Alignment of HL_20811.4 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
3
I

8
3

4
9
2
I

10
2

5
11
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
HL_20811.4_Instance_1 HL_20811.4,HL_1QF6_001,C13_G22CAGUUGGUAG
HL_20811.4_Sequence_1 HL_20811.41QF6_C13_G22CAGUUGGUAGtrue98000.25
HL_20811.4_Instance_2 HL_20811.4,HL_7MRL_001,C13_G22CAGUCGGUAG
HL_20811.4_Sequence_2 HL_20811.47MRL_C13_G22CAGUCGGUAGtrue87001.35
HL_20811.4_Instance_3 HL_20811.4,HL_5AXM_001,C13_G22CAGUUGGGAG
HL_20811.4_Sequence_3 HL_20811.45AXM_C13_G22CAGUUGGGAGtrue99000.14
HL_20811.4_Instance_4 HL_20811.4,HL_5B63_003,C913_G923CAAUUGGAUAG
HL_20811.4_Sequence_4 HL_20811.45B63_C913_G923CAAUUGGAUAGtrue35006.75
HL_20811.4_Instance_5 HL_20811.4,HL_7LYF_001,C13_G22CAGUCGGUAG
HL_20811.4_Sequence_5 HL_20811.47LYF_C13_G22CAGUCGGUAGtrue87001.35
HL_20811.4_Instance_6 HL_20811.4,HL_2AZX_004,C513_G522CAAUGGUAG
HL_20811.4_Sequence_6 HL_20811.42AZX_C513_G522CAAUGGUAGtrue89001.19
HL_20811.4_Instance_7 HL_20811.4,HL_8SP9_001,C13_G22CAGUCGGUAG
HL_20811.4_Sequence_7 HL_20811.48SP9_C13_G22CAGUCGGUAGtrue87001.35
HL_20811.4_Instance_8 HL_20811.4,HL_6JXM_001,C13_G21CAGUGGUAG
HL_20811.4_Sequence_8 HL_20811.46JXM_C13_G21CAGUGGUAGtrue100000.00
HL_20811.4_Instance_9 HL_20811.4,HL_3AL0_001,U13_G22UAACGGUAG
HL_20811.4_Sequence_9 HL_20811.43AL0_U13_G22UAACGGUAGtrue62004.01
HL_20811.4_Instance_10 HL_20811.4,HL_1FIR_004,C13_G22CAGUCGGUAG
HL_20811.4_Sequence_10 HL_20811.41FIR_C13_G22CAGUCGGUAGtrue87001.35
HL_20811.4_Instance_11 HL_20811.4,HL_4V90_032,C13_G22CAGCCGGUAG
HL_20811.4_Sequence_11 HL_20811.44V90_C13_G22CAGCCGGUAGtrue77002.44
HL_20811.4_Instance_12 HL_20811.4,HL_7UQ6_001,C13_G21CAGUGGUAG
HL_20811.4_Sequence_12 HL_20811.47UQ6_C13_G21CAGUGGUAGtrue100000.00
HL_20811.4_Instance_13 HL_20811.4,HL_7EQJ_004,C13_G22CAGCUGGGAG
HL_20811.4_Sequence_13 HL_20811.47EQJ_C13_G22CAGCUGGGAGtrue88001.23
HL_20811.4_Instance_14 HL_20811.4,HL_5DO4_001,C11_G16CUGAAG
HL_20811.4_Sequence_14 HL_20811.45DO4_C11_G16CUGAAGtrue64003.75

Conserved interactions between motif group positions in HL_20811.4:
1 5 cWW 
2 3 s35 
2 4 cWS 
2 5 s55
JAR3D SCFG/MRF model for HL_20811.4:
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 [5] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008641986,0.015101999,0.010021227,0.167541786,0.000000000],[0.036181325,0.009855924,0.290364393,0.012482375,0.000000000],[0.010143497,0.171090989,0.001947520,0.020434044,0.000000000],[0.172809267,0.011977354,0.052143724,0.009262590,0.000000000],[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 [5] // Basepair C13 - G22 cWW 
BasepairNode | Deletion Probability [0.0000000000000011] | Pair Probability [[0.309286920,0.179597796,0.189796487,0.183457017,0.000000000],[0.014349823,0.011703948,0.001952518,0.011877933,0.000000000],[0.019403364,0.001952518,0.024868800,0.009287685,0.000000000],[0.022438637,0.007353082,0.005818941,0.006854529,0.000000000],[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 [0.000253248,0.070909413,0.000253248,0.001025654,0.285663636,0.568541545,0.072986046,0.000354547,0.000012662] | Right Letter Distribution [0.038461538,0.130769231,0.438461538,0.392307692,0.000000000] | Left Index [2] | Right Index [4] // Basepair A14 - A21 cWS 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node G15:G15
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.218750000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.031250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.718750000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.031250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G15
Sequences of instances from HL_20811.4:
> HL_20811.4  1QF6 C   13 G   22
CAGUUGGUAG
> HL_20811.4  7MRL C   13 G   22
CAGUCGGUAG
> HL_20811.4  5AXM C   13 G   22
CAGUUGGGAG
> HL_20811.4  5B63 C  913 G  923
CAAUUGGAUAG
> HL_20811.4  7LYF C   13 G   22
CAGUCGGUAG
> HL_20811.4  2AZX C  513 G  522
CAAUGGUAG
> HL_20811.4  8SP9 C   13 G   22
CAGUCGGUAG
> HL_20811.4  6JXM C   13 G   21
CAGUGGUAG
> HL_20811.4  3AL0 U   13 G   22
UAACGGUAG
> HL_20811.4  1FIR C   13 G   22
CAGUCGGUAG
> HL_20811.4  4V90 C   13 G   22
CAGCCGGUAG
> HL_20811.4  7UQ6 C   13 G   21
CAGUGGUAG
> HL_20811.4  7EQJ C   13 G   22
CAGCUGGGAG
> HL_20811.4  5DO4 C   11 G   16
CUGAAG