Alignment of HL_79299.9 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for HL_79299.9
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
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_79299.9_Instance_1 HL_79299.9_HL_5Y85_004_C28_G33CUUCGG
HL_79299.9_Sequence_1 HL_79299.9_HL_5Y85_004_C28_G33CUUCGGtrue100000.00
HL_79299.9_Instance_2 HL_79299.9_HL_5D5L_003_C60_G65CUUCGG
HL_79299.9_Sequence_2 HL_79299.9_HL_5D5L_003_C60_G65CUUCGGtrue100000.00
HL_79299.9_Instance_3 HL_79299.9_HL_5J7L_011_C419_G424CUUCGG
HL_79299.9_Sequence_3 HL_79299.9_HL_5J7L_011_C419_G424CUUCGGtrue100000.00
HL_79299.9_Instance_4 HL_79299.9_HL_5LYS_002_C48_G60CUUCGG
HL_79299.9_Sequence_4 HL_79299.9_HL_5LYS_002_C48_G60CUUCGGtrue100000.00
HL_79299.9_Instance_5 HL_79299.9_HL_4Y4O_144_C1691_G1696CUUCGG
HL_79299.9_Sequence_5 HL_79299.9_HL_4Y4O_144_C_1691_G_1696CUUCGGtrue100000.00
HL_79299.9_Instance_6 HL_79299.9_HL_4JF2_003_C60_G65CUUCGG
HL_79299.9_Sequence_6 HL_79299.9_HL_4JF2_003_C60_G65CUUCGGtrue100000.00
HL_79299.9_Instance_7 HL_79299.9_HL_4LFB_011_C419_G424CUUCGG
HL_79299.9_Sequence_7 HL_79299.9_HL_4LFB_011_C419_G424CUUCGGtrue100000.00
HL_79299.9_Instance_8 HL_79299.9_HL_5J7L_175_C1691_G1696CUUCGG
HL_79299.9_Sequence_8 HL_79299.9_HL_5J7L_175_C_1691_G_1696CUUCGGtrue100000.00
HL_79299.9_Instance_9 HL_79299.9_HL_4V9F_044_C1769_G1774CUUCGG
HL_79299.9_Sequence_9 HL_79299.9_HL_4V9F_044_C_1769_G_1774CUUCGGtrue100000.00
HL_79299.9_Instance_10 HL_79299.9_HL_4PDB_001_C17_G22CUUCGG
HL_79299.9_Sequence_10 HL_79299.9_HL_4PDB_001_C17_G22CUUCGGtrue100000.00
HL_79299.9_Instance_11 HL_79299.9_HL_4PMI_005_C53_G58CUUCGG
HL_79299.9_Sequence_11 HL_79299.9_HL_4PMI_005_C53_G58CUUCGGtrue100000.00
HL_79299.9_Instance_12 HL_79299.9_HL_4PMI_003_C53_G58CUUCGG
HL_79299.9_Sequence_12 HL_79299.9_HL_4PMI_003_C53_G58CUUCGGtrue100000.00
HL_79299.9_Instance_13 HL_79299.9_HL_4PMI_001_C53_G58CUUCGG
HL_79299.9_Sequence_13 HL_79299.9_HL_4PMI_001_C53_G58CUUCGGtrue100000.00
HL_79299.9_Instance_14 HL_79299.9_HL_4PMI_004_C53_G58CUUCGG
HL_79299.9_Sequence_14 HL_79299.9_HL_4PMI_004_C53_G58CUUCGGtrue100000.00
HL_79299.9_Instance_15 HL_79299.9_HL_4PMI_002_C53_G58CUUCGG
HL_79299.9_Sequence_15 HL_79299.9_HL_4PMI_002_C53_G58CUUCGGtrue100000.00
HL_79299.9_Instance_16 HL_79299.9_HL_4PMI_006_C53_G58CUUCGG
HL_79299.9_Sequence_16 HL_79299.9_HL_4PMI_006_C53_G58CUUCGGtrue100000.00
HL_79299.9_Instance_17 HL_79299.9_HL_6QN3_001_C9_G14CUUCGG
