Alignment of HL_93727.3 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
3

2
5
3
I

6
4

3
7
4
I

8
4

4
9
4
I

10
4

5
11
4
I

12
4

6
13
3
I

14
3

7
15
2
I

16
2

8
17
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_93727.3_Instance_1 HL_93727.3_HL_5AOX_001_G11_C18GGUGGCUC
HL_93727.3_Sequence_1 HL_93727.3_HL_5AOX_001_G11_C18GGUGGCUCtrue72002.94
HL_93727.3_Instance_2 HL_93727.3_HL_1E8O_001_G110_C117GGUGGCGC
HL_93727.3_Sequence_2 HL_93727.3_HL_1E8O_001_G110_C117GGUGGCGCtrue79002.23
HL_93727.3_Instance_3 HL_93727.3_HL_5J7L_154_G712_C719GGUAACAC
HL_93727.3_Sequence_3 HL_93727.3_HL_5J7L_154_G712_C719GGUAACACtrue100000.00
HL_93727.3_Instance_4 HL_93727.3_HL_3HHN_010_G92_C99GUUAAAAC
HL_93727.3_Sequence_4 HL_93727.3_HL_3HHN_010_G92_C99GUUAAAACtrue93000.78
HL_93727.3_Instance_5 HL_93727.3_HL_4Y4O_124_G712_C719GGUGAGAC
HL_93727.3_Sequence_5 HL_93727.3_HL_4Y4O_124_G712_C719GGUGAGACtrue80002.09
HL_93727.3_Instance_6 HL_93727.3_HL_1MMS_002_C1092_G1099CGUAACAG
HL_93727.3_Sequence_6 HL_93727.3_HL_1MMS_002_C_1092_G_1099CGUAACAGtrue99000.10
HL_93727.3_Instance_7 HL_93727.3_HL_5D8H_002_C1202_G1209CGUAACAG
HL_93727.3_Sequence_7 HL_93727.3_HL_5D8H_002_C_1202_G_1209CGUAACAGtrue99000.10
HL_93727.3_Instance_8 HL_93727.3_HL_1U9S_003_G181_C189GGUAAGAGC
HL_93727.3_Sequence_8 HL_93727.3_HL_1U9S_003_G181_C189GGUAAGAGCtrue77002.47
HL_93727.3_Instance_9 HL_93727.3_HL_4LFB_006_G259_C267GGUAAUGGC
HL_93727.3_Sequence_9 HL_93727.3_HL_4LFB_006_G259_C267GGUAAUGGCtrue87001.40
HL_93727.3_Instance_10 HL_93727.3_HL_6PRV_002_C1092_G1099CGUAAUAG
HL_93727.3_Sequence_10 HL_93727.3_HL_6PRV_002_C_1092_G_1099CGUAAUAGtrue97000.37
HL_93727.3_Instance_11 HL_93727.3_HL_5J7L_006_G259_C267GGUAACGGC
HL_93727.3_Sequence_11 HL_93727.3_HL_5J7L_006_G259_C267GGUAACGGCtrue89001.13
HL_93727.3_Instance_12 HL_93727.3_HL_4WF9_004_A136_U143AGUUAUGU
HL_93727.3_Sequence_12 HL_93727.3_HL_4WF9_004_A136_U143AGUUAUGUtrue72002.91
HL_93727.3_Instance_13 HL_93727.3_HL_4V88_193_G330_C338GAUAGUGGC
HL_93727.3_Sequence_13 HL_93727.3_HL_4V88_193_G330_C338GAUAGUGGCtrue51005.20
HL_93727.3_Instance_14 HL_93727.3_HL_7A0S_056_C2334_G2341CUGACACG
HL_93727.3_Sequence_14 HL_93727.3_HL_7A0S_056_C_2334_G_2341CUGACACGtrue53004.99
HL_93727.3_Instance_15 HL_93727.3_HL_4KQY_003_C94_G102CUCGAACAG
HL_93727.3_Sequence_15 HL_93727.3_HL_4KQY_003_C94_G102CUCGAACAGtrue49005.36
HL_93727.3_Instance_16 HL_93727.3_HL_4KQY_006_C94_G102CUCGAACAG
HL_93727.3_Sequence_16 HL_93727.3_HL_4KQY_006_C94_G102CUCGAACAGtrue49005.36
HL_93727.3_Instance_17 HL_93727.3_HL_6CZR_077_G255_C263GGUAAUGGC
HL_93727.3_Sequence_17 HL_93727.3_HL_6CZR_077_G255_C263GGUAAUGGCtrue87001.40
HL_93727.3_Instance_18 HL_93727.3_HL_4WF9_053_C2382_G2389CCUACAAG
HL_93727.3_Sequence_18 HL_93727.3_HL_4WF9_053_C_2382_G_2389CCUACAAGtrue80002.16
HL_93727.3_Instance_19 HL_93727.3_HL_4Y4O_160_C2355_G2362CCUGCAAG
HL_93727.3_Sequence_19 HL_93727.3_HL_4Y4O_160_C_2355_G_2362CCUGCAAGtrue71003.03
HL_93727.3_Instance_20 HL_93727.3_HL_7A0S_029_C1103_G1110CGUAAUAG
HL_93727.3_Sequence_20 HL_93727.3_HL_7A0S_029_C_1103_G_1110CGUAAUAGtrue97000.37
HL_93727.3_Instance_21 HL_93727.3_HL_4WF9_041_G1761_C1768GUUAACGC
HL_93727.3_Sequence_21 HL_93727.3_HL_4WF9_041_G_1761_C_1768GUUAACGCtrue79002.20
HL_93727.3_Instance_22 HL_93727.3_HL_6UFM_004_G13_C20GCCAUCAC
HL_93727.3_Sequence_22 HL_93727.3_HL_6UFM_004_G13_C20GCCAUCACtrue58004.41

