Alignment of HL_31585.4 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
3
I

6
3

3
7
3
I

8
3

4
9
3
I

10
3

5
11
3
I

12
3

6
13
2
I

14
2

7
15
1
I


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Alignment
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HL_31585.4_Instance_1 HL_31585.4,HL_4XNR_002,G46_C53GUUUCUAC
HL_31585.4_Sequence_1 HL_31585.44XNR_G46_C53GUUUCUACtrue100000.00
HL_31585.4_Instance_2 HL_31585.4,HL_1Y26_002,G46_C53GUUUCUAC
HL_31585.4_Sequence_2 HL_31585.41Y26_G46_C53GUUUCUACtrue100000.00
HL_31585.4_Instance_3 HL_31585.4,HL_4FEN_002,G46_C53GUUUCUAC
HL_31585.4_Sequence_3 HL_31585.44FEN_G46_C53GUUUCUACtrue100000.00
HL_31585.4_Instance_4 HL_31585.4,HL_1Y27_002,G46_C53GUUUCUAC
HL_31585.4_Sequence_4 HL_31585.41Y27_G46_C53GUUUCUACtrue100000.00
HL_31585.4_Instance_5 HL_31585.4,HL_4LX6_002,G46_C53GCUUCCAC
HL_31585.4_Sequence_5 HL_31585.44LX6_G46_C53GCUUCCACtrue81001.79
HL_31585.4_Instance_6 HL_31585.4,HL_3RKF_008,G46_C53GUUUCUAC
HL_31585.4_Sequence_6 HL_31585.43RKF_G46_C53GUUUCUACtrue100000.00
HL_31585.4_Instance_7 HL_31585.4,HL_9IWF_005,G32_C39GUUUCGAC
HL_31585.4_Sequence_7 HL_31585.49IWF_G32_C39GUUUCGACtrue93000.64
HL_31585.4_Instance_8 HL_31585.4,HL_3LA5_002,G46_C53GCUUCCAC
HL_31585.4_Sequence_8 HL_31585.43LA5_G46_C53GCUUCCACtrue81001.79
HL_31585.4_Instance_9 HL_31585.4,HL_7TZS_001,C27_G33CUGCGUG
HL_31585.4_Sequence_9 HL_31585.47TZS_C27_G33CUGCGUGtrue46005.09
HL_31585.4_Instance_10 HL_31585.4,HL_4LFB_002,G80_C89GUUUUAC
HL_31585.4_Sequence_10 HL_31585.44LFB_G80_C89GUUUUACtrue84001.50
HL_31585.4_Instance_11 HL_31585.4,HL_5VPO_138,U32_A39UUCGGGGA
HL_31585.4_Sequence_11 HL_31585.45VPO_U32_A39UUCGGGGAtrue12008.33
HL_31585.4_Instance_12 HL_31585.4,HL_6UFH_003,G70_C77GGUUGGCC
HL_31585.4_Sequence_12 HL_31585.46UFH_G70_C77GGUUGGCCtrue71002.74
HL_31585.4_Instance_13 HL_31585.4,HL_9DFE_059,U2528_G2535UGAAGAAG
HL_31585.4_Sequence_13 HL_31585.49DFE_U_2528_G_2535UGAAGAAGtrue74002.48
HL_31585.4_Instance_14 HL_31585.4,HL_6JXM_002,G41_C48GCUAAAAC
HL_31585.4_Sequence_14 HL_31585.46JXM_G41_C48GCUAAAACtrue70002.90
HL_31585.4_Instance_15 HL_31585.4,HL_4V9F_063,U2563_G2570UGCAGAAG
HL_31585.4_Sequence_15 HL_31585.44V9F_U_2563_G_2570UGCAGAAGtrue80001.86
HL_31585.4_Instance_16 HL_31585.4,HL_7A0S_060,U2507_G2514UGAAGAAG
HL_31585.4_Sequence_16 HL_31585.47A0S_U_2507_G_2514UGAAGAAGtrue74002.48
HL_31585.4_Instance_17 HL_31585.4,HL_5J7L_194,U2528_G2535UGAAGUAG
HL_31585.4_Sequence_17 HL_31585.45J7L_U_2528_G_2535UGAAGUAGtrue77002.21
HL_31585.4_Instance_18 HL_31585.4,HL_4WF9_057,U2555_G2562UGUAGUCG
HL_31585.4_Sequence_18 HL_31585.44WF9_U_2555_G_2562UGUAGUCGtrue69002.91
HL_31585.4_Instance_19 HL_31585.4,HL_8CRE_061,A2869_U2876AGCAGAAU
HL_31585.4_Sequence_19 HL_31585.48CRE_A_2869_U_2876AGCAGAAUtrue82001.68
HL_31585.4_Instance_20 HL_31585.4,HL_8P9A_173,A2897_U2904AGCAGAAU
HL_31585.4_Sequence_20 HL_31585.48P9A_A_2897_U_2904AGCAGAAUtrue82001.68