HL_79299.9_Sequence_17 HL_79299.9_HL_6QN3_001_C9_G14CUUCGGtrue100000.00
HL_79299.9_Instance_18 HL_79299.9_HL_4LFB_009_C342_G347CUACGG
HL_79299.9_Sequence_18 HL_79299.9_HL_4LFB_009_C342_G347CUACGGtrue83001.71
HL_79299.9_Instance_19 HL_79299.9_HL_2HW8_001_C15_G20CUUCGG
HL_79299.9_Sequence_19 HL_79299.9_HL_2HW8_001_C15_G20CUUCGGtrue100000.00
HL_79299.9_Instance_20 HL_79299.9_HL_6SY6_001_C19_G24CUUCGG
HL_79299.9_Sequence_20 HL_79299.9_HL_6SY6_001_C19_G24CUUCGGtrue100000.00
HL_79299.9_Instance_21 HL_79299.9_HL_1UN6_003_C15_G64CUACGG
HL_79299.9_Sequence_21 HL_79299.9_HL_1UN6_003_C15_G64CUACGGtrue83001.71
HL_79299.9_Instance_22 HL_79299.9_HL_6QN3_003_C9_G14CUUCGG
HL_79299.9_Sequence_22 HL_79299.9_HL_6QN3_003_C9_G14CUUCGGtrue100000.00
HL_79299.9_Instance_23 HL_79299.9_HL_4LFB_031_C1449_G1454CUACGG
HL_79299.9_Sequence_23 HL_79299.9_HL_4LFB_031_C_1449_G_1454CUACGGtrue83001.71
HL_79299.9_Instance_24 HL_79299.9_HL_4V88_196_C414_G419CCAAGG
HL_79299.9_Sequence_24 HL_79299.9_HL_4V88_196_C414_G419CCAAGGtrue25007.60
HL_79299.9_Instance_25 HL_79299.9_HL_5J7L_030_C1449_G1454CUUCGG
HL_79299.9_Sequence_25 HL_79299.9_HL_5J7L_030_C_1449_G_1454CUUCGGtrue100000.00
HL_79299.9_Instance_26 HL_79299.9_HL_4AY2_001_C8_G13CUUCGG
HL_79299.9_Sequence_26 HL_79299.9_HL_4AY2_001_C8_G13CUUCGGtrue100000.00
HL_79299.9_Instance_27 HL_79299.9_HL_6CZR_080_C338_G343CUACGG
HL_79299.9_Sequence_27 HL_79299.9_HL_6CZR_080_C338_G343CUACGGtrue83001.71
HL_79299.9_Instance_28 HL_79299.9_HL_3U4M_001_C2143_G2148CUCCGG
HL_79299.9_Sequence_28 HL_79299.9_HL_3U4M_001_C_2143_G_2148CUCCGGtrue78002.22
HL_79299.9_Instance_29 HL_79299.9_HL_7A0S_042_C1708_G1713CUUCGG
HL_79299.9_Sequence_29 HL_79299.9_HL_7A0S_042_C_1708_G_1713CUUCGGtrue100000.00
HL_79299.9_Instance_30 HL_79299.9_HL_1KUQ_001_C8_G13CUUCGG
HL_79299.9_Sequence_30 HL_79299.9_HL_1KUQ_001_C8_G13CUUCGGtrue100000.00
HL_79299.9_Instance_31 HL_79299.9_HL_1I6U_001_C16_G21CUUCGG
HL_79299.9_Sequence_31 HL_79299.9_HL_1I6U_001_C16_G21CUUCGGtrue100000.00
HL_79299.9_Instance_32 HL_79299.9_HL_5J7L_009_C342_G347CUACGG
HL_79299.9_Sequence_32 HL_79299.9_HL_5J7L_009_C342_G347CUACGGtrue83001.71
HL_79299.9_Instance_33 HL_79299.9_HL_4WF9_040_C1735_G1740CUUCGG
HL_79299.9_Sequence_33 HL_79299.9_HL_4WF9_040_C_1735_G_1740CUUCGGtrue100000.00
HL_79299.9_Instance_34 HL_79299.9_HL_5TBW_043_C1923_G1928CUUCGG
HL_79299.9_Sequence_34 HL_79299.9_HL_5TBW_043_C_1923_G_1928CUUCGGtrue100000.00
