Alignment of HL_49941.1 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
3
I

12
3

6
13
2
I

14
2

7
15
1
I


In
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HL_49941.1_Instance_1 HL_49941.1,HL_1FFY_001,C13_G22CAGGUGGUUAG
HL_49941.1_Sequence_1 HL_49941.11FFY_C13_G22CAGGUGGUUAGtrue100000.00
HL_49941.1_Instance_2 HL_49941.1,HL_1QU2_001,C13_G22CAGGUGGUUAG
HL_49941.1_Sequence_2 HL_49941.11QU2_C13_G22CAGGUGGUUAGtrue100000.00
HL_49941.1_Instance_3 HL_49941.1,HL_2CSX_001,C13_G22CAGCUGGUCAG
HL_49941.1_Sequence_3 HL_49941.12CSX_C13_G22CAGCUGGUCAGtrue92001.47
HL_49941.1_Instance_4 HL_49941.1,HL_6NWY_033,C13_G22CAGCCUGGUAG
HL_49941.1_Sequence_4 HL_49941.16NWY_C13_G22CAGCCUGGUAGtrue90001.86

Conserved interactions between motif group positions in HL_49941.1:
1 7 cWW 
2 3 s35 
2 6 cWS 
2 7 s55 
4 5 s55
JAR3D SCFG/MRF model for HL_49941.1:
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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009353183,0.016772504,0.010752635,0.194966481,0.000000000],[0.019886467,0.009525946,0.243418233,0.013525436,0.000000000],[0.010873390,0.199167485,0.002049567,0.023014932,0.000000000],[0.197494026,0.013031497,0.026256418,0.009911799,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair C13 - G22 cWW 
BasepairNode | Deletion Probability [0.0000000000000572] | Pair Probability [[0.278194135,0.191981782,0.202883713,0.196107112,0.000000000],[0.015339301,0.012510983,0.002087152,0.012696964,0.000000000],[0.020741304,0.002087152,0.026583603,0.009928108,0.000000000],[0.007451226,0.007860106,0.006220181,0.007327176,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.000000000,0.000000000,0.003046923,0.252894576,0.734308349,0.009293114,0.000457038] | Right Letter Distribution [0.029411765,0.088235294,0.500000000,0.382352941,0.000000000] | Left Index [2] | Right Index [6] // Basepair A14 - A21A cWS 
HairpinNode  | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node G15:U17
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.750000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G15
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.416666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G16
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.750000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U17
Insertion    | Location [1] | Length Distribution [0.741082411,0.255227552,0.003536285,0.000153752] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 3, position 1
Sequences of instances from HL_49941.1:
> HL_49941.1  1FFY C   13 G   22
CAGGUGGUUAG
> HL_49941.1  1QU2 C   13 G   22
CAGGUGGUUAG
> HL_49941.1  2CSX C   13 G   22
CAGCUGGUCAG
> HL_49941.1  6NWY C   13 G   22
CAGCCUGGUAG