Conserved interactions between motif group positions in HL_31585.4:
1 2 s35 
1 7 cWW 
3 4 s35 
4 5 s35 
5 6 s35 
6 7 s35
JAR3D SCFG/MRF model for HL_31585.4:
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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000022428100038] | Pair Probability [[0.008518620,0.015792015,0.009945643,0.152846956,0.000000000],[0.075570096,0.012046715,0.146005822,0.011553536,0.000000000],[0.009958931,0.230842878,0.002028488,0.022130526,0.000000000],[0.153470380,0.011507991,0.128249135,0.009532268,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.598829244,0.400049819,0.001071117,0.000049819] | Left Letter Distribution [0.050000000,0.050000000,0.850000000,0.050000000,0.000000000] | Right Length Distribution [0.947519322,0.052231364,0.000243082,0.000006233] | Right Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Left Index [1] | Right Index [7] // Basepair G46 - C53 cWW 
HairpinNode  | Num Bases [5] | Left Index [2] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node U47:A52
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.159090909,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.295454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.022727273,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.522727273,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U47
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.386363636,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.068181818,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.068181818,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.477272727,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U49
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.068181818,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.431818182,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.431818182,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.068181818,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C50
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.295454545,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.113636364,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.204545455,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.386363636,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U51
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.750000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.113636364,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.068181818,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.068181818,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A52
Insertion    | Location [1] | Length Distribution [0.549066002,0.449688667,0.001189290,0.000056040] | Letter Distribution [0.045454545,0.045454545,0.045454545,0.863636364,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_31585.4:
> HL_31585.4  4XNR G   46 C   53
GUUUCUAC
> HL_31585.4  1Y26 G   46 C   53
GUUUCUAC
> HL_31585.4  4FEN G   46 C   53
GUUUCUAC
> HL_31585.4  1Y27 G   46 C   53
GUUUCUAC
> HL_31585.4  4LX6 G   46 C   53
GCUUCCAC
> HL_31585.4  3RKF G   46 C   53
GUUUCUAC
> HL_31585.4  9IWF G   32 C   39
GUUUCGAC
> HL_31585.4  3LA5 G   46 C   53
GCUUCCAC
> HL_31585.4  7TZS C   27 G   33
CUGCGUG
> HL_31585.4  4LFB G   80 C   89
GUUUUAC
> HL_31585.4  5VPO U   32 A   39
UUCGGGGA
> HL_31585.4  6UFH G   70 C   77
GGUUGGCC
> HL_31585.4  9DFE U 2528 G 2535
UGAAGAAG
> HL_31585.4  6JXM G   41 C   48
GCUAAAAC
> HL_31585.4  4V9F U 2563 G 2570
UGCAGAAG
> HL_31585.4  7A0S U 2507 G 2514
UGAAGAAG
> HL_31585.4  5J7L U 2528 G 2535
UGAAGUAG
> HL_31585.4  4WF9 U 2555 G 2562
UGUAGUCG
> HL_31585.4  8CRE A 2869 U 2876
AGCAGAAU
> HL_31585.4  8P9A A 2897 U 2904
AGCAGAAU