Alignment of IL_24982.5 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
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
4

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_24982.5_Instance_1 IL_24982.5_IL_3U5F_053_C990_G1014CGAAGCGUAG
IL_24982.5_Sequence_1 IL_24982.5_IL_3U5F_053_C990_G_1014CGAAG*CGUAGtrue97000.31
IL_24982.5_Instance_2 IL_24982.5_IL_4BPP_049_C968_G992CAAAGCGUAG
IL_24982.5_Sequence_2 IL_24982.5_IL_4BPP_049_C968_G992CAAAG*CGUAGtrue91000.93
IL_24982.5_Instance_3 IL_24982.5_IL_1FJG_033_C779_G803CAAACGGUAG
IL_24982.5_Sequence_3 IL_24982.5_IL_1FJG_033_C779_G803CAAAC*GGUAGtrue89001.23
IL_24982.5_Instance_4 IL_24982.5_IL_3U5F_035_U968_G631UCAAGCGUAG
IL_24982.5_Sequence_4 IL_24982.5_IL_3U5F_035_U968_G631UCAAG*CGUAGtrue95000.56
IL_24982.5_Instance_5 IL_24982.5_IL_4BPP_035_U946_G625UCAAGCGUAG
IL_24982.5_Sequence_5 IL_24982.5_IL_4BPP_035_U946_G625UCAAG*CGUAGtrue95000.56
IL_24982.5_Instance_6 IL_24982.5_IL_2AW7_040_C779_G803CAAACGGUAG
IL_24982.5_Sequence_6 IL_24982.5_IL_2AW7_040_C779_G803CAAAC*GGUAGtrue89001.23
IL_24982.5_Instance_7 IL_24982.5_IL_2AW7_030_U757_G584UCAGGCGCAG
IL_24982.5_Sequence_7 IL_24982.5_IL_2AW7_030_U757_G584UCAGG*CGCAGtrue80002.09
IL_24982.5_Instance_8 IL_24982.5_IL_1FJG_023_U757_G584UGAGGUGUAG
IL_24982.5_Sequence_8 IL_24982.5_IL_1FJG_023_U757_G584UGAGG*UGUAGtrue92000.87
IL_24982.5_Instance_9 IL_24982.5_IL_2QBG_052_C1357_G1374CGAGGCGUAG
IL_24982.5_Sequence_9 IL_24982.5_IL_2QBG_052_C_1357_G_1374CGAGG*CGUAGtrue97000.30
IL_24982.5_Instance_10 IL_24982.5_IL_1S72_023_C719_G709CGAGGCGCAG
IL_24982.5_Sequence_10 IL_24982.5_IL_1S72_023_C719_G709CGAGG*CGCAGtrue83001.84
IL_24982.5_Instance_11 IL_24982.5_IL_4IOA_051_U1370_G1387UGAGGCGCAG
IL_24982.5_Sequence_11 IL_24982.5_IL_4IOA_051_U_1370_G_1387UGAGG*CGCAGtrue86001.53
IL_24982.5_Instance_12 IL_24982.5_IL_1S72_055_U1639_G1546UCAACGGUCG
IL_24982.5_Sequence_12 IL_24982.5_IL_1S72_055_U_1639_G_1546UCAAC*GGUCGtrue89001.18
IL_24982.5_Instance_13 IL_24982.5_IL_3V2F_050_U1357_G1374UGAAGCGUAG
IL_24982.5_Sequence_13 IL_24982.5_IL_3V2F_050_U_1357_G_1374UGAAG*CGUAGtrue100000.00
IL_24982.5_Instance_14 IL_24982.5_IL_2QBG_058_U1513_G1478UGAGGUGUAG
IL_24982.5_Sequence_14 IL_24982.5_IL_2QBG_058_U_1513_G_1478UGAGG*UGUAGtrue92000.87
IL_24982.5_Instance_15 IL_24982.5_IL_2QWY_004_A46_U20AAAAGCGUAU
IL_24982.5_Sequence_15 IL_24982.5_IL_2QWY_004_A46_U20AAAAG*CGUAUtrue87001.37
IL_24982.5_Instance_16 IL_24982.5_IL_4IOA_026_C927_G875CGAAGUGUAG
IL_24982.5_Sequence_16 IL_24982.5_IL_4IOA_026_C927_G875CGAAG*UGUAGtrue89001.19

Conserved interactions between motif group positions in IL_24982.5:
1 2 s35 
1 10 cWW 
2 7 s33 
2 8 s33 
2 9 tSH 
2 10 s55 
3 4 s35 
3 8 tHW 
3 9 s55 
4 5 s35 
4 7 tHS 
4 8 s55 
5 6 cWW 
5 7 s55 
6 7 s35 
7 8 s35 
8 9 s35 
9 10 s35 
7 3 6BPh
2 8 6BPh
9 2 6BR
JAR3D SCFG/MRF model for IL_24982.5:
