Alignment of HL_59710.7 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_59710.7
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
4
I

10
4

5
11
4
I

12
4

6
13
4
I

14
4

7
15
3
I

16
3

8
17
2
I

18
2

9
19
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_59710.7_Instance_1 HL_59710.7_HL_4TUE_034_G31_C39GCUCAUAAC
HL_59710.7_Sequence_1 HL_59710.7_HL_4TUE_034_G31_C39GCUCAUAACtrue95000.74
HL_59710.7_Instance_2 HL_59710.7_HL_4V9Q_214_G31_C39GCUCAUAAC
HL_59710.7_Sequence_2 HL_59710.7_HL_4V9Q_214_G31_C39GCUCAUAACtrue95000.74
HL_59710.7_Instance_3 HL_59710.7_HL_4V50_137_G31_C39GCUCAUAAC
HL_59710.7_Sequence_3 HL_59710.7_HL_4V50_137_G31_C39GCUCAUAACtrue95000.74
HL_59710.7_Instance_4 HL_59710.7_HL_2AZX_005_A531_U539ACUCCAGAU
HL_59710.7_Sequence_4 HL_59710.7_HL_2AZX_005_A531_U539ACUCCAGAUtrue87001.96
HL_59710.7_Instance_5 HL_59710.7_HL_2AZX_008_A531_U539ACUCCAGAU
HL_59710.7_Sequence_5 HL_59710.7_HL_2AZX_008_A531_U539ACUCCAGAUtrue87001.96
HL_59710.7_Instance_6 HL_59710.7_HL_4WT8_216_G32_C40GCUCAUAAC
HL_59710.7_Sequence_6 HL_59710.7_HL_4WT8_216_G32_C40GCUCAUAACtrue95000.74
HL_59710.7_Instance_7 HL_59710.7_HL_6UFG_007_G32_C40GCUGAUAAC
HL_59710.7_Sequence_7 HL_59710.7_HL_6UFG_007_G32_C40GCUGAUAACtrue95000.74
HL_59710.7_Instance_8 HL_59710.7_HL_5IBB_210_C31_G39CCUUACAAG
HL_59710.7_Sequence_8 HL_59710.7_HL_5IBB_210_C31_G39CCUUACAAGtrue82002.69
HL_59710.7_Instance_9 HL_59710.7_HL_6ORD_036_C31_G39CUUGGCAAG
HL_59710.7_Sequence_9 HL_59710.7_HL_6ORD_036_C31_G39CUUGGCAAGtrue66005.06
HL_59710.7_Instance_10 HL_59710.7_HL_4P95_002_G241_C249GCUAAUCAC
HL_59710.7_Sequence_10 HL_59710.7_HL_4P95_002_G241_C249GCUAAUCACtrue67004.87
HL_59710.7_Instance_11 HL_59710.7_HL_4V9I_039_U31_A39UCUCGAAAA
HL_59710.7_Sequence_11 HL_59710.7_HL_4V9I_039_U31_A39UCUCGAAAAtrue88001.86
HL_59710.7_Instance_12 HL_59710.7_HL_4R4V_001_C626_G634CGUCGUCGG
HL_59710.7_Sequence_12 HL_59710.7_HL_4R4V_001_C626_G634CGUCGUCGGtrue55006.78
HL_59710.7_Instance_13 HL_59710.7_HL_4R4V_005_C626_G634CGUCGUCGG
HL_59710.7_Sequence_13 HL_59710.7_HL_4R4V_005_C626_G634CGUCGUCGGtrue55006.78
HL_59710.7_Instance_14 HL_59710.7_HL_4V9K_034_A31_U39ACUCAUAAU
HL_59710.7_Sequence_14 HL_59710.7_HL_4V9K_034_A31_U39ACUCAUAAUtrue97000.45
HL_59710.7_Instance_15 HL_59710.7_HL_4YCO_002_A31_U39AUUGAAAAU
HL_59710.7_Sequence_15 HL_59710.7_HL_4YCO_002_A31_U39AUUGAAAAUtrue84002.44
