Alignment of HL_81538.2 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
4
I

12
4

6
13
3
I

14
3

7
15
2
I

16
2

8
17
1
I


In
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Full
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Alignment
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HL_81538.2_Instance_1 HL_81538.2,HL_5J7L_154,G712_C719GGUAACAC
HL_81538.2_Sequence_1 HL_81538.25J7L_G712_C719GGUAACACtrue100000.00
HL_81538.2_Instance_2 HL_81538.2,HL_8CRE_027,U1263_A1270UGUAACAA
HL_81538.2_Sequence_2 HL_81538.28CRE_U_1263_A_1270UGUAACAAtrue98000.18
HL_81538.2_Instance_3 HL_81538.2,HL_5D8H_002,C1202_G1209CGUAACAG
HL_81538.2_Sequence_3 HL_81538.25D8H_C_1202_G_1209CGUAACAGtrue100000.04
HL_81538.2_Instance_4 HL_81538.2,HL_1MMS_002,C1092_G1099CGUAACAG
HL_81538.2_Sequence_4 HL_81538.21MMS_C_1092_G_1099CGUAACAGtrue100000.04
HL_81538.2_Instance_5 HL_81538.2,HL_6PRV_002,C1092_G1099CGUAAUAG
HL_81538.2_Sequence_5 HL_81538.26PRV_C_1092_G_1099CGUAAUAGtrue89001.14
HL_81538.2_Instance_6 HL_81538.2,HL_8P9A_140,U1267_A1274UGUAACAA
HL_81538.2_Sequence_6 HL_81538.28P9A_U_1267_A_1274UGUAACAAtrue98000.18
HL_81538.2_Instance_7 HL_81538.2,HL_3HHN_010,G92_C99GUUAAAAC
HL_81538.2_Sequence_7 HL_81538.23HHN_G92_C99GUUAAAACtrue94000.61
HL_81538.2_Instance_8 HL_81538.2,HL_5AOX_001,G11_C18GGUGGCUC
HL_81538.2_Sequence_8 HL_81538.25AOX_G11_C18GGUGGCUCtrue80002.13
HL_81538.2_Instance_9 HL_81538.2,HL_9DFE_020,G712_C719GGUGAGAC
HL_81538.2_Sequence_9 HL_81538.29DFE_G712_C719GGUGAGACtrue82001.88
HL_81538.2_Instance_10 HL_81538.2,HL_4WF9_004,A136_U143AGUUAUGU
HL_81538.2_Sequence_10 HL_81538.24WF9_A136_U143AGUUAUGUtrue65003.73
HL_81538.2_Instance_11 HL_81538.2,HL_1E8O_001,G110_C117GGUGGCGC
HL_81538.2_Sequence_11 HL_81538.21E8O_G110_C117GGUGGCGCtrue78002.39
HL_81538.2_Instance_12 HL_81538.2,HL_8CRE_217,A1223_U1232AUUGAGAGCU
HL_81538.2_Sequence_12 HL_81538.28CRE_A_1223_U_1232AUUGAGAGCUtrue53005.05
HL_81538.2_Instance_13 HL_81538.2,HL_4KQY_003,C94_G102CUCGAACAG
HL_81538.2_Sequence_13 HL_81538.24KQY_C94_G102CUCGAACAGtrue46005.83
HL_81538.2_Instance_14 HL_81538.2,HL_4V9F_043,C1705_G1713CGGCGAAAG
HL_81538.2_Sequence_14 HL_81538.24V9F_C_1705_G_1713CGGCGAAAGtrue22008.32
HL_81538.2_Instance_15 HL_81538.2,HL_8P9A_216,A1238_U1247AUUGAGAGCU
HL_81538.2_Sequence_15 HL_81538.28P9A_A_1238_U_1247AUUGAGAGCUtrue53005.05
HL_81538.2_Instance_16 HL_81538.2,HL_5J7L_012,G462_C470GUUAAUACC
HL_81538.2_Sequence_16 HL_81538.25J7L_G462_C470GUUAAUACCtrue74002.77

Conserved interactions between motif group positions in HL_81538.2:
1 2 s35 
1 8 cWW 
2 3 s35 
2 7 tSH 
2 8 s55 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
3 6 6BPh
JAR3D SCFG/MRF model for HL_81538.2:
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 [8] // Initial node
BasepairNode | Deletion Probability [0.0000174430812709] | Pair Probability [[0.008353585,0.016940947,0.009391314,0.202101094,0.000000000],[0.016520558,0.008476384,0.221136226,0.011091595,0.000000000],[0.009383500,0.230218785,0.001824372,0.026580370,0.000000000],[0.192895631,0.011155907,0.024744258,0.009185475,0.000000000],[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 [0.934446650,0.065203005,0.000340613,0.000009732] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [1] | Right Index [8] // Basepair G712 - C719 cWW 
BasepairNode | Deletion Probability [0.0000125283626446] | Pair Probability [[0.081226792,0.082728655,0.001605616,0.056569188,0.000000000],[0.079151969,0.080275490,0.001605616,0.001605616,0.000000000],[0.172043477,0.001605616,0.079807645,0.103057189,0.000000000],[0.107394601,0.148111299,0.001605616,0.001605616,0.000000000],[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 [0.872188059,0.127267066,0.000525414,0.000019460] | Right Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair G713 - A718 tSH 
HairpinNode  | Num Bases [4] | Left Index [3] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node U714:C717
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.004385965,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.065789474,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.065789474,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.864035088,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U714
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.472222222,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.361111111,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A715
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.750000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.027777778,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.194444444,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.027777778,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A716
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.361111111,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.416666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.138888889,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C717
Insertion    | Location [3] | Length Distribution [0.747743542,0.251322751,0.000894802,0.000038904] | Letter Distribution [0.250000000,0.083333333,0.416666667,0.250000000,0.000000000]// Insertion in Hairpin after nucleotide 5, position 3
Sequences of instances from HL_81538.2:
> HL_81538.2  5J7L G  712 C  719
GGUAACAC
> HL_81538.2  8CRE U 1263 A 1270
UGUAACAA
> HL_81538.2  5D8H C 1202 G 1209
CGUAACAG
> HL_81538.2  1MMS C 1092 G 1099
CGUAACAG
> HL_81538.2  6PRV C 1092 G 1099
CGUAAUAG
> HL_81538.2  8P9A U 1267 A 1274
UGUAACAA
> HL_81538.2  3HHN G   92 C   99
GUUAAAAC
> HL_81538.2  5AOX G   11 C   18
GGUGGCUC
> HL_81538.2  9DFE G  712 C  719
GGUGAGAC
> HL_81538.2  4WF9 A  136 U  143
AGUUAUGU
> HL_81538.2  1E8O G  110 C  117
GGUGGCGC
> HL_81538.2  8CRE A 1223 U 1232
AUUGAGAGCU
> HL_81538.2  4KQY C   94 G  102
CUCGAACAG
> HL_81538.2  4V9F C 1705 G 1713
CGGCGAAAG
> HL_81538.2  8P9A A 1238 U 1247
AUUGAGAGCU
> HL_81538.2  5J7L G  462 C  470
GUUAAUACC