3
7
4
I

8
5

4
9
5
I

10
6

5
11
6
I

12
7


13
6
I

14
6

6
15
5
I

16
5

7
17
4
I

18
3

8
19
3
I

20
3

9
21
2
I

22
2

10
23
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_39585.1_Instance_1 IL_39585.1_IL_3V2F_098_U2636_G2782UUGAGCAAGAUGAG
IL_39585.1_Sequence_1 IL_39585.1_IL_3V2F_098_U_2636_G_2782UUGAG*CAAGAUGAGtrue73003.40
IL_39585.1_Instance_2 IL_39585.1_IL_4IOA_095_U2615_G2762UUGAGCAAGAUGAG
IL_39585.1_Sequence_2 IL_39585.1_IL_4IOA_095_U_2615_G_2762UUGAG*CAAGAUGAGtrue73003.40
IL_39585.1_Instance_3 IL_39585.1_IL_1S72_089_C2672_G2817CUGACGGAAAAGAG
IL_39585.1_Sequence_3 IL_39585.1_IL_1S72_089_C_2672_G_2817CUGAC*GGAAAAGAGtrue67004.14
IL_39585.1_Instance_4 IL_39585.1_IL_3V2F_071_U1851_G1891UCAAGCGAAG
IL_39585.1_Sequence_4 IL_39585.1_IL_3V2F_071_U_1851_G_1891UCAAG*CGAAGtrue100000.00
IL_39585.1_Instance_5 IL_39585.1_IL_4IOA_069_U1843_G1874UCAAGUGAAG
IL_39585.1_Sequence_5 IL_39585.1_IL_4IOA_069_U_1843_G_1874UCAAG*UGAAGtrue93000.92
IL_39585.1_Instance_6 IL_39585.1_IL_4IOA_050_C1389_G1368CGAUGCUAAG
IL_39585.1_Sequence_6 IL_39585.1_IL_4IOA_050_C_1389_G_1368CGAUG*CUAAGtrue67004.14

Conserved interactions between motif group positions in IL_39585.1:
1 2 s35 
1 10 cWW 
2 3 s35 
2 8 tWH 
2 9 tSH 
2 10 s55 
3 4 s35 
3 7 s33 
3 8 s55 
3 9 tSH 
4 5 s35 
4 7 tHS 
4 9 s55 
5 6 cWW 
5 7 s55 
6 7 s35 
8 9 s53 
8 10 s35 
9 10 s35 
4 7 6BR
JAR3D SCFG/MRF model for IL_39585.1:
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 [10] // Initial node U2636 - G2782 from junction 
BasepairNode | Deletion Probability [0.0000000082449969] | Pair Probability [[0.011568670,0.015004905,0.013717942,0.086563999,0.000000000],[0.210007908,0.013051939,0.116859137,0.015670913,0.000000000],[0.013991452,0.091895298,0.002952919,0.017566300,0.000000000],[0.091345969,0.014368361,0.272912695,0.012521592,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [0.493624023,0.004113534,0.004319210,0.493624023,0.004113534,0.000205677] | Right Letter Distribution [0.409090909,0.045454545,0.318181818,0.227272727,0.000000000] | Left Index [1] | Right Index [10] // Basepair U2636 - G2782 cWW 
ClusterNode  | Deletion Probability [0.0000000000425867] | Num Left Bases [2] | Num Right Bases [2] | Left Index [2] | Right Index [9] | Norm Constant [0.135108635236567] // Cluster node U2637:G2638 and A2776:A2778
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.022193440,0.004032174,0.068294143,0.004032174,0.000000000],[0.144395317,0.030088333,0.108454026,0.004032174,0.000000000],[0.031964102,0.004032174,0.042564995,0.024183430,0.000000000],[0.346043401,0.004032174,0.042578165,0.119079776,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U2637 - A2776 tWH 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.118423907,0.109714818,0.001277960,0.007504879,0.000000000],[0.140269246,0.096413576,0.001277960,0.001277960,0.000000000],[0.122838246,0.001277960,0.008044388,0.043009991,0.000000000],[0.232162706,0.113950484,0.001277960,0.001277960,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U2637 - A2778 tSH 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.211954656,0.114102715,0.001179443,0.005616359,0.000000000],[0.098760399,0.103515300,0.001179443,0.001179443,0.000000000],[0.146246221,0.001179443,0.005714155,0.098106004,0.000000000],[0.106402395,0.102505136,0.001179443,0.001179443,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2638 - A2778 tSH 
Insertion    | Location [3] | Length Distribution [0.497737557,0.497737557,0.004319210,0.000205677] | Letter Distribution [0.300000000,0.100000000,0.500000000,0.100000000,0.000000000]// Insertion after nucleotide 8, position 3 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 [4] | Right Index [7] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.143107073,0.122479494,0.173101272,0.122989924,0.000000000],[0.118256878,0.083202990,0.001347441,0.118428795,0.000000000],[0.001347441,0.001347441,0.009331305,0.001347441,0.000000000],[0.008716688,0.001347441,0.060405157,0.033243218,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [4] | Right Index [7] // Basepair A2639 - A2775 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010795257,0.065846457,0.011939594,0.162136419,0.000000000],[0.016688363,0.008619217,0.183721697,0.013216907,0.000000000],[0.011812838,0.216159781,0.002277618,0.086324791,0.000000000],[0.160516374,0.013801104,0.022111314,0.014032271,0.000000000],[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 [5] | Right Index [6] // Basepair G2640 - C2774 cWW 
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_39585.1:
> IL_39585.1 IL_3V2F_098 U 2636 G 2782
UUGAG*CAAGAUGAG
> IL_39585.1 IL_4IOA_095 U 2615 G 2762
UUGAG*CAAGAUGAG
> IL_39585.1 IL_1S72_089 C 2672 G 2817
CUGAC*GGAAAAGAG
> IL_39585.1 IL_3V2F_071 U 1851 G 1891
UCAAG*CGAAG
> IL_39585.1 IL_4IOA_069 U 1843 G 1874
UCAAG*UGAAG
> IL_39585.1 IL_4IOA_050 C 1389 G 1368
CGAUG*CUAAG