Alignment of HL_19210.3 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
3

3
7
3
I

8
3

4
9
3
I

10
3

5
11
3
I

12
3

6
13
3
I

14
3

7
15
3
I

16
3

8
17
3
I

18
3

9
19
2
I

20
2

10
21
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
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Alignment
score
deficit
HL_19210.3_Instance_1 HL_19210.3,HL_1MMS_001,C1064_G1074CUUAGAAGCAG
HL_19210.3_Sequence_1 HL_19210.31MMS_C_1064_G_1074CUUAGAAGCAGtrue100000.00
HL_19210.3_Instance_2 HL_19210.3,HL_5D8H_001,C1174_G1184CUUAGAAGCAG
HL_19210.3_Sequence_2 HL_19210.35D8H_C_1174_G_1184CUUAGAAGCAGtrue100000.00
HL_19210.3_Instance_3 HL_19210.3,HL_6PRV_001,C1064_G1074CUUAGAAGCAG
HL_19210.3_Sequence_3 HL_19210.36PRV_C_1064_G_1074CUUAGAAGCAGtrue100000.00
HL_19210.3_Instance_4 HL_19210.3,HL_5J7L_161,C1064_G1074CUUAGAAGCAG
HL_19210.3_Sequence_4 HL_19210.35J7L_C_1064_G_1074CUUAGAAGCAGtrue100000.00
HL_19210.3_Instance_5 HL_19210.3,HL_8CRE_026,C1235_G1245CAUGGAAGUCG
HL_19210.3_Sequence_5 HL_19210.38CRE_C_1235_G_1245CAUGGAAGUCGtrue89002.01
HL_19210.3_Instance_6 HL_19210.3,HL_8P9A_139,C1239_G1249CAUGGAAGUCG
HL_19210.3_Sequence_6 HL_19210.38P9A_C_1239_G_1249CAUGGAAGUCGtrue89002.01
HL_19210.3_Instance_7 HL_19210.3,HL_7OSM_117,G53_C62GUUCGAUUCC
HL_19210.3_Sequence_7 HL_19210.37OSM_G53_C62GUUCGAUUCCtrue73004.86

Conserved interactions between motif group positions in HL_19210.3:
1 2 s35 
1 10 cWW 
2 3 s35 
4 5 s35 
5 6 s35 
6 9 s35 
7 8 s35 
9 10 s35 
3 6 6BPh
2 6 6BR
9 6 7BR
JAR3D SCFG/MRF model for HL_19210.3:
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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009117787,0.016733999,0.010467584,0.189844861,0.000000000],[0.018895995,0.009236003,0.254474892,0.013077223,0.000000000],[0.010551423,0.203726527,0.001992038,0.022818912,0.000000000],[0.191599712,0.012734286,0.025069445,0.009659312,0.000000000],[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 C1064 - G1074 cWW 
HairpinNode  | Num Bases [8] | Left Index [2] | Right Index [9] | Norm Constant [1.000000000000000] // Hairpin node U1065:A1073
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.283783784,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.013513514,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.013513514,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.689189189,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U1065
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.009803922,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.009803922,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.009803922,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.970588235,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U1066
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.277777778,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A1067
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.833333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G1068
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.833333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A1069
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.722222222,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G1071
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.388888889,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C1072
Interaction  | Interacting Bases [8,8] | Pair Probability [[0.554054054,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.418918919,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.013513514,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.013513514,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A1073
Insertion    | Location [5] | Length Distribution [0.146977400,0.846630090,0.006090502,0.000302008] | Letter Distribution [0.812500000,0.062500000,0.062500000,0.062500000,0.000000000]// Insertion in Hairpin after nucleotide 6, position 5
Sequences of instances from HL_19210.3:
> HL_19210.3  1MMS C 1064 G 1074
CUUAGAAGCAG
> HL_19210.3  5D8H C 1174 G 1184
CUUAGAAGCAG
> HL_19210.3  6PRV C 1064 G 1074
CUUAGAAGCAG
> HL_19210.3  5J7L C 1064 G 1074
CUUAGAAGCAG
> HL_19210.3  8CRE C 1235 G 1245
CAUGGAAGUCG
> HL_19210.3  8P9A C 1239 G 1249
CAUGGAAGUCG
> HL_19210.3  7OSM G   53 C   62
GUUCGAUUCC