HL_59710.7_Instance_16 HL_59710.7_HL_1U0B_002_A31_U39AUUGCAAAU
HL_59710.7_Sequence_16 HL_59710.7_HL_1U0B_002_A31_U39AUUGCAAAUtrue79003.16
HL_59710.7_Instance_17 HL_59710.7_HL_3TUP_002_A31_U39ACUGAAAAU
HL_59710.7_Sequence_17 HL_59710.7_HL_3TUP_002_A31_U39ACUGAAAAUtrue100000.00
HL_59710.7_Instance_18 HL_59710.7_HL_1N78_002_C531_G539CCUCUCAAG
HL_59710.7_Sequence_18 HL_59710.7_HL_1N78_002_C531_G539CCUCUCAAGtrue81002.88
HL_59710.7_Instance_19 HL_59710.7_HL_6UFM_002_G32_C40GCUGAUAAC
HL_59710.7_Sequence_19 HL_59710.7_HL_6UFM_002_G32_C40GCUGAUAACtrue95000.74
HL_59710.7_Instance_20 HL_59710.7_HL_3WFS_002_A31_U39ACUGAAAAU
HL_59710.7_Sequence_20 HL_59710.7_HL_3WFS_002_A31_U39ACUGAAAAUtrue100000.00
HL_59710.7_Instance_21 HL_59710.7_HL_4V90_033_A31_U39AUUGAAAAU
HL_59710.7_Sequence_21 HL_59710.7_HL_4V90_033_A31_U39AUUGAAAAUtrue84002.44
HL_59710.7_Instance_22 HL_59710.7_HL_5T83_002_U56_A64UUUCACAAA
HL_59710.7_Sequence_22 HL_59710.7_HL_5T83_002_U56_A64UUUCACAAAtrue74003.87
HL_59710.7_Instance_23 HL_59710.7_HL_3W3S_002_A31_U39ACUUCAAAU
HL_59710.7_Sequence_23 HL_59710.7_HL_3W3S_002_A31_U39ACUUCAAAUtrue86002.14
HL_59710.7_Instance_24 HL_59710.7_HL_3W3S_006_A31_U39ACUUCAAAU
HL_59710.7_Sequence_24 HL_59710.7_HL_3W3S_006_A31_U39ACUUCAAAUtrue86002.14
HL_59710.7_Instance_25 HL_59710.7_HL_2AKE_002_A31_U39ACUCCAGAU
HL_59710.7_Sequence_25 HL_59710.7_HL_2AKE_002_A31_U39ACUCCAGAUtrue87001.96
HL_59710.7_Instance_26 HL_59710.7_HL_2AKE_005_A31_U39ACUCCAGAU
HL_59710.7_Sequence_26 HL_59710.7_HL_2AKE_005_A31_U39ACUCCAGAUtrue87001.96
HL_59710.7_Instance_27 HL_59710.7_HL_2IY5_002_A31_U39ACUGAAAAU
HL_59710.7_Sequence_27 HL_59710.7_HL_2IY5_002_A31_U39ACUGAAAAUtrue100000.00
HL_59710.7_Instance_28 HL_59710.7_HL_2IY5_005_A31_U39ACUGAAAAU
HL_59710.7_Sequence_28 HL_59710.7_HL_2IY5_005_A31_U39ACUGAAAAUtrue100000.00
HL_59710.7_Instance_29 HL_59710.7_HL_4P5J_002_C25_G33CUCGACACG
HL_59710.7_Sequence_29 HL_59710.7_HL_4P5J_002_C25_G33CUCGACACGtrue44008.36
HL_59710.7_Instance_30 HL_59710.7_HL_7KGA_001_U22_G31UCAAGCCUAG
HL_59710.7_Sequence_30 HL_59710.7_HL_7KGA_001_U22_G31UCAAGCCUAGtrue70013.84
HL_59710.7_Instance_31 HL_59710.7_HL_1J1U_002_A532_U540ACUGUAGAU
HL_59710.7_Sequence_31 HL_59710.7_HL_1J1U_002_A532_U540ACUGUAGAUtrue81002.85
HL_59710.7_Instance_32 HL_59710.7_HL_1J1U_005_A532_U540ACUGUAGAU
HL_59710.7_Sequence_32 HL_59710.7_HL_1J1U_005_A532_U540ACUGUAGAUtrue81002.85

