Alignment of HL_02361.5 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
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_02361.5_Instance_1 HL_02361.5_HL_6VMY_001_U223_A229UGAACAA
HL_02361.5_Sequence_1 HL_02361.5_HL_6VMY_001_U223_A229UGAACAAtrue99000.10
HL_02361.5_Instance_2 HL_02361.5_HL_5O7H_001_C32_G38CGCACAG
HL_02361.5_Sequence_2 HL_02361.5_HL_5O7H_001_C32_G38CGCACAGtrue85001.44
HL_02361.5_Instance_3 HL_02361.5_HL_5J7L_174_A1630_U1636AGAGAAU
HL_02361.5_Sequence_3 HL_02361.5_HL_5J7L_174_A_1630_U_1636AGAGAAUtrue74002.43
HL_02361.5_Instance_4 HL_02361.5_HL_4Y4O_123_C641_G647CGAACAG
HL_02361.5_Sequence_4 HL_02361.5_HL_4Y4O_123_C641_G647CGAACAGtrue100000.00
HL_02361.5_Instance_5 HL_02361.5_HL_2XLK_001_C10_G16CGUAUAG
HL_02361.5_Sequence_5 HL_02361.5_HL_2XLK_001_C10_G16CGUAUAGtrue88001.10
HL_02361.5_Instance_6 HL_02361.5_HL_1XJR_001_G21_C27GGAGUAC
HL_02361.5_Sequence_6 HL_02361.5_HL_1XJR_001_G21_C27GGAGUACtrue83001.57
HL_02361.5_Instance_7 HL_02361.5_HL_4AL5_001_C10_G16CGUAUAG
HL_02361.5_Sequence_7 HL_02361.5_HL_4AL5_001_C10_G16CGUAUAGtrue88001.10
HL_02361.5_Instance_8 HL_02361.5_HL_5LM7_001_U21_A27UGAAGAA
HL_02361.5_Sequence_8 HL_02361.5_HL_5LM7_001_U21_A27UGAAGAAtrue85001.40
HL_02361.5_Instance_9 HL_02361.5_HL_5TBW_042_U1862_G1868UGAACAG
HL_02361.5_Sequence_9 HL_02361.5_HL_5TBW_042_U_1862_G_1868UGAACAGtrue96000.42
HL_02361.5_Instance_10 HL_02361.5_HL_4WF9_021_U686_G692UGAAUAG
HL_02361.5_Sequence_10 HL_02361.5_HL_4WF9_021_U686_G692UGAAUAGtrue96000.42
HL_02361.5_Instance_11 HL_02361.5_HL_4V9F_016_U493_G499UCAGAAG
HL_02361.5_Sequence_11 HL_02361.5_HL_4V9F_016_U493_G499UCAGAAGtrue65003.33
HL_02361.5_Instance_12 HL_02361.5_HL_3D0U_003_G121_C127GGAAUAC
HL_02361.5_Sequence_12 HL_02361.5_HL_3D0U_003_G121_C127GGAAUACtrue98000.21
HL_02361.5_Instance_13 HL_02361.5_HL_7A0S_046_C1797_G1803CGAACAG
HL_02361.5_Sequence_13 HL_02361.5_HL_7A0S_046_C_1797_G_1803CGAACAGtrue100000.00
HL_02361.5_Instance_14 HL_02361.5_HL_5TBW_074_U73_G78UUGCAG
HL_02361.5_Sequence_14 HL_02361.5_HL_5TBW_074_U73_G78UUGCAGtrue38005.84
HL_02361.5_Instance_15 HL_02361.5_HL_5VSU_001_U70_A75UGCAUA
HL_02361.5_Sequence_15 HL_02361.5_HL_5VSU_001_U70_A75UGCAUAtrue71002.76
HL_02361.5_Instance_16 HL_02361.5_HL_7A0S_004_C133_G138CGUAAG
HL_02361.5_Sequence_16 HL_02361.5_HL_7A0S_004_C133_G138CGUAAGtrue84001.55

Conserved interactions between motif group positions in HL_02361.5:
1 2 s35 
1 6 cWW 
2 5 tSH 
3 4 s35 
4 5 s35 
5 6 s35 
4 2 7BR
JAR3D SCFG/MRF model for HL_02361.5:
Character Definition | A,C,G,U,* // Define characters here
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Initial node U223 - A229 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008686343,0.015043492,0.010150759,0.148076819,0.000000000],[0.079668596,0.012543602,0.195405288,0.011922454,0.000000000],[0.010248665,0.158198059,0.002094714,0.020629282,0.000000000],[0.177529753,0.011440134,0.128618680,0.009743362,0.000000000],[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 U223 - A229 cWW 
BasepairNode | Deletion Probability [0.0000003315588406] | Pair Probability [[0.100363935,0.096106402,0.001186342,0.005620556,0.000000000],[0.109991044,0.102350464,0.001186342,0.001186342,0.000000000],[0.235374957,0.001186342,0.006030461,0.107664908,0.000000000],[0.125126743,0.104252476,0.001186342,0.001186342,0.000000000],[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 [0.188939376,0.808380908,0.002553497,0.000126218] | Right Letter Distribution [0.166666667,0.366666667,0.100000000,0.366666667,0.000000000] | Left Index [2] | Right Index [5] // Basepair G224 - A228 tSH 
HairpinNode  | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A225:A226
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.583333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.138888889,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.194444444,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A225
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.737804878,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.067073171,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.189024390,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.006097561,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A226
Sequences of instances from HL_02361.5:
> HL_02361.5 HL_6VMY_001 U  223 A  229
UGAACAA
> HL_02361.5 HL_5O7H_001 C   32 G   38
CGCACAG
> HL_02361.5 HL_5J7L_174 A 1630 U 1636
AGAGAAU
> HL_02361.5 HL_4Y4O_123 C  641 G  647
CGAACAG
> HL_02361.5 HL_2XLK_001 C   10 G   16
CGUAUAG
> HL_02361.5 HL_1XJR_001 G   21 C   27
GGAGUAC
> HL_02361.5 HL_4AL5_001 C   10 G   16
CGUAUAG
> HL_02361.5 HL_5LM7_001 U   21 A   27
UGAAGAA
> HL_02361.5 HL_5TBW_042 U 1862 G 1868
UGAACAG
> HL_02361.5 HL_4WF9_021 U  686 G  692
UGAAUAG
> HL_02361.5 HL_4V9F_016 U  493 G  499
UCAGAAG
> HL_02361.5 HL_3D0U_003 G  121 C  127
GGAAUAC
> HL_02361.5 HL_7A0S_046 C 1797 G 1803
CGAACAG
> HL_02361.5 HL_5TBW_074 U   73 G   78
UUGCAG
> HL_02361.5 HL_5VSU_001 U   70 A   75
UGCAUA
> HL_02361.5 HL_7A0S_004 C  133 G  138
CGUAAG