Alignment of HL_87219.4 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
4
I

6
7

3
7
7
I

8
8

4
9
8
I

10
8

5
11
8
I

12
8

6
13
8
I

14
8

7
15
7
I

16
7

8
17
6
I

18
5

9
19
2
I

20
2

10
21
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
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distance

Alignment
score
deficit
HL_87219.4_Instance_1 HL_87219.4_HL_5J7L_017_G786_C796GAUUAGAUACC
HL_87219.4_Sequence_1 HL_87219.4_HL_5J7L_017_G786_C796GAUUAGAUACCtrue93001.07
HL_87219.4_Instance_2 HL_87219.4_HL_4LFB_017_G786_C796GAUUAGAUACC
HL_87219.4_Sequence_2 HL_87219.4_HL_4LFB_017_G786_C796GAUUAGAUACCtrue93001.07
HL_87219.4_Instance_3 HL_87219.4_HL_6CZR_088_G770_C780GAUUAGAUACC
HL_87219.4_Sequence_3 HL_87219.4_HL_6CZR_088_G770_C780GAUUAGAUACCtrue93001.07
HL_87219.4_Instance_4 HL_87219.4_HL_4V88_208_G997_C1007GAUCAGAUACC
HL_87219.4_Sequence_4 HL_87219.4_HL_4V88_208_G997_C_1007GAUCAGAUACCtrue80003.20
HL_87219.4_Instance_5 HL_87219.4_HL_5J7L_015_C689_G698CGGUGAAAUG
HL_87219.4_Sequence_5 HL_87219.4_HL_5J7L_015_C689_G698CGGUGAAAUGtrue100000.00
HL_87219.4_Instance_6 HL_87219.4_HL_4LFB_015_C689_G698CGGUGAAAUG
HL_87219.4_Sequence_6 HL_87219.4_HL_4LFB_015_C689_G698CGGUGAAAUGtrue100000.00
HL_87219.4_Instance_7 HL_87219.4_HL_6CZR_086_C673_G682CGGUGAAAUG
HL_87219.4_Sequence_7 HL_87219.4_HL_6CZR_086_C673_G682CGGUGAAAUGtrue100000.00
HL_87219.4_Instance_8 HL_87219.4_HL_4V88_206_A900_U909AGGUGAAAUU
HL_87219.4_Sequence_8 HL_87219.4_HL_4V88_206_A900_U909AGGUGAAAUUtrue100000.05
HL_87219.4_Instance_9 HL_87219.4_HL_3R9X_001_A1513_U1522AGGGGAACCU
HL_87219.4_Sequence_9 HL_87219.4_HL_3R9X_001_A_1513_U_1522AGGGGAACCUtrue75003.85
HL_87219.4_Instance_10 HL_87219.4_HL_5TBW_028_G1266_C1275GUGUAACAAC
HL_87219.4_Sequence_10 HL_87219.4_HL_5TBW_028_G_1266_C_1275GUGUAACAACtrue72004.38
HL_87219.4_Instance_11 HL_87219.4_HL_4WSM_226_G63_C73GGUUCAAGUCC
HL_87219.4_Sequence_11 HL_87219.4_HL_4WSM_226_G63_C73GGUUCAAGUCCtrue71004.56

Conserved interactions between motif group positions in HL_87219.4:
1 2 s35 
1 10 cWW 
2 3 s35 
2 10 s55 
3 4 s35 
3 8 tSH 
5 6 s35 
6 7 s35 
7 8 s35 
8 9 s35 
9 10 s35 
4 7 6BPh
JAR3D SCFG/MRF model for HL_87219.4:
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 [10] // Initial node G786 - C796 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008819762,0.018124088,0.009959712,0.202847942,0.000000000],[0.016578175,0.008818938,0.213602497,0.011845166,0.000000000],[0.009925645,0.242528718,0.001911957,0.028187187,0.000000000],[0.182832453,0.012083152,0.022313377,0.009621229,0.000000000],[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 [10] // Basepair G786 - C796 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.346153846,0.038461538,0.500000000,0.115384615,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.115384615,0.500000000,0.038461538,0.346153846,0.000000000] | Position [2] | Left Index [3] | Right Index [9] // 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 [3] | Right Index [8] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000021781539185] | Pair Probability [[0.100852388,0.100252221,0.001170348,0.005618559,0.000000000],[0.101441703,0.101511325,0.001170348,0.001170348,0.000000000],[0.170762009,0.022353694,0.006364883,0.098409479,0.000000000],[0.160531682,0.104866972,0.001170348,0.022353694,0.000000000],[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 [0.543801687,0.453920502,0.002175207,0.000102604] | Right Letter Distribution [0.071428571,0.071428571,0.214285714,0.642857143,0.000000000] | Left Index [3] | Right Index [8] // Basepair U788 - A794 tSH 
HairpinNode  | Num Bases [4] | Left Index [4] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node U789:A792
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.006329114,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.094936709,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.094936709,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.803797468,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U789
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.423076923,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.115384615,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.423076923,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.038461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A790
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.576923077,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.346153846,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.038461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G791
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.807692308,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.115384615,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.038461538,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.038461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A792
Sequences of instances from HL_87219.4:
> HL_87219.4 HL_5J7L_017 G  786 C  796
GAUUAGAUACC
> HL_87219.4 HL_4LFB_017 G  786 C  796
GAUUAGAUACC
> HL_87219.4 HL_6CZR_088 G  770 C  780
GAUUAGAUACC
> HL_87219.4 HL_4V88_208 G  997 C 1007
GAUCAGAUACC
> HL_87219.4 HL_5J7L_015 C  689 G  698
CGGUGAAAUG
> HL_87219.4 HL_4LFB_015 C  689 G  698
CGGUGAAAUG
> HL_87219.4 HL_6CZR_086 C  673 G  682
CGGUGAAAUG
> HL_87219.4 HL_4V88_206 A  900 U  909
AGGUGAAAUU
> HL_87219.4 HL_3R9X_001 A 1513 U 1522
AGGGGAACCU
> HL_87219.4 HL_5TBW_028 G 1266 C 1275
GUGUAACAAC
> HL_87219.4 HL_4WSM_226 G   63 C   73
GGUUCAAGUCC