Alignment of HL_04783.2 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
3
I

8
3

4
9
2
I

10
2

5
11
1
I


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HL_04783.2_Instance_1 HL_04783.2,HL_5J7L_179,C1806_G1811CGAAAG
HL_04783.2_Sequence_1 HL_04783.25J7L_C_1806_G_1811CGAAAGtrue100000.00
HL_04783.2_Instance_2 HL_04783.2,HL_3OXE_002,G49_C54GGAAAC
HL_04783.2_Sequence_2 HL_04783.23OXE_G49_C54GGAAACtrue99000.10
HL_04783.2_Instance_3 HL_04783.2,HL_8G9Z_003,C47C_G47HCUAGCG
HL_04783.2_Sequence_3 HL_04783.28G9Z_C47C_G47HCUAGCGtrue82001.67
HL_04783.2_Instance_4 HL_04783.2,HL_3IGI_004,G135_C141GGAACAC
HL_04783.2_Sequence_4 HL_04783.23IGI_G135_C141GGAACACtrue68003.09
HL_04783.2_Instance_5 HL_04783.2,HL_3FOZ_005,A31_U39AUUGAAAAU
HL_04783.2_Sequence_5 HL_04783.23FOZ_A31_U39AUUGAAAAUtrue42005.47
HL_04783.2_Instance_6 HL_04783.2,HL_3EPH_002,A31_U39AUUGCAAAU
HL_04783.2_Sequence_6 HL_04783.23EPH_A31_U39AUUGCAAAUtrue32006.43
HL_04783.2_Instance_7 HL_04783.2,HL_1OOA_001,U13_G18UGUAAG
HL_04783.2_Sequence_7 HL_04783.21OOA_U13_G18UGUAAGtrue77002.14
HL_04783.2_Instance_8 HL_04783.2,HL_4V9F_007,C195_G201CGCAACG
HL_04783.2_Sequence_8 HL_04783.24V9F_C195_G201CGCAACGtrue61003.69
HL_04783.2_Instance_9 HL_04783.2,HL_4C9D_002,C21_G25CGUAG
HL_04783.2_Sequence_9 HL_04783.24C9D_C21_G25CGUAGtrue93000.71

Conserved interactions between motif group positions in HL_04783.2:
1 2 s35 
1 5 cWW 
2 4 tSH 
2 5 s55 
3 4 s55 
4 5 s35
JAR3D SCFG/MRF model for HL_04783.2:
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 [5] // Initial node
BasepairNode | Deletion Probability [0.0000132986348294] | Pair Probability [[0.009090134,0.017359147,0.010410901,0.189212021,0.000000000],[0.047087928,0.010922828,0.210611007,0.012319268,0.000000000],[0.010464996,0.191014404,0.002071820,0.027916884,0.000000000],[0.174803083,0.012212817,0.064348592,0.010154170,0.000000000],[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 [0.883805084,0.115305590,0.000858659,0.000030666] | Right Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Left Index [1] | Right Index [5] // Basepair C1806 - G1811 cWW 
BasepairNode | Deletion Probability [0.0000000034875273] | Pair Probability [[0.107308342,0.106426886,0.001262313,0.005985159,0.000000000],[0.108203585,0.110221448,0.001262313,0.001262313,0.000000000],[0.178074529,0.001262313,0.006421620,0.099223162,0.000000000],[0.148044015,0.122517377,0.001262313,0.001262313,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.222432705,0.441810016,0.113721776,0.220721684,0.001252712,0.000061108] | Left Letter Distribution [0.464285714,0.178571429,0.178571429,0.178571429,0.000000000] | Right Length Distribution [0.663420013,0.334466599,0.002021501,0.000091886] | Right Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Left Index [2] | Right Index [4] // Basepair G1807 - A1810 tSH 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node A1809:A1809
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.136363636,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.136363636,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.227272727,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A1809
Sequences of instances from HL_04783.2:
> HL_04783.2  5J7L C 1806 G 1811
CGAAAG
> HL_04783.2  3OXE G   49 C   54
GGAAAC
> HL_04783.2  8G9Z C  47C G  47H
CUAGCG
> HL_04783.2  3IGI G  135 C  141
GGAACAC
> HL_04783.2  3FOZ A   31 U   39
AUUGAAAAU
> HL_04783.2  3EPH A   31 U   39
AUUGCAAAU
> HL_04783.2  1OOA U   13 G   18
UGUAAG
> HL_04783.2  4V9F C  195 G  201
CGCAACG
> HL_04783.2  4C9D C   21 G   25
CGUAG