HL_79299.9_Instance_35 HL_79299.9_HL_1NBS_006_C152_G157CUUCGG
HL_79299.9_Sequence_35 HL_79299.9_HL_1NBS_006_C152_G157CUUCGGtrue100000.00
HL_79299.9_Instance_36 HL_79299.9_HL_5ML7_002_C2187_G2192CGCUAG
HL_79299.9_Sequence_36 HL_79299.9_HL_5ML7_002_C_2187_G_2192CGCUAGtrue30007.03
HL_79299.9_Instance_37 HL_79299.9_HL_5J7L_171_C1533_G1538CUACGG
HL_79299.9_Sequence_37 HL_79299.9_HL_5J7L_171_C_1533_G_1538CUACGGtrue83001.71
HL_79299.9_Instance_38 HL_79299.9_HL_6DLR_002_A61_U66AUUCGU
HL_79299.9_Sequence_38 HL_79299.9_HL_6DLR_002_A61_U66AUUCGUtrue89001.12
HL_79299.9_Instance_39 HL_79299.9_HL_3IGI_008_G338_C343GUUCGC
HL_79299.9_Sequence_39 HL_79299.9_HL_3IGI_008_G338_C343GUUCGCtrue90001.06
HL_79299.9_Instance_40 HL_79299.9_HL_6CZR_082_C415_G420CUUCGG
HL_79299.9_Sequence_40 HL_79299.9_HL_6CZR_082_C415_G420CUUCGGtrue100000.00
HL_79299.9_Instance_41 HL_79299.9_HL_5J7L_005_C207_G212CUUCGG
HL_79299.9_Sequence_41 HL_79299.9_HL_5J7L_005_C207_G212CUUCGGtrue100000.00
HL_79299.9_Instance_42 HL_79299.9_HL_3V7E_002_C65_G70CUUCGG
HL_79299.9_Sequence_42 HL_79299.9_HL_3V7E_002_C65_G70CUUCGGtrue100000.00
HL_79299.9_Instance_43 HL_79299.9_HL_4U7U_001_C51_G56CGCCAG
HL_79299.9_Sequence_43 HL_79299.9_HL_4U7U_001_C51_G56CGCCAGtrue54004.70
HL_79299.9_Instance_44 HL_79299.9_HL_2NUE_001_C21_G26CGCAAG
HL_79299.9_Sequence_44 HL_79299.9_HL_2NUE_001_C21_G26CGCAAGtrue25007.62
HL_79299.9_Instance_45 HL_79299.9_HL_6JQ6_004_C45_G50CUUCGG
HL_79299.9_Sequence_45 HL_79299.9_HL_6JQ6_004_C45_G50CUUCGGtrue100000.00
HL_79299.9_Instance_46 HL_79299.9_HL_6JQ6_002_C45_G50CUUCGG
HL_79299.9_Sequence_46 HL_79299.9_HL_6JQ6_002_C45_G50CUUCGGtrue100000.00
HL_79299.9_Instance_47 HL_79299.9_HL_6CK5_001_A27_U32AUUUGU
HL_79299.9_Sequence_47 HL_79299.9_HL_6CK5_001_A27_U32AUUUGUtrue66003.45
HL_79299.9_Instance_48 HL_79299.9_HL_1P6V_001_C26_G31CUUCGG
HL_79299.9_Sequence_48 HL_79299.9_HL_1P6V_001_C26_G31CUUCGGtrue100000.00
HL_79299.9_Instance_49 HL_79299.9_HL_5J7L_200_C2795_G2801CUUUAAG
HL_79299.9_Sequence_49 HL_79299.9_HL_5J7L_200_C_2795_G_2801CUUUAAGtrue5009.59
HL_79299.9_Instance_50 HL_79299.9_HL_6DME_002_C57_G62CUUCGG
HL_79299.9_Sequence_50 HL_79299.9_HL_6DME_002_C57_G62CUUCGGtrue100000.00
HL_79299.9_Instance_51 HL_79299.9_HL_4Y4O_111_G271I_C271OGCUUGUC
HL_79299.9_Sequence_51 HL_79299.9_HL_4Y4O_111_G_271I_C_271OGCUUGUCtrue-40010.54
HL_79299.9_Instance_52 HL_79299.9_HL_2CZJ_007_G25_C30GUUCGC
HL_79299.9_Sequence_52 HL_79299.9_HL_2CZJ_007_G25_C30GUUCGCtrue90001.06

