Alignment of HL_08002.5 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
7

2
5
7
I

6
8

3
7
8
I

8
8

4
9
7
I

10
7

5
11
6
I

12
5

6
13
4
I

14
3

7
15
2
I

16
2

8
17
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_08002.5_Instance_1 HL_08002.5_HL_6DN2_004_G88_C95GUAGAGUC
HL_08002.5_Sequence_1 HL_08002.5_HL_6DN2_004_G88_C95GUAGAGUCtrue99000.17
HL_08002.5_Instance_2 HL_08002.5_HL_3F2X_005_G88_C95GUAGAGUC
HL_08002.5_Sequence_2 HL_08002.5_HL_3F2X_005_G88_C95GUAGAGUCtrue99000.17
HL_08002.5_Instance_3 HL_08002.5_HL_5C45_004_G88_C95GUAGAGUC
HL_08002.5_Sequence_3 HL_08002.5_HL_5C45_004_G88_C95GUAGAGUCtrue99000.17
HL_08002.5_Instance_4 HL_08002.5_HL_4FRG_003_G58_C66GUUAUACUC
HL_08002.5_Sequence_4 HL_08002.5_HL_4FRG_003_G58_C66GUUAUACUCtrue83002.44
HL_08002.5_Instance_5 HL_08002.5_HL_5C45_002_G36_C43GUAUAGUC
HL_08002.5_Sequence_5 HL_08002.5_HL_5C45_002_G36_C43GUAUAGUCtrue100000.00
HL_08002.5_Instance_6 HL_08002.5_HL_3F2X_002_G36_C43GUAUAGUC
HL_08002.5_Sequence_6 HL_08002.5_HL_3F2X_002_G36_C43GUAUAGUCtrue100000.00
HL_08002.5_Instance_7 HL_08002.5_HL_4FRN_007_G56_C64GUUAUACUC
HL_08002.5_Sequence_7 HL_08002.5_HL_4FRN_007_G56_C64GUUAUACUCtrue83002.44
HL_08002.5_Instance_8 HL_08002.5_HL_6DN2_002_G36_C43GUAUAGUC
HL_08002.5_Sequence_8 HL_08002.5_HL_6DN2_002_G36_C43GUAUAGUCtrue100000.00
HL_08002.5_Instance_9 HL_08002.5_HL_4WF9_012_G370_C378GUAAUAAUC
HL_08002.5_Sequence_9 HL_08002.5_HL_4WF9_012_G370_C378GUAAUAAUCtrue81002.61
HL_08002.5_Instance_10 HL_08002.5_HL_5J7L_144_G327_C335GUGACAGCC
HL_08002.5_Sequence_10 HL_08002.5_HL_5J7L_144_G327_C335GUGACAGCCtrue83002.46
HL_08002.5_Instance_11 HL_08002.5_HL_7A0S_012_G338_C346GUGAGAGUC
HL_08002.5_Sequence_11 HL_08002.5_HL_7A0S_012_G338_C346GUGAGAGUCtrue97000.48
HL_08002.5_Instance_12 HL_08002.5_HL_4Y4O_114_G327_C335GUGAAAGCC
HL_08002.5_Sequence_12 HL_08002.5_HL_4Y4O_114_G327_C335GUGAAAGCCtrue79002.97
HL_08002.5_Instance_13 HL_08002.5_HL_4V9F_012_G334_C342GUGACAACC
HL_08002.5_Sequence_13 HL_08002.5_HL_4V9F_012_G334_C342GUGACAACCtrue75003.46
HL_08002.5_Instance_14 HL_08002.5_HL_5TBW_007_G216_C224GUGAGAAUC
HL_08002.5_Sequence_14 HL_08002.5_HL_5TBW_007_G216_C224GUGAGAAUCtrue89001.48

Conserved interactions between motif group positions in HL_08002.5:
1 2 s35 
1 8 cWW 
2 5 tWH 
3 4 perp 
5 8 s35 
6 7 s35 
8 7 7BPh
JAR3D SCFG/MRF model for HL_08002.5:
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 [8] // Initial node G88 - C95 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003421372,0.049878455,0.003896030,0.070763821,0.000000000],[0.006009733,0.023484994,0.071363436,0.004669298,0.000000000],[0.003852762,0.636871337,0.000734378,0.009407902,0.000000000],[0.069858180,0.033923966,0.008246450,0.003617885,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair G88 - C95 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.031250000,0.218750000,0.031250000,0.718750000,0.000000000] | Position [2] | Left Index [2] | Right Index [7] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [6] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.218750000,0.156250000,0.593750000,0.031250000,0.000000000] | Position [2] | Left Index [2] | Right Index [6] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [5] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000011805868568] | Pair Probability [[0.016670989,0.003689317,0.017315551,0.003689317,0.000000000],[0.037100939,0.297288410,0.003689317,0.003689317,0.000000000],[0.003689317,0.008843535,0.028056941,0.016408810,0.000000000],[0.498434800,0.003689317,0.021404972,0.036339155,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.428133005,0.569660385,0.002105156,0.000101453] | Left Letter Distribution [0.150000000,0.050000000,0.550000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [5] // Basepair U89 - A92 tWH 
HairpinNode  | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A90:G91
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.906250000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.031250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.031250000,0.000000000,0.000000000],[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 A90
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.093750000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.156250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.343750000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.406250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G91
Sequences of instances from HL_08002.5:
> HL_08002.5 HL_6DN2_004 G   88 C   95
GUAGAGUC
> HL_08002.5 HL_3F2X_005 G   88 C   95
GUAGAGUC
> HL_08002.5 HL_5C45_004 G   88 C   95
GUAGAGUC
> HL_08002.5 HL_4FRG_003 G   58 C   66
GUUAUACUC
> HL_08002.5 HL_5C45_002 G   36 C   43
GUAUAGUC
> HL_08002.5 HL_3F2X_002 G   36 C   43
GUAUAGUC
> HL_08002.5 HL_4FRN_007 G   56 C   64
GUUAUACUC
> HL_08002.5 HL_6DN2_002 G   36 C   43
GUAUAGUC
> HL_08002.5 HL_4WF9_012 G  370 C  378
GUAAUAAUC
> HL_08002.5 HL_5J7L_144 G  327 C  335
GUGACAGCC
> HL_08002.5 HL_7A0S_012 G  338 C  346
GUGAGAGUC
> HL_08002.5 HL_4Y4O_114 G  327 C  335
GUGAAAGCC
> HL_08002.5 HL_4V9F_012 G  334 C  342
GUGACAACC
> HL_08002.5 HL_5TBW_007 G  216 C  224
GUGAGAAUC