Conserved interactions between motif group positions in HL_59710.7:
1 2 s35 
1 9 cWW 
2 3 s35 
2 8 bif 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
8 9 s35 
3 6 6BPh
JAR3D SCFG/MRF model for HL_59710.7:
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 [9] // Initial node G31 - C39 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.007321517,0.015593468,0.008115979,0.273288254,0.000000000],[0.020966448,0.007871885,0.195605409,0.009166410,0.000000000],[0.008114035,0.204048003,0.001623127,0.029951416,0.000000000],[0.165611877,0.009372059,0.034868952,0.008481159,0.000000000],[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 [9] // Basepair G31 - C39 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.020608131,0.023150601,0.005028382,0.005028382,0.000000000],[0.703315889,0.058889179,0.005028382,0.005028382,0.000000000],[0.005028382,0.005028382,0.043715289,0.032191143,0.000000000],[0.061566671,0.016336040,0.005028382,0.005028382,0.000000000],[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 [2] | Right Index [8] // Basepair C32 - A38 bif 
HairpinNode  | Num Bases [5] | Left Index [3] | Right Index [7] | Norm Constant [0.999999999999999] // Hairpin node U33:A37
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.033185841,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.033185841,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.002212389,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.931415929,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U33
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.044117647,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.426470588,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.426470588,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.102941176,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C34
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.514705882,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.132352941,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.102941176,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A35
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.485294118,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.191176471,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.014705882,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.308823529,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U36
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.661764706,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.102941176,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.191176471,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.044117647,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A37
Insertion    | Location [1] | Length Distribution [0.967164848,0.032708413,0.000124302,0.000002437] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 3, position 1
Sequences of instances from HL_59710.7:
> HL_59710.7 HL_4TUE_034 G   31 C   39
GCUCAUAAC
> HL_59710.7 HL_4V9Q_214 G   31 C   39
GCUCAUAAC
> HL_59710.7 HL_4V50_137 G   31 C   39
GCUCAUAAC
> HL_59710.7 HL_2AZX_005 A  531 U  539
ACUCCAGAU
> HL_59710.7 HL_2AZX_008 A  531 U  539
ACUCCAGAU
> HL_59710.7 HL_4WT8_216 G   32 C   40
GCUCAUAAC
> HL_59710.7 HL_6UFG_007 G   32 C   40
GCUGAUAAC
> HL_59710.7 HL_5IBB_210 C   31 G   39
CCUUACAAG
> HL_59710.7 HL_6ORD_036 C   31 G   39
CUUGGCAAG
> HL_59710.7 HL_4P95_002 G  241 C  249
GCUAAUCAC
> HL_59710.7 HL_4V9I_039 U   31 A   39
UCUCGAAAA
> HL_59710.7 HL_4R4V_001 C  626 G  634
CGUCGUCGG
> HL_59710.7 HL_4R4V_005 C  626 G  634
CGUCGUCGG
> HL_59710.7 HL_4V9K_034 A   31 U   39
ACUCAUAAU
> HL_59710.7 HL_4YCO_002 A   31 U   39
AUUGAAAAU
> HL_59710.7 HL_1U0B_002 A   31 U   39
AUUGCAAAU
> HL_59710.7 HL_3TUP_002 A   31 U   39
ACUGAAAAU
> HL_59710.7 HL_1N78_002 C  531 G  539
CCUCUCAAG
> HL_59710.7 HL_6UFM_002 G   32 C   40
GCUGAUAAC
> HL_59710.7 HL_3WFS_002 A   31 U   39
ACUGAAAAU
> HL_59710.7 HL_4V90_033 A   31 U   39
AUUGAAAAU
> HL_59710.7 HL_5T83_002 U   56 A   64
UUUCACAAA
> HL_59710.7 HL_3W3S_002 A   31 U   39
ACUUCAAAU
> HL_59710.7 HL_3W3S_006 A   31 U   39
ACUUCAAAU
> HL_59710.7 HL_2AKE_002 A   31 U   39
ACUCCAGAU
> HL_59710.7 HL_2AKE_005 A   31 U   39
ACUCCAGAU
> HL_59710.7 HL_2IY5_002 A   31 U   39
ACUGAAAAU
> HL_59710.7 HL_2IY5_005 A   31 U   39
ACUGAAAAU
> HL_59710.7 HL_4P5J_002 C   25 G   33
CUCGACACG
> HL_59710.7 HL_7KGA_001 U   22 G   31
UCAAGCCUAG
> HL_59710.7 HL_1J1U_002 A  532 U  540
ACUGUAGAU
> HL_59710.7 HL_1J1U_005 A  532 U  540
ACUGUAGAU