Alignment of HL_98995.6 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
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_98995.6_Instance_1 HL_98995.6_HL_7A0S_064_U2680_A2685UACCAA
HL_98995.6_Sequence_1 HL_98995.6_HL_7A0S_064_U_2680_A_2685UACCAAtrue90000.96
HL_98995.6_Instance_2 HL_98995.6_HL_5J7L_198_U2701_A2706UGCCAA
HL_98995.6_Sequence_2 HL_98995.6_HL_5J7L_198_U_2701_A_2706UGCCAAtrue100000.00
HL_98995.6_Instance_3 HL_98995.6_HL_4WF9_061_U2728_A2733UGCCAA
HL_98995.6_Sequence_3 HL_98995.6_HL_4WF9_061_U_2728_A_2733UGCCAAtrue100000.00
HL_98995.6_Instance_4 HL_98995.6_HL_4V9F_067_C2737_G2742CGAGAG
HL_98995.6_Sequence_4 HL_98995.6_HL_4V9F_067_C_2737_G_2742CGAGAGtrue83001.59
HL_98995.6_Instance_5 HL_98995.6_HL_5TBW_066_U3068_A3073UGAUCA
HL_98995.6_Sequence_5 HL_98995.6_HL_5TBW_066_U_3068_A_3073UGAUCAtrue74002.46
HL_98995.6_Instance_6 HL_98995.6_HL_6UFM_005_G50_C55GGAAAC
HL_98995.6_Sequence_6 HL_98995.6_HL_6UFM_005_G50_C55GGAAACtrue89001.03
HL_98995.6_Instance_7 HL_98995.6_HL_4GXY_003_G65_C71GUCCCGC
HL_98995.6_Sequence_7 HL_98995.6_HL_4GXY_003_G65_C71GUCCCGCtrue41005.57
HL_98995.6_Instance_8 HL_98995.6_HL_1U6B_002_C70_G75CGCCCG
HL_98995.6_Sequence_8 HL_98995.6_HL_1U6B_002_C70_G75CGCCCGtrue89001.04
HL_98995.6_Instance_9 HL_98995.6_HL_6JXM_002_G41_C48GCUAAAAC
HL_98995.6_Sequence_9 HL_98995.6_HL_6JXM_002_G41_C48GCUAAAACtrue39005.83

Conserved interactions between motif group positions in HL_98995.6:
1 6 cWW 
2 3 s35 
3 4 s35 
4 5 s35 
5 6 s35 
JAR3D SCFG/MRF model for HL_98995.6:
Character Definition | A,C,G,U,* // Define characters here
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Initial node U2680 - A2685 from junction 
BasepairNode | Deletion Probability [0.0000040911808346] | Pair Probability [[0.008776738,0.017176466,0.009858911,0.185786150,0.000000000],[0.018717789,0.009086084,0.207059807,0.011605009,0.000000000],[0.009854156,0.215798955,0.001936477,0.022814115,0.000000000],[0.225586024,0.011378544,0.035050500,0.009514275,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.772932054,0.115234914,0.111158785,0.000643599,0.000030648] | Left Letter Distribution [0.100000000,0.300000000,0.100000000,0.500000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair U2680 - A2685 cWW 
HairpinNode  | Num Bases [4] | Left Index [2] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A2681:A2684
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.227272727,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.136363636,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.590909091,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.045454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2681
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.409090909,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.045454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C2682
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.227272727,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.136363636,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.136363636,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C2683
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.590909091,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.227272727,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.136363636,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.045454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2684
Sequences of instances from HL_98995.6:
> HL_98995.6 HL_7A0S_064 U 2680 A 2685
UACCAA
> HL_98995.6 HL_5J7L_198 U 2701 A 2706
UGCCAA
> HL_98995.6 HL_4WF9_061 U 2728 A 2733
UGCCAA
> HL_98995.6 HL_4V9F_067 C 2737 G 2742
CGAGAG
> HL_98995.6 HL_5TBW_066 U 3068 A 3073
UGAUCA
> HL_98995.6 HL_6UFM_005 G   50 C   55
GGAAAC
> HL_98995.6 HL_4GXY_003 G   65 C   71
GUCCCGC
> HL_98995.6 HL_1U6B_002 C   70 G   75
CGCCCG
> HL_98995.6 HL_6JXM_002 G   41 C   48
GCUAAAAC