Alignment of HL_65794.5 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
3
I

6
3

3
7
3
I

8
3

4
9
3
I

10
3

5
11
2
I

12
2

6
13
1
I


In
acceptance
region

Cutoff
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Full
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distance
Interior
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Alignment
score
deficit
HL_65794.5_Instance_1 HL_65794.5,HL_8CRE_065,U3040_A3045UGAUCA
HL_65794.5_Sequence_1 HL_65794.58CRE_U_3040_A_3045UGAUCAtrue82001.71
HL_65794.5_Instance_2 HL_65794.5,HL_8P9A_177,U3068_A3073UGAUCA
HL_65794.5_Sequence_2 HL_65794.58P9A_U_3068_A_3073UGAUCAtrue82001.71
HL_65794.5_Instance_3 HL_65794.5,HL_4V9F_067,C2737_G2742CGAGAG
HL_65794.5_Sequence_3 HL_65794.54V9F_C_2737_G_2742CGAGAGtrue82001.67
HL_65794.5_Instance_4 HL_65794.5,HL_7A0S_064,U2680_A2685UACCAA
HL_65794.5_Sequence_4 HL_65794.57A0S_U_2680_A_2685UACCAAtrue88001.10
HL_65794.5_Instance_5 HL_65794.5,HL_5J7L_198,U2701_A2706UGCCAA
HL_65794.5_Sequence_5 HL_65794.55J7L_U_2701_A_2706UGCCAAtrue100000.00
HL_65794.5_Instance_6 HL_65794.5,HL_6UFM_005,G50_C55GGAAAC
HL_65794.5_Sequence_6 HL_65794.56UFM_G50_C55GGAAACtrue77002.15
HL_65794.5_Instance_7 HL_65794.5,HL_4WF9_061,U2728_A2733UGCCAA
HL_65794.5_Sequence_7 HL_65794.54WF9_U_2728_A_2733UGCCAAtrue100000.00
HL_65794.5_Instance_8 HL_65794.5,HL_1U6B_002,C70_G75CGCCCG
HL_65794.5_Sequence_8 HL_65794.51U6B_C70_G75CGCCCGtrue91000.90
HL_65794.5_Instance_9 HL_65794.5,HL_3R4F_005,U52_G57UGGUUG
HL_65794.5_Sequence_9 HL_65794.53R4F_U52_G57UGGUUGtrue46005.16
HL_65794.5_Instance_10 HL_65794.5,HL_4PQV_002,C28_G34CGCCGAG
HL_65794.5_Sequence_10 HL_65794.54PQV_C28_G34CGCCGAGtrue57004.11
HL_65794.5_Instance_11 HL_65794.5,HL_4GXY_003,G65_C71GUCCCGC
HL_65794.5_Sequence_11 HL_65794.54GXY_G65_C71GUCCCGCtrue52004.59
HL_65794.5_Instance_12 HL_65794.5,HL_8KEB_002,G34_C40GCAAUAC
HL_65794.5_Sequence_12 HL_65794.58KEB_G34_C40GCAAUACtrue59003.93
HL_65794.5_Instance_13 HL_65794.5,HL_8K1E_001,G23_C29GCACGGC
HL_65794.5_Sequence_13 HL_65794.58K1E_G23_C29GCACGGCtrue49004.84
HL_65794.5_Instance_14 HL_65794.5,HL_7YSE_002,U32_A38UUGCCAA
HL_65794.5_Sequence_14 HL_65794.57YSE_U32_A38UUGCCAAtrue81001.78

Conserved interactions between motif group positions in HL_65794.5:
1 6 cWW 
2 3 s35 
3 4 s35 
4 5 s35 
5 6 s35
JAR3D SCFG/MRF model for HL_65794.5:
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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000036211996515] | Pair Probability [[0.008499787,0.016082502,0.009648129,0.167242462,0.000000000],[0.036046458,0.009858622,0.196525230,0.011299980,0.000000000],[0.009667655,0.204373191,0.001929949,0.021116849,0.000000000],[0.225943325,0.010988494,0.061468053,0.009309314,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.711910021,0.286896692,0.001142509,0.000050778] | Left Letter Distribution [0.083333333,0.416666667,0.083333333,0.416666667,0.000000000] | Right Length Distribution [0.925121325,0.074446731,0.000419239,0.000012704] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [1] | Right Index [6] // Basepair U3040 - A3045 cWW 
HairpinNode  | Num Bases [4] | Left Index [2] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node G3041:C3044
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.218750000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.093750000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.656250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.031250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G3041
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.343750000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.531250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.093750000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.031250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A3042
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.093750000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.468750000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.156250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.281250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U3043
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.468750000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.218750000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.218750000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.093750000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C3044
Sequences of instances from HL_65794.5:
> HL_65794.5  8CRE U 3040 A 3045
UGAUCA
> HL_65794.5  8P9A U 3068 A 3073
UGAUCA
> HL_65794.5  4V9F C 2737 G 2742
CGAGAG
> HL_65794.5  7A0S U 2680 A 2685
UACCAA
> HL_65794.5  5J7L U 2701 A 2706
UGCCAA
> HL_65794.5  6UFM G   50 C   55
GGAAAC
> HL_65794.5  4WF9 U 2728 A 2733
UGCCAA
> HL_65794.5  1U6B C   70 G   75
CGCCCG
> HL_65794.5  3R4F U   52 G   57
UGGUUG
> HL_65794.5  4PQV C   28 G   34
CGCCGAG
> HL_65794.5  4GXY G   65 C   71
GUCCCGC
> HL_65794.5  8KEB G   34 C   40
GCAAUAC
> HL_65794.5  8K1E G   23 C   29
GCACGGC
> HL_65794.5  7YSE U   32 A   38
UUGCCAA