Alignment of HL_07886.3 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
2
I

10
2

5
11
1
I


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HL_07886.3_Instance_1 HL_07886.3,HL_8CRE_068,C3205_G3212CGGAAAGG
HL_07886.3_Sequence_1 HL_07886.38CRE_C_3205_G_3212CGGAAAGGtrue85001.40
HL_07886.3_Instance_2 HL_07886.3,HL_8P9A_180,C3240_G3247CGGAAAGG
HL_07886.3_Sequence_2 HL_07886.38P9A_C_3240_G_3247CGGAAAGGtrue85001.40
HL_07886.3_Instance_3 HL_07886.3,HL_2QUX_002,G10_C17GAUAUGGC
HL_07886.3_Sequence_3 HL_07886.32QUX_G10_C17GAUAUGGCtrue56004.19
HL_07886.3_Instance_4 HL_07886.3,HL_5B2P_003,A64_U68AUUUU
HL_07886.3_Sequence_4 HL_07886.35B2P_A64_U68AUUUUtrue48004.93
HL_07886.3_Instance_5 HL_07886.3,HL_8JY0_002,U30_A36UGAAGGA
HL_07886.3_Sequence_5 HL_07886.38JY0_U30_A36UGAAGGAtrue100000.00
HL_07886.3_Instance_6 HL_07886.3,HL_9DXL_002,U14_A20UGAAGGA
HL_07886.3_Sequence_6 HL_07886.39DXL_U14_A20UGAAGGAtrue100000.00

Conserved interactions between motif group positions in HL_07886.3:
1 2 s35 
1 5 cWW 
2 4 s33 
2 5 s55 
3 4 s55
JAR3D SCFG/MRF model for HL_07886.3:
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 [0.0000002938397278] | Pair Probability [[0.009006543,0.017894042,0.010062967,0.201190266,0.000000000],[0.019126021,0.009336196,0.212781293,0.011757893,0.000000000],[0.010085822,0.201995530,0.001988429,0.027746318,0.000000000],[0.212339272,0.011569435,0.033134779,0.009985193,0.000000000],[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 [0.170928484,0.821824149,0.006905511,0.000341857] | Right Letter Distribution [0.071428571,0.071428571,0.785714286,0.071428571,0.000000000] | Left Index [1] | Right Index [5] // Basepair C3205 - G3212 cWW 
HairpinNode  | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G3206:A3210
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.187500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.562500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.187500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G3206
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.437500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.312500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.187500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G3207
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.437500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.187500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A3210
Insertion    | Location [1] | Length Distribution [0.826344012,0.171868555,0.001718686,0.000068747] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Insertion    | Location [2] | Length Distribution [0.168193628,0.496376316,0.332353343,0.002939970,0.000136743] | Letter Distribution [0.722222222,0.055555556,0.055555556,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2
Sequences of instances from HL_07886.3:
> HL_07886.3  8CRE C 3205 G 3212
CGGAAAGG
> HL_07886.3  8P9A C 3240 G 3247
CGGAAAGG
> HL_07886.3  2QUX G   10 C   17
GAUAUGGC
> HL_07886.3  5B2P A   64 U   68
AUUUU
> HL_07886.3  8JY0 U   30 A   36
UGAAGGA
> HL_07886.3  9DXL U   14 A   20
UGAAGGA