Alignment of HL_19870.4 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
6

6
13
6
I

14
6

7
15
5
I

16
5

8
17
4
I

18
4

9
19
3
I

20
3

10
21
2
I

22
2

11
23
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_19870.4_Instance_1 HL_19870.4_HL_4WF9_050_C2291_G2303CUAAAAGGUAACG
HL_19870.4_Sequence_1 HL_19870.4_HL_4WF9_050_C_2291_G_2303CUAAAAGGUAACGtrue100000.00
HL_19870.4_Instance_2 HL_19870.4_HL_4Y4O_157_C2264_G2276CUAAAAGGUAACG
HL_19870.4_Sequence_2 HL_19870.4_HL_4Y4O_157_C_2264_G_2276CUAAAAGGUAACGtrue100000.00
HL_19870.4_Instance_3 HL_19870.4_HL_5J7L_187_C2264_G2276CUAAAGAGUAACG
HL_19870.4_Sequence_3 HL_19870.4_HL_5J7L_187_C_2264_G_2276CUAAAGAGUAACGtrue89002.20
HL_19870.4_Instance_4 HL_19870.4_HL_4V9F_056_C2298_G2310CGAAAAGAUAUCG
HL_19870.4_Sequence_4 HL_19870.4_HL_4V9F_056_C_2298_G_2310CGAAAAGAUAUCGtrue95000.97
HL_19870.4_Instance_5 HL_19870.4_HL_7A0S_053_C2243_G2255CCAAAAUGUAACG
HL_19870.4_Sequence_5 HL_19870.4_HL_7A0S_053_C_2243_G_2255CCAAAAUGUAACGtrue92001.51
HL_19870.4_Instance_6 HL_19870.4_HL_5TBW_055_U2633_G2645UUAAACGAUAACG
HL_19870.4_Sequence_6 HL_19870.4_HL_5TBW_055_U_2633_G_2645UUAAACGAUAACGtrue87002.66

Conserved interactions between motif group positions in HL_19870.4:
1 2 s35 
1 11 cWW 
2 3 s33 
2 10 tSH 
2 11 s55 
3 4 s53 
3 8 s53 
3 9 tHH 
4 8 tWW 
5 6 s35 
6 7 s35 
7 8 s35 
9 10 s35 
10 11 s35 
3 9 6BPh
JAR3D SCFG/MRF model for HL_19870.4:
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 [11] // Initial node C2291 - G2303 from junction 
BasepairNode | Deletion Probability [0.0000001231336240] | Pair Probability [[0.009450884,0.015956080,0.011081266,0.165384558,0.000000000],[0.064779646,0.012271176,0.221537108,0.013630044,0.000000000],[0.011230126,0.168795395,0.002205978,0.021170298,0.000000000],[0.175296480,0.013008887,0.083924597,0.010277478,0.000000000],[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 [0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.062500000,0.812500000,0.062500000,0.062500000,0.000000000] | Left Index [1] | Right Index [11] // Basepair C2291 - G2303 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.112258085,0.084762344,0.001522367,0.007953908,0.000000000],[0.119230564,0.096930765,0.001522367,0.001522367,0.000000000],[0.135910265,0.001522367,0.010001683,0.123254686,0.000000000],[0.180699689,0.119863808,0.001522367,0.001522367,0.000000000],[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 [10] // Basepair U2292 - A2301 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.417171827,0.289668157,0.017287202,0.017637068,0.000000000],[0.067920990,0.000772046,0.065817481,0.007336049,0.000000000],[0.003849208,0.064976341,0.001927026,0.000772046,0.000000000],[0.005243791,0.038076678,0.000772046,0.000772046,0.000000000],[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 [9] // Basepair A2293 - A2300 tHH 
BasepairNode | Deletion Probability [0.0000001231336240] | Pair Probability [[0.016557184,0.040914681,0.003463595,0.402963250,0.000000000],[0.016259194,0.037312069,0.014424190,0.040003847,0.000000000],[0.003463595,0.017168579,0.016577471,0.277450101,0.000000000],[0.039566434,0.033214493,0.017074679,0.023586638,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Left Letter Distribution [0.812500000,0.062500000,0.062500000,0.062500000,0.000000000] | 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 [8] // Basepair A2294 - U2299 tWW 
HairpinNode  | Num Bases [3] | Left Index [5] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node A2296:G2298
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.562500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.187500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2296
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.187500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.562500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.187500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2297
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.562500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2298
Sequences of instances from HL_19870.4:
> HL_19870.4 HL_4WF9_050 C 2291 G 2303
CUAAAAGGUAACG
> HL_19870.4 HL_4Y4O_157 C 2264 G 2276
CUAAAAGGUAACG
> HL_19870.4 HL_5J7L_187 C 2264 G 2276
CUAAAGAGUAACG
> HL_19870.4 HL_4V9F_056 C 2298 G 2310
CGAAAAGAUAUCG
> HL_19870.4 HL_7A0S_053 C 2243 G 2255
CCAAAAUGUAACG
> HL_19870.4 HL_5TBW_055 U 2633 G 2645
UUAAACGAUAACG