Alignment of HL_54035.5 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
4

3
7
4
I

8
4

4
9
4
I

10
4

5
11
3
I

12
3

6
13
2
I

14
2

7
15
1
I


In
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Full
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distance

Interior
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Alignment
score
deficit
HL_54035.5_Instance_1 HL_54035.5_HL_3R4F_001_A24_U31AUUGAGUU
HL_54035.5_Sequence_1 HL_54035.5_HL_3R4F_001_A24_U31AUUGAGUUtrue95000.56
HL_54035.5_Instance_2 HL_54035.5_HL_3R4F_003_A24_U31AUUGAGUU
HL_54035.5_Sequence_2 HL_54035.5_HL_3R4F_003_A24_U31AUUGAGUUtrue95000.56
HL_54035.5_Instance_3 HL_54035.5_HL_5J7L_024_G1089_C1096GUUAAGUC
HL_54035.5_Sequence_3 HL_54035.5_HL_5J7L_024_G_1089_C_1096GUUAAGUCtrue100000.00
HL_54035.5_Instance_4 HL_54035.5_HL_5TBW_008_U278_G287UUUGGGAAUG
HL_54035.5_Sequence_4 HL_54035.5_HL_5TBW_008_U278_G287UUUGGGAAUGtrue29008.46
HL_54035.5_Instance_5 HL_54035.5_HL_4LFB_025_G1089_C1096GUUAAGUC
HL_54035.5_Sequence_5 HL_54035.5_HL_4LFB_025_G_1089_C_1096GUUAAGUCtrue100000.00
HL_54035.5_Instance_6 HL_54035.5_HL_5TBW_024_C1076_G1083CUUAAUUG
HL_54035.5_Sequence_6 HL_54035.5_HL_5TBW_024_C_1076_G_1083CUUAAUUGtrue91001.05
HL_54035.5_Instance_7 HL_54035.5_HL_4V88_215_C1309_G1316CUUAAUUG
HL_54035.5_Sequence_7 HL_54035.5_HL_4V88_215_C_1309_G_1316CUUAAUUGtrue91001.05
HL_54035.5_Instance_8 HL_54035.5_HL_6CZR_096_G1072_C1079GUUAAGUC
HL_54035.5_Sequence_8 HL_54035.5_HL_6CZR_096_G_1072_C_1079GUUAAGUCtrue100000.00
HL_54035.5_Instance_9 HL_54035.5_HL_5TBW_038_G1719_C1725GUUUAUC
HL_54035.5_Sequence_9 HL_54035.5_HL_5TBW_038_G_1719_C_1725GUUUAUCtrue78002.59

Conserved interactions between motif group positions in HL_54035.5:
1 2 s35 
1 7 cWW 
2 3 s35 
2 6 cWW 
3 6 s55 
4 5 s35 
5 6 s35 
6 7 s35 
JAR3D SCFG/MRF model for HL_54035.5:
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 [7] // Initial node A24 - U31 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009131124,0.018018440,0.010435981,0.189738429,0.000000000],[0.046426872,0.010887920,0.191025320,0.012213912,0.000000000],[0.010438876,0.210580642,0.002071721,0.028602908,0.000000000],[0.174257789,0.012316895,0.063660197,0.010192977,0.000000000],[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 [7] // Basepair A24 - U31 cWW 
BasepairNode | Deletion Probability [0.0000000679767832] | Pair Probability [[0.014436950,0.264791255,0.012889761,0.022512775,0.000000000],[0.015956256,0.017204790,0.019243046,0.014149980,0.000000000],[0.012620538,0.019602827,0.003979087,0.050833588,0.000000000],[0.019666410,0.015324417,0.016310825,0.480477495,0.000000000],[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 [0.114201960,0.770099850,0.004916181,0.110140768,0.000610706,0.000030535] | Right Letter Distribution [0.208333333,0.041666667,0.541666667,0.208333333,0.000000000] | Left Index [2] | Right Index [6] // Basepair U25 - U30 cWW 
HairpinNode  | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node U26:A28
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.045454545,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.863636364,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U26
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.318181818,0.000000000,0.000000000],[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 G27
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.772727273,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[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 A28
Sequences of instances from HL_54035.5:
> HL_54035.5 HL_3R4F_001 A   24 U   31
AUUGAGUU
> HL_54035.5 HL_3R4F_003 A   24 U   31
AUUGAGUU
> HL_54035.5 HL_5J7L_024 G 1089 C 1096
GUUAAGUC
> HL_54035.5 HL_5TBW_008 U  278 G  287
UUUGGGAAUG
> HL_54035.5 HL_4LFB_025 G 1089 C 1096
GUUAAGUC
> HL_54035.5 HL_5TBW_024 C 1076 G 1083
CUUAAUUG
> HL_54035.5 HL_4V88_215 C 1309 G 1316
CUUAAUUG
> HL_54035.5 HL_6CZR_096 G 1072 C 1079
GUUAAGUC
> HL_54035.5 HL_5TBW_038 G 1719 C 1725
GUUUAUC