Alignment of HL_01008.4 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_01008.4
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
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_01008.4_Instance_1 HL_01008.4_HL_5MSF_001_G7_C12GAUCAC
HL_01008.4_Sequence_1 HL_01008.4_HL_5MSF_001_G7_C12GAUCACtrue100000.00
HL_01008.4_Instance_2 HL_01008.4_HL_5MSF_005_G7_C12GAUCAC
HL_01008.4_Sequence_2 HL_01008.4_HL_5MSF_005_G7_C12GAUCACtrue100000.00
HL_01008.4_Instance_3 HL_01008.4_HL_1U1Y_005_G7_C12GAUCAC
HL_01008.4_Sequence_3 HL_01008.4_HL_1U1Y_005_G7_C12GAUCACtrue100000.00
HL_01008.4_Instance_4 HL_01008.4_HL_1U1Y_001_G7_C12GAUCAC
HL_01008.4_Sequence_4 HL_01008.4_HL_1U1Y_001_G7_C12GAUCACtrue100000.00
HL_01008.4_Instance_5 HL_01008.4_HL_2IZN_005_G8_C13GAUUAC
HL_01008.4_Sequence_5 HL_01008.4_HL_2IZN_005_G8_C13GAUUACtrue88001.23
HL_01008.4_Instance_6 HL_01008.4_HL_2IZN_001_G8_C13GAUUAC
HL_01008.4_Sequence_6 HL_01008.4_HL_2IZN_001_G8_C13GAUUACtrue88001.23
HL_01008.4_Instance_7 HL_01008.4_HL_7MSF_005_C5_G10CAACAG
HL_01008.4_Sequence_7 HL_01008.4_HL_7MSF_005_C5_G10CAACAGtrue93000.74
HL_01008.4_Instance_8 HL_01008.4_HL_7MSF_001_C5_G10CAACAG
HL_01008.4_Sequence_8 HL_01008.4_HL_7MSF_001_C5_G10CAACAGtrue93000.74
HL_01008.4_Instance_9 HL_01008.4_HL_6CZR_102_C1430_G1435CUACGG
HL_01008.4_Sequence_9 HL_01008.4_HL_6CZR_102_C_1430_G_1435CUACGGtrue59004.21

Conserved interactions between motif group positions in HL_01008.4:
1 2 s35 
1 5 cWW 
2 4 s35 
2 5 s55 
4 3 7BPh
JAR3D SCFG/MRF model for HL_01008.4:
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 [5] // Initial node G7 - C12 from junction 
BasepairNode | Deletion Probability [0.0000001233099223] | Pair Probability [[0.009047108,0.017980999,0.010334636,0.187602286,0.000000000],[0.016991075,0.008984252,0.219366759,0.012588934,0.000000000],[0.010296248,0.248730076,0.001955254,0.024017273,0.000000000],[0.186798784,0.012745957,0.022986810,0.009573550,0.000000000],[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 [0.005492996,0.988739357,0.005492996,0.000274650] | Right Letter Distribution [0.772727273,0.045454545,0.136363636,0.045454545,0.000000000] | Left Index [1] | Right Index [5] // Basepair G7 - C12 cWW 
HairpinNode  | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A8:C10
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.772727273,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.136363636,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A8
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.318181818,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.590909091,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U9
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.007692308,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.761538462,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.007692308,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.223076923,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C10
Sequences of instances from HL_01008.4:
> HL_01008.4 HL_5MSF_001 G    7 C   12
GAUCAC
> HL_01008.4 HL_5MSF_005 G    7 C   12
GAUCAC
> HL_01008.4 HL_1U1Y_005 G    7 C   12
GAUCAC
> HL_01008.4 HL_1U1Y_001 G    7 C   12
GAUCAC
> HL_01008.4 HL_2IZN_005 G    8 C   13
GAUUAC
> HL_01008.4 HL_2IZN_001 G    8 C   13
GAUUAC
> HL_01008.4 HL_7MSF_005 C    5 G   10
CAACAG
> HL_01008.4 HL_7MSF_001 C    5 G   10
CAACAG
> HL_01008.4 HL_6CZR_102 C 1430 G 1435
CUACGG