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 C990 - G1014 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.010090714,0.014463119,0.011862728,0.111472694,0.000000000],[0.148456487,0.010868877,0.173513261,0.013600691,0.000000000],[0.012073761,0.107968823,0.002496283,0.017487865,0.000000000],[0.105870687,0.012603264,0.235985582,0.011185164,0.000000000],[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 [1] | Right Index [10] // Basepair C990 - G1014 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.137769253,0.091987757,0.001095288,0.007668052,0.000000000],[0.146471273,0.106633920,0.001319392,0.001319392,0.000000000],[0.256993336,0.001930613,0.010231048,0.138556003,0.000000000],[0.049284353,0.047658021,0.000541150,0.000541150,0.000000000],[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 [2] | Right Index [9] // Basepair G991 - A1013 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.021617428,0.107604254,0.004245584,0.502765553,0.000000000],[0.004245584,0.033679913,0.004245584,0.004245584,0.000000000],[0.043285658,0.065999338,0.047545948,0.049058839,0.000000000],[0.004245584,0.004245584,0.022292533,0.080677030,0.000000000],[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 [3] | Right Index [8] // Basepair A992 - U1012 tHW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.031448730,0.031127007,0.294456641,0.032960893,0.000000000],[0.034877929,0.031675905,0.004217122,0.031579695,0.000000000],[0.000674008,0.000674008,0.297759431,0.000674008,0.000000000],[0.032388063,0.000674008,0.174138545,0.000674008,0.000000000],[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 A993 - G1011 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009977130,0.065408444,0.010976641,0.145413475,0.000000000],[0.015265187,0.007936705,0.182128792,0.012129373,0.000000000],[0.010862667,0.246003737,0.002105170,0.101876728,0.000000000],[0.143870840,0.012657470,0.020116733,0.013270908,0.000000000],[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 G994 - C1010 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_24982.5:
> IL_24982.5 IL_3U5F_053 C  990 G 1014
CGAAG*CGUAG
> IL_24982.5 IL_4BPP_049 C  968 G  992
CAAAG*CGUAG
> IL_24982.5 IL_1FJG_033 C  779 G  803
CAAAC*GGUAG
> IL_24982.5 IL_3U5F_035 U  968 G  631
UCAAG*CGUAG
> IL_24982.5 IL_4BPP_035 U  946 G  625
UCAAG*CGUAG
> IL_24982.5 IL_2AW7_040 C  779 G  803
CAAAC*GGUAG
> IL_24982.5 IL_2AW7_030 U  757 G  584
UCAGG*CGCAG
> IL_24982.5 IL_1FJG_023 U  757 G  584
UGAGG*UGUAG
> IL_24982.5 IL_2QBG_052 C 1357 G 1374
CGAGG*CGUAG
> IL_24982.5 IL_1S72_023 C  719 G  709
CGAGG*CGCAG
> IL_24982.5 IL_4IOA_051 U 1370 G 1387
UGAGG*CGCAG
> IL_24982.5 IL_1S72_055 U 1639 G 1546
UCAAC*GGUCG
> IL_24982.5 IL_3V2F_050 U 1357 G 1374
UGAAG*CGUAG
> IL_24982.5 IL_2QBG_058 U 1513 G 1478
UGAGG*UGUAG
> IL_24982.5 IL_2QWY_004 A   46 U   20
AAAAG*CGUAU
> IL_24982.5 IL_4IOA_026 C  927 G  875
CGAAG*UGUAG