Alignment of HL_38808.1 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
3

3
7
2
I

8
2

4
9
1
I


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HL_38808.1_Instance_1 HL_38808.1,HL_4QEI_002,A31_U39AUUCCCAUU
HL_38808.1_Sequence_1 HL_38808.14QEI_A31_U39AUUCCCAUUtrue100000.00
HL_38808.1_Instance_2 HL_38808.1,HL_5E6M_002,A31_U39AUUCCCAUU
HL_38808.1_Sequence_2 HL_38808.15E6M_A31_U39AUUCCCAUUtrue100000.00
HL_38808.1_Instance_3 HL_38808.1,HL_2DU3_002,A930_U938ACUGCAGAU
HL_38808.1_Sequence_3 HL_38808.12DU3_A930_U938ACUGCAGAUtrue79002.67
HL_38808.1_Instance_4 HL_38808.1,HL_6ZDP_003,C1303_G1312CUAAUUAGUG
HL_38808.1_Sequence_4 HL_38808.16ZDP_C_1303_G_1312CUAAUUAGUGtrue72003.66

Conserved interactions between motif group positions in HL_38808.1:
1 2 s35 
1 4 cWW 
2 3 cWW 
3 4 s35
JAR3D SCFG/MRF model for HL_38808.1:
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 [4] // Initial node
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009166602,0.020383573,0.009980938,0.227730182,0.000000000],[0.017857579,0.009428504,0.203678568,0.011001082,0.000000000],[0.009996931,0.194467451,0.002013816,0.044896561,0.000000000],[0.193563959,0.011369935,0.023491652,0.010972668,0.000000000],[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 [4] // Basepair A31 - U39 cWW 
HairpinNode  | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node U32:U38
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.014086870,0.211727087,0.013618649,0.025251500,0.000000000],[0.110187822,0.023575027,0.023667479,0.015016014,0.000000000],[0.013490860,0.022612825,0.004008091,0.043681523,0.000000000],[0.024951543,0.015593912,0.093375434,0.345155364,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U32 - U38 cWW 
Insertion    | Location [1] | Length Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.009140768,0.734308349,0.252894576,0.003503961,0.000152346] | Letter Distribution [0.282608696,0.326086957,0.152173913,0.239130435,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_38808.1:
> HL_38808.1  4QEI A   31 U   39
AUUCCCAUU
> HL_38808.1  5E6M A   31 U   39
AUUCCCAUU
> HL_38808.1  2DU3 A  930 U  938
ACUGCAGAU
> HL_38808.1  6ZDP C 1303 G 1312
CUAAUUAGUG