Alignment of HL_56334.1 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
2
I

6
2

3
7
1
I


In
acceptance
region

Cutoff
score
Full
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distance
Interior
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Alignment
score
deficit
HL_56334.1_Instance_1 HL_56334.1,HL_4V9F_004,U125_A129UCUAA
HL_56334.1_Sequence_1 HL_56334.14V9F_U125_A129UCUAAtrue78002.05
HL_56334.1_Instance_2 HL_56334.1,HL_6AJK_001,U933_A938UGGAAA
HL_56334.1_Sequence_2 HL_56334.16AJK_U933_A938UGGAAAtrue69002.92
HL_56334.1_Instance_3 HL_56334.1,HL_8SP9_002,C67_G71CAUUG
HL_56334.1_Sequence_3 HL_56334.18SP9_C67_G71CAUUGtrue90000.90
HL_56334.1_Instance_4 HL_56334.1,HL_6TQB_001,A10_U14AUAUU
HL_56334.1_Sequence_4 HL_56334.16TQB_A10_U14AUAUUtrue100000.00
HL_56334.1_Instance_5 HL_56334.1,HL_6TQA_003,A9_U13AUAUU
HL_56334.1_Sequence_5 HL_56334.16TQA_A9_U13AUAUUtrue100000.00
HL_56334.1_Instance_6 HL_56334.1,HL_4ZLD_001,C7_G11CUGUG
HL_56334.1_Sequence_6 HL_56334.14ZLD_C7_G11CUGUGtrue99000.06
HL_56334.1_Instance_7 HL_56334.1,HL_8UIW_004,U105_A110UCCUUA
HL_56334.1_Sequence_7 HL_56334.18UIW_U105_A110UCCUUAtrue72002.62
HL_56334.1_Instance_8 HL_56334.1,HL_6AAX_001,U933_A938UGGAAA
HL_56334.1_Sequence_8 HL_56334.16AAX_U933_A938UGGAAAtrue69002.92
HL_56334.1_Instance_9 HL_56334.1,HL_4QOZ_001,U11_A16UUUUCA
HL_56334.1_Sequence_9 HL_56334.14QOZ_U11_A16UUUUCAtrue96000.35
HL_56334.1_Instance_10 HL_56334.1,HL_4QI2_003,C10_G14CUGUG
HL_56334.1_Sequence_10 HL_56334.14QI2_C10_G14CUGUGtrue99000.06
HL_56334.1_Instance_11 HL_56334.1,HL_4QIL_002,C8_G12CUGUG
HL_56334.1_Sequence_11 HL_56334.14QIL_C8_G12CUGUGtrue99000.06
HL_56334.1_Instance_12 HL_56334.1,HL_4TUW_002,U13_A18UUUUCA
HL_56334.1_Sequence_12 HL_56334.14TUW_U13_A18UUUUCAtrue96000.35
HL_56334.1_Instance_13 HL_56334.1,HL_4Z31_001,C6_G10CUGUG
HL_56334.1_Sequence_13 HL_56334.14Z31_C6_G10CUGUGtrue99000.06
HL_56334.1_Instance_14 HL_56334.1,HL_1ZBH_001,U11_A16UUUUCA
HL_56334.1_Sequence_14 HL_56334.11ZBH_U11_A16UUUUCAtrue96000.35
HL_56334.1_Instance_15 HL_56334.1,HL_4OOG_001,G14_C19GAGUCC
HL_56334.1_Sequence_15 HL_56334.14OOG_G14_C19GAGUCCtrue72002.65
HL_56334.1_Instance_16 HL_56334.1,HL_5T16_002,G16_C21GAGUCC
HL_56334.1_Sequence_16 HL_56334.15T16_G16_C21GAGUCCtrue72002.65

Conserved interactions between motif group positions in HL_56334.1:
1 2 s35 
1 3 cWW 
2 3 s55
JAR3D SCFG/MRF model for HL_56334.1:
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 [3] // Initial node
BasepairNode | Deletion Probability [0.0000000000439613] | Pair Probability [[0.008186185,0.016096044,0.009133004,0.191953022,0.000000000],[0.017856649,0.008553250,0.219962121,0.010637082,0.000000000],[0.009158620,0.192433570,0.001814643,0.024105290,0.000000000],[0.237709580,0.010369727,0.032966724,0.009064488,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.001358485,0.436461730,0.560277907,0.001814547,0.000087331] | Left Letter Distribution [0.129629630,0.129629630,0.240740741,0.500000000,0.000000000] | Right Length Distribution [0.065025816,0.931907295,0.002921309,0.000145580] | Right Letter Distribution [0.147058824,0.323529412,0.029411765,0.500000000,0.000000000] | Left Index [1] | Right Index [3] // Basepair U125 - A129 cWW 
HairpinNode  | Num Bases [1] | Left Index [2] | Right Index [2] | Norm Constant [1.000000000000000] // Hairpin node A128:A128
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.305555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.027777778,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.416666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A128
Sequences of instances from HL_56334.1:
> HL_56334.1  4V9F U  125 A  129
UCUAA
> HL_56334.1  6AJK U  933 A  938
UGGAAA
> HL_56334.1  8SP9 C   67 G   71
CAUUG
> HL_56334.1  6TQB A   10 U   14
AUAUU
> HL_56334.1  6TQA A    9 U   13
AUAUU
> HL_56334.1  4ZLD C    7 G   11
CUGUG
> HL_56334.1  8UIW U  105 A  110
UCCUUA
> HL_56334.1  6AAX U  933 A  938
UGGAAA
> HL_56334.1  4QOZ U   11 A   16
UUUUCA
> HL_56334.1  4QI2 C   10 G   14
CUGUG
> HL_56334.1  4QIL C    8 G   12
CUGUG
> HL_56334.1  4TUW U   13 A   18
UUUUCA
> HL_56334.1  4Z31 C    6 G   10
CUGUG
> HL_56334.1  1ZBH U   11 A   16
UUUUCA
> HL_56334.1  4OOG G   14 C   19
GAGUCC
> HL_56334.1  5T16 G   16 C   21
GAGUCC