Alignment of HL_49922.4 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
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Cutoff
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Full
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Alignment
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HL_49922.4_Instance_1 HL_49922.4,HL_6QCW_001,U3_A8UAGUAA
HL_49922.4_Sequence_1 HL_49922.46QCW_U3_A8UAGUAAtrue100000.00
HL_49922.4_Instance_2 HL_49922.4,HL_5FMZ_001,U3_A8UAGUAA
HL_49922.4_Sequence_2 HL_49922.45FMZ_U3_A8UAGUAAtrue100000.00
HL_49922.4_Instance_3 HL_49922.4,HL_7Z42_002,U3_A8UAGUAA
HL_49922.4_Sequence_3 HL_49922.47Z42_U3_A8UAGUAAtrue100000.00
HL_49922.4_Instance_4 HL_49922.4,HL_4WSB_001,U3_A8UAGUAA
HL_49922.4_Sequence_4 HL_49922.44WSB_U3_A8UAGUAAtrue100000.00
HL_49922.4_Instance_5 HL_49922.4,HL_9F37_001,U3_A8UAGUAA
HL_49922.4_Sequence_5 HL_49922.49F37_U3_A8UAGUAAtrue100000.00
HL_49922.4_Instance_6 HL_49922.4,HL_7Z4O_002,U3_A8UAGUAA
HL_49922.4_Sequence_6 HL_49922.47Z4O_U3_A8UAGUAAtrue100000.00
HL_49922.4_Instance_7 HL_49922.4,HL_7EL1_002,C59_G65CAAAAUG
HL_49922.4_Sequence_7 HL_49922.47EL1_C59_G65CAAAAUGtrue62003.59
HL_49922.4_Instance_8 HL_49922.4,HL_7ENI_002,C59_G65CAAAAUG
HL_49922.4_Sequence_8 HL_49922.47ENI_C59_G65CAAAAUGtrue62003.59
HL_49922.4_Instance_9 HL_49922.4,HL_5J7L_185,G2209_C2215GUAAUCC
HL_49922.4_Sequence_9 HL_49922.45J7L_G_2209_C_2215GUAAUCCtrue51004.62
HL_49922.4_Instance_10 HL_49922.4,HL_4WF9_048,C2236_G2242CUUAUCG
HL_49922.4_Sequence_10 HL_49922.44WF9_C_2236_G_2242CUUAUCGtrue52004.52

Conserved interactions between motif group positions in HL_49922.4:
1 2 s35 
1 5 cWW 
2 3 s33 
2 4 cSW 
4 5 s35 
3 3 2BPh
JAR3D SCFG/MRF model for HL_49922.4:
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 [0.0000083361642801] | Pair Probability [[0.008581857,0.016398307,0.009591246,0.183193464,0.000000000],[0.019490383,0.009056960,0.213825451,0.011213075,0.000000000],[0.009624836,0.193146236,0.001912411,0.021832549,0.000000000],[0.242725585,0.010746714,0.039273889,0.009387036,0.000000000],[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 [0.796024845,0.202732919,0.001192547,0.000049689] | Right Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair U3 - A8 cWW 
BasepairNode | Deletion Probability [0.0000000420189757] | Pair Probability [[0.271662348,0.014620519,0.019769390,0.007102071,0.000000000],[0.182985740,0.011924733,0.001989351,0.007491791,0.000000000],[0.193376820,0.001989351,0.025337927,0.005928710,0.000000000],[0.186917762,0.052456767,0.009462889,0.006983833,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.796024845,0.202732919,0.001192547,0.000049689] | Left Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Right Length Distribution [0.004949270,0.989853997,0.004949270,0.000247463] | Right Letter Distribution [0.208333333,0.041666667,0.041666667,0.708333333,0.000000000] | Left Index [2] | Right Index [4] // Basepair A4 - A7 cSW 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node G5:G5
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.395833333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.006944444,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.590277778,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.006944444,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G5
Sequences of instances from HL_49922.4:
> HL_49922.4  6QCW U    3 A    8
UAGUAA
> HL_49922.4  5FMZ U    3 A    8
UAGUAA
> HL_49922.4  7Z42 U    3 A    8
UAGUAA
> HL_49922.4  4WSB U    3 A    8
UAGUAA
> HL_49922.4  9F37 U    3 A    8
UAGUAA
> HL_49922.4  7Z4O U    3 A    8
UAGUAA
> HL_49922.4  7EL1 C   59 G   65
CAAAAUG
> HL_49922.4  7ENI C   59 G   65
CAAAAUG
> HL_49922.4  5J7L G 2209 C 2215
GUAAUCC
> HL_49922.4  4WF9 C 2236 G 2242
CUUAUCG