Alignment of HL_53890.2 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
3

3
7
3
I

8
3

4
9
2
I

10
2

5
11
1
I


In
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Cutoff
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Full
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Interior
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Alignment
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HL_53890.2_Instance_1 HL_53890.2,HL_7A0S_007,A202_U207AGAAUU
HL_53890.2_Sequence_1 HL_53890.27A0S_A202_U207AGAAUUtrue100000.00
HL_53890.2_Instance_2 HL_53890.2,HL_9DFE_006,A225_U230AGAAAU
HL_53890.2_Sequence_2 HL_53890.29DFE_A225_U230AGAAAUtrue96000.37
HL_53890.2_Instance_3 HL_53890.2,HL_4WF9_007,A228_U233AAAAUU
HL_53890.2_Sequence_3 HL_53890.24WF9_A228_U233AAAAUUtrue100000.00
HL_53890.2_Instance_4 HL_53890.2,HL_8CRE_002,C68_G73CAACAG
HL_53890.2_Sequence_4 HL_53890.28CRE_C68_G73CAACAGtrue89001.02
HL_53890.2_Instance_5 HL_53890.2,HL_8P9A_114,C69_G74CAACCG
HL_53890.2_Sequence_5 HL_53890.28P9A_C69_G74CAACCGtrue83001.61
HL_53890.2_Instance_6 HL_53890.2,HL_2NUE_001,C21_G26CGCAAG
HL_53890.2_Sequence_6 HL_53890.22NUE_C21_G26CGCAAGtrue95000.50
HL_53890.2_Instance_7 HL_53890.2,HL_8CRE_076,C108_G114CACAUUG
HL_53890.2_Sequence_7 HL_53890.28CRE_C108_G114CACAUUGtrue75002.39
HL_53890.2_Instance_8 HL_53890.2,HL_7A0S_023,U792_G798UGAAAAG
HL_53890.2_Sequence_8 HL_53890.27A0S_U792_G798UGAAAAGtrue74002.48
HL_53890.2_Instance_9 HL_53890.2,HL_8P9A_188,C108_G114CACAUUG
HL_53890.2_Sequence_9 HL_53890.28P9A_C108_G114CACAUUGtrue75002.39
HL_53890.2_Instance_10 HL_53890.2,HL_8P9A_193,C190_G195CCUUUG
HL_53890.2_Sequence_10 HL_53890.28P9A_C190_G195CCUUUGtrue79001.99
HL_53890.2_Instance_11 HL_53890.2,HL_4UYK_003,U98_G103UGUAAG
HL_53890.2_Sequence_11 HL_53890.24UYK_U98_G103UGUAAGtrue74002.47
HL_53890.2_Instance_12 HL_53890.2,HL_6VMY_004,C287_G293CCAAGCG
HL_53890.2_Sequence_12 HL_53890.26VMY_C287_G293CCAAGCGtrue72002.70
HL_53890.2_Instance_13 HL_53890.2,HL_8P9A_194,C230_G235CUUCGG
HL_53890.2_Sequence_13 HL_53890.28P9A_C230_G235CUUCGGtrue64003.46
HL_53890.2_Instance_14 HL_53890.2,HL_8S95_003,C67_G73CCACGUG
HL_53890.2_Sequence_14 HL_53890.28S95_C67_G73CCACGUGtrue77002.18
HL_53890.2_Instance_15 HL_53890.2,HL_1P6V_001,C26_G31CUUCGG
HL_53890.2_Sequence_15 HL_53890.21P6V_C26_G31CUUCGGtrue64003.46

Conserved interactions between motif group positions in HL_53890.2:
1 2 s35 
1 5 cWW 
2 3 s35 
2 5 s55 
4 5 s35
JAR3D SCFG/MRF model for HL_53890.2:
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 [0.0000003539658436] | Pair Probability [[0.008615710,0.015670354,0.009929952,0.184248347,0.000000000],[0.050875518,0.010748113,0.249976806,0.011888244,0.000000000],[0.010036296,0.159358136,0.001988751,0.025050456,0.000000000],[0.164034985,0.011548940,0.076402288,0.009627104,0.000000000],[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 [0.201424549,0.795759483,0.002683452,0.000132516] | Right Letter Distribution [0.321428571,0.178571429,0.035714286,0.464285714,0.000000000] | Left Index [1] | Right Index [5] // Basepair A202 - U207 cWW 
HairpinNode  | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G203:A205
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.323529412,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.205882353,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.323529412,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.147058824,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G203
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.323529412,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.029411765,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.147058824,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A204
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.382352941,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.147058824,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.264705882,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.205882353,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A205
Insertion    | Location [1] | Length Distribution [0.598440869,0.400066346,0.001426439,0.000066346] | Letter Distribution [0.437500000,0.187500000,0.062500000,0.312500000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Insertion    | Location [2] | Length Distribution [0.863704278,0.135687012,0.000586575,0.000022135] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2
Sequences of instances from HL_53890.2:
> HL_53890.2  7A0S A  202 U  207
AGAAUU
> HL_53890.2  9DFE A  225 U  230
AGAAAU
> HL_53890.2  4WF9 A  228 U  233
AAAAUU
> HL_53890.2  8CRE C   68 G   73
CAACAG
> HL_53890.2  8P9A C   69 G   74
CAACCG
> HL_53890.2  2NUE C   21 G   26
CGCAAG
> HL_53890.2  8CRE C  108 G  114
CACAUUG
> HL_53890.2  7A0S U  792 G  798
UGAAAAG
> HL_53890.2  8P9A C  108 G  114
CACAUUG
> HL_53890.2  8P9A C  190 G  195
CCUUUG
> HL_53890.2  4UYK U   98 G  103
UGUAAG
> HL_53890.2  6VMY C  287 G  293
CCAAGCG
> HL_53890.2  8P9A C  230 G  235
CUUCGG
> HL_53890.2  8S95 C   67 G   73
CCACGUG
> HL_53890.2  1P6V C   26 G   31
CUUCGG