Alignment of HL_78347.4 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
4

3
7
4
I

8
4

4
9
3
I

10
3

5
11
2
I

12
2

6
13
1
I


In
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HL_78347.4_Instance_1 HL_78347.4,HL_5HR6_001,U12_G22UAGAGGCCCAG
HL_78347.4_Sequence_1 HL_78347.45HR6_U12_G22UAGAGGCCCAGtrue71002.79
HL_78347.4_Instance_2 HL_78347.4,HL_5HR7_004,U13_G22UAGAGGCCCAG
HL_78347.4_Sequence_2 HL_78347.45HR7_U13_G22UAGAGGCCCAGtrue71002.79
HL_78347.4_Instance_3 HL_78347.4,HL_2DER_004,U13_G22UAGAGGCCCAG
HL_78347.4_Sequence_3 HL_78347.42DER_U13_G22UAGAGGCCCAGtrue71002.79
HL_78347.4_Instance_4 HL_78347.4,HL_1N78_001,U513_G522UAGCGGUUAG
HL_78347.4_Sequence_4 HL_78347.41N78_U513_G522UAGCGGUUAGtrue45005.24
HL_78347.4_Instance_5 HL_78347.4,HL_6WBR_004,C55_G63CCUUCGUGG
HL_78347.4_Sequence_5 HL_78347.46WBR_C55_G63CCUUCGUGGtrue27006.89
HL_78347.4_Instance_6 HL_78347.4,HL_1QU2_002,C31_G39CCUGAUAAG
HL_78347.4_Sequence_6 HL_78347.41QU2_C31_G39CCUGAUAAGtrue63003.51
HL_78347.4_Instance_7 HL_78347.4,HL_1FFY_002,C31_G39CCUGAUAAG
HL_78347.4_Sequence_7 HL_78347.41FFY_C31_G39CCUGAUAAGtrue63003.51
HL_78347.4_Instance_8 HL_78347.4,HL_8CRE_194,U188_G193UGUUUG
HL_78347.4_Sequence_8 HL_78347.48CRE_U188_G193UGUUUGtrue100000.00
HL_78347.4_Instance_9 HL_78347.4,HL_3DIL_004,G149_C154GGUCUC
HL_78347.4_Sequence_9 HL_78347.43DIL_G149_C154GGUCUCtrue80001.94

Conserved interactions between motif group positions in HL_78347.4:
1 2 s35 
1 6 cWW 
2 3 s35 
2 5 cWS 
2 6 s55 
3 4 tSW 
4 5 s55 
5 6 s35
JAR3D SCFG/MRF model for HL_78347.4:
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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009833399,0.014712099,0.011994876,0.102318351,0.000000000],[0.165385301,0.018553059,0.135836702,0.014018666,0.000000000],[0.012182980,0.113542111,0.002587876,0.017730307,0.000000000],[0.128285815,0.013209500,0.228540820,0.011268139,0.000000000],[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 [6] // Basepair U12 - G22 cWW 
BasepairNode | Deletion Probability [0.0000003956735078] | Pair Probability [[0.175775332,0.128015309,0.135336267,0.131473956,0.000000000],[0.064601867,0.014924013,0.031365422,0.015177872,0.000000000],[0.031593855,0.003077618,0.025182612,0.201671876,0.000000000],[0.011021707,0.011085180,0.008824412,0.010872701,0.000000000],[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 [0.224265942,0.771181521,0.004338660,0.000213878] | Right Letter Distribution [0.277777778,0.388888889,0.055555556,0.277777778,0.000000000] | Left Index [2] | Right Index [5] // Basepair A13 - A21 cWS 
HairpinNode  | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G14:C19
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.008992623,0.008290293,0.004770392,0.091936205,0.000000000],[0.008336522,0.009367869,0.071519356,0.077768288,0.000000000],[0.008263668,0.413602616,0.004770392,0.034546006,0.000000000],[0.008134846,0.040749331,0.068709294,0.140242298,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G14 - C19 tSW 
Insertion    | Location [1] | Length Distribution [0.219988390,0.003055394,0.330654771,0.113660668,0.330685325,0.001863791,0.000091662] | Letter Distribution [0.239130435,0.239130435,0.456521739,0.065217391,0.000000000]// Insertion in Hairpin after nucleotide 3, position 1
Sequences of instances from HL_78347.4:
> HL_78347.4  5HR6 U   12 G   22
UAGAGGCCCAG
> HL_78347.4  5HR7 U   13 G   22
UAGAGGCCCAG
> HL_78347.4  2DER U   13 G   22
UAGAGGCCCAG
> HL_78347.4  1N78 U  513 G  522
UAGCGGUUAG
> HL_78347.4  6WBR C   55 G   63
CCUUCGUGG
> HL_78347.4  1QU2 C   31 G   39
CCUGAUAAG
> HL_78347.4  1FFY C   31 G   39
CCUGAUAAG
> HL_78347.4  8CRE U  188 G  193
UGUUUG
> HL_78347.4  3DIL G  149 C  154
GGUCUC