Conserved interactions between motif group positions in HL_93727.3:
1 2 s35 
1 8 cWW 
2 3 s35 
2 7 tSH 
2 8 s55 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
3 6 6BPh
JAR3D SCFG/MRF model for HL_93727.3:
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 [8] // Initial node G11 - C18 from junction 
BasepairNode | Deletion Probability [0.0000045283410407] | Pair Probability [[0.008053456,0.015930260,0.009181313,0.175754462,0.000000000],[0.015397884,0.008038891,0.245211997,0.011168415,0.000000000],[0.009166555,0.270570173,0.001745108,0.022254230,0.000000000],[0.166956691,0.011251217,0.020730033,0.008589315,0.000000000],[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 [0.680425536,0.318740281,0.000798138,0.000036045] | Right Letter Distribution [0.277777778,0.055555556,0.611111111,0.055555556,0.000000000] | Left Index [1] | Right Index [8] // Basepair G11 - C18 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.065340768,0.060719131,0.015625149,0.106197426,0.000000000],[0.103735802,0.060596947,0.001890102,0.001890102,0.000000000],[0.140329191,0.001890102,0.158604543,0.078639827,0.000000000],[0.084541987,0.102483673,0.015625149,0.001890102,0.000000000],[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 [7] // Basepair G12 - U17 tSH 
HairpinNode  | Num Bases [4] | Left Index [3] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node U13:C16
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.003205128,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.137820513,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.048076923,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.810897436,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U13
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.645833333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.020833333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.270833333,0.000000000,0.000000000],[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 G14
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.645833333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.145833333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.145833333,0.000000000,0.000000000],[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 G15
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.270833333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.354166667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.104166667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.270833333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C16
Sequences of instances from HL_93727.3:
> HL_93727.3 HL_5AOX_001 G   11 C   18
GGUGGCUC
> HL_93727.3 HL_1E8O_001 G  110 C  117
GGUGGCGC
> HL_93727.3 HL_5J7L_154 G  712 C  719
GGUAACAC
> HL_93727.3 HL_3HHN_010 G   92 C   99
GUUAAAAC
> HL_93727.3 HL_4Y4O_124 G  712 C  719
GGUGAGAC
> HL_93727.3 HL_1MMS_002 C 1092 G 1099
CGUAACAG
> HL_93727.3 HL_5D8H_002 C 1202 G 1209
CGUAACAG
> HL_93727.3 HL_1U9S_003 G  181 C  189
GGUAAGAGC
> HL_93727.3 HL_4LFB_006 G  259 C  267
GGUAAUGGC
> HL_93727.3 HL_6PRV_002 C 1092 G 1099
CGUAAUAG
> HL_93727.3 HL_5J7L_006 G  259 C  267
GGUAACGGC
> HL_93727.3 HL_4WF9_004 A  136 U  143
AGUUAUGU
> HL_93727.3 HL_4V88_193 G  330 C  338
GAUAGUGGC
> HL_93727.3 HL_7A0S_056 C 2334 G 2341
CUGACACG
> HL_93727.3 HL_4KQY_003 C   94 G  102
CUCGAACAG
> HL_93727.3 HL_4KQY_006 C   94 G  102
CUCGAACAG
> HL_93727.3 HL_6CZR_077 G  255 C  263
GGUAAUGGC
> HL_93727.3 HL_4WF9_053 C 2382 G 2389
CCUACAAG
> HL_93727.3 HL_4Y4O_160 C 2355 G 2362
CCUGCAAG
> HL_93727.3 HL_7A0S_029 C 1103 G 1110
CGUAAUAG
> HL_93727.3 HL_4WF9_041 G 1761 C 1768
GUUAACGC
> HL_93727.3 HL_6UFM_004 G   13 C   20
GCCAUCAC