Alignment of HL_75660.5 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
2
I

6
2

3
7
1
I


In
acceptance
region

Cutoff
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Full
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distance
Interior
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Alignment
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HL_75660.5_Instance_1 HL_75660.5,HL_8CRE_006,C207_G211CACAG
HL_75660.5_Sequence_1 HL_75660.58CRE_C207_G211CACAGtrue84001.52
HL_75660.5_Instance_2 HL_75660.5,HL_8P9A_118,C208_G212CAUAG
HL_75660.5_Sequence_2 HL_75660.58P9A_C208_G212CAUAGtrue97000.28
HL_75660.5_Instance_3 HL_75660.5,HL_4V9F_011,G326_C330GAUAC
HL_75660.5_Sequence_3 HL_75660.54V9F_G326_C330GAUACtrue96000.42
HL_75660.5_Instance_4 HL_75660.5,HL_8G9Z_001,G15_C20AGUGGUC
HL_75660.5_Sequence_4 HL_75660.58G9Z_G15_C20AGUGGUCtrue60003.82
HL_75660.5_Instance_5 HL_75660.5,HL_5J7L_143,G319_C323GAUAC
HL_75660.5_Sequence_5 HL_75660.55J7L_G319_C323GAUACtrue96000.42
HL_75660.5_Instance_6 HL_75660.5,HL_5U3G_001,C18_G23CGAAAG
HL_75660.5_Sequence_6 HL_75660.55U3G_C18_G23CGAAAGtrue84001.49
HL_75660.5_Instance_7 HL_75660.5,HL_9DFE_010,C319_G323CAGAG
HL_75660.5_Sequence_7 HL_75660.59DFE_C319_G323CAGAGtrue92000.77
HL_75660.5_Instance_8 HL_75660.5,HL_7A0S_011,C330_G334CUCAG
HL_75660.5_Sequence_8 HL_75660.57A0S_C330_G334CUCAGtrue76002.26
HL_75660.5_Instance_9 HL_75660.5,HL_4WF9_011,C362_G366CAAAG
HL_75660.5_Sequence_9 HL_75660.54WF9_C362_G366CAAAGtrue100000.00
HL_75660.5_Instance_10 HL_75660.5,HL_4WF9_003,G122_C127GGAAAC
HL_75660.5_Sequence_10 HL_75660.54WF9_G122_C127GGAAACtrue83001.63
HL_75660.5_Instance_11 HL_75660.5,HL_7KI3_001,C10_G15CUGAUG
HL_75660.5_Sequence_11 HL_75660.57KI3_C10_G15CUGAUGtrue69002.91
HL_75660.5_Instance_12 HL_75660.5,HL_8K0Y_001,G10_C15GGUGGC
HL_75660.5_Sequence_12 HL_75660.58K0Y_G10_C15GGUGGCtrue64003.45
HL_75660.5_Instance_13 HL_75660.5,HL_2ZNI_001,C13_G21CGAAUAG
HL_75660.5_Sequence_13 HL_75660.52ZNI_C13_G21CGAAUAGtrue50004.72
HL_75660.5_Instance_14 HL_75660.5,HL_2Y9H_003,C11_G16CGCGUG
HL_75660.5_Sequence_14 HL_75660.52Y9H_C11_G16CGCGUGtrue57004.06
HL_75660.5_Instance_15 HL_75660.5,HL_1WZ2_007,C950_G955CGUAGG
HL_75660.5_Sequence_15 HL_75660.51WZ2_C950_G955CGUAGGtrue73002.54
HL_75660.5_Instance_16 HL_75660.5,HL_8CRE_052,C2543_G2547CUCUG
HL_75660.5_Sequence_16 HL_75660.58CRE_C_2543_G_2547CUCUGtrue73002.54
HL_75660.5_Instance_17 HL_75660.5,HL_8KAL_003,G87_C91GAGUC
HL_75660.5_Sequence_17 HL_75660.58KAL_G87_C91GAGUCtrue88001.19
HL_75660.5_Instance_18 HL_75660.5,HL_4V9F_003,G118_C122GAAUC
HL_75660.5_Sequence_18 HL_75660.54V9F_G118_C122GAAUCtrue96000.42
HL_75660.5_Instance_19 HL_75660.5,HL_8CRE_038,A1756_U1761AAUUUU
HL_75660.5_Sequence_19 HL_75660.58CRE_A_1756_U_1761AAUUUUtrue75002.35

Conserved interactions between motif group positions in HL_75660.5:
1 2 s35 
1 3 cWW 
2 3 s55
JAR3D SCFG/MRF model for HL_75660.5:
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 [3] // Initial node
BasepairNode | Deletion Probability [0.0000000000379806] | Pair Probability [[0.008225014,0.015880974,0.009388019,0.179833887,0.000000000],[0.016251474,0.008266210,0.269012122,0.011505740,0.000000000],[0.009409375,0.234446656,0.001788876,0.022497665,0.000000000],[0.171530720,0.011445019,0.021731843,0.008786407,0.000000000],[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 [0.000000000,0.001377610,0.524593777,0.420308722,0.053520137,0.000192865,0.000006888] | Right Letter Distribution [0.410000000,0.090000000,0.190000000,0.310000000,0.000000000] | Left Index [1] | Right Index [3] // Basepair C207 - G211 cWW 
HairpinNode  | Num Bases [1] | Left Index [2] | Right Index [2] | Norm Constant [1.000000000000000] // Hairpin node A208:A208
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.452380952,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.023809524,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.309523810,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.214285714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A208
Sequences of instances from HL_75660.5:
> HL_75660.5  8CRE C  207 G  211
CACAG
> HL_75660.5  8P9A C  208 G  212
CAUAG
> HL_75660.5  4V9F G  326 C  330
GAUAC
> HL_75660.5  8G9Z G   15 C  20A
GUGGUC
> HL_75660.5  5J7L G  319 C  323
GAUAC
> HL_75660.5  5U3G C   18 G   23
CGAAAG
> HL_75660.5  9DFE C  319 G  323
CAGAG
> HL_75660.5  7A0S C  330 G  334
CUCAG
> HL_75660.5  4WF9 C  362 G  366
CAAAG
> HL_75660.5  4WF9 G  122 C  127
GGAAAC
> HL_75660.5  7KI3 C   10 G   15
CUGAUG
> HL_75660.5  8K0Y G   10 C   15
GGUGGC
> HL_75660.5  2ZNI C   13 G   21
CGAAUAG
> HL_75660.5  2Y9H C   11 G   16
CGCGUG
> HL_75660.5  1WZ2 C  950 G  955
CGUAGG
> HL_75660.5  8CRE C 2543 G 2547
CUCUG
> HL_75660.5  8KAL G   87 C   91
GAGUC
> HL_75660.5  4V9F G  118 C  122
GAAUC
> HL_75660.5  8CRE A 1756 U 1761
AAUUUU