Conserved interactions between motif group positions in HL_79299.9:
1 2 s35 
1 5 cWW 
2 3 s35 
2 4 tSW 
2 5 s55 
3 4 s53 
4 5 s55 
JAR3D SCFG/MRF model for HL_79299.9:
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 C28 - G33 from junction 
BasepairNode | Deletion Probability [0.0000200614746445] | Pair Probability [[0.006400631,0.011725369,0.007334658,0.146791473,0.000000000],[0.013412271,0.006507835,0.448831520,0.009146058,0.000000000],[0.007404072,0.156071103,0.001401062,0.016642554,0.000000000],[0.134888076,0.008877364,0.017739748,0.006826206,0.000000000],[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 [0.960570113,0.039344916,0.000083123,0.000001847] | Right Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair C28 - G33 cWW 
BasepairNode | Deletion Probability [0.0000001236064579] | Pair Probability [[0.021859428,0.020602182,0.002599796,0.114316387,0.000000000],[0.022423262,0.011513474,0.028467930,0.017499452,0.000000000],[0.046688647,0.004562412,0.002599796,0.012071054,0.000000000],[0.025636978,0.012048993,0.554616470,0.102493738,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.000959647,0.998032724,0.000959647,0.000047982] | Left Letter Distribution [0.138888889,0.083333333,0.009259259,0.768518519,0.000000000] | 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 [4] // Basepair U29 - G32 tSW 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node C31:C31
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.046296296,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.861111111,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.009259259,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C31
Sequences of instances from HL_79299.9:
> HL_79299.9 HL_5Y85_004 C   28 G   33
CUUCGG
> HL_79299.9 HL_5D5L_003 C   60 G   65
CUUCGG
> HL_79299.9 HL_5J7L_011 C  419 G  424
CUUCGG
> HL_79299.9 HL_5LYS_002 C   48 G   60
CUUCGG
> HL_79299.9 HL_4Y4O_144 C 1691 G 1696
CUUCGG
> HL_79299.9 HL_4JF2_003 C   60 G   65
CUUCGG
> HL_79299.9 HL_4LFB_011 C  419 G  424
CUUCGG
> HL_79299.9 HL_5J7L_175 C 1691 G 1696
CUUCGG
> HL_79299.9 HL_4V9F_044 C 1769 G 1774
CUUCGG
> HL_79299.9 HL_4PDB_001 C   17 G   22
CUUCGG
> HL_79299.9 HL_4PMI_005 C   53 G   58
CUUCGG
> HL_79299.9 HL_4PMI_003 C   53 G   58
CUUCGG
> HL_79299.9 HL_4PMI_001 C   53 G   58
CUUCGG
> HL_79299.9 HL_4PMI_004 C   53 G   58
CUUCGG
> HL_79299.9 HL_4PMI_002 C   53 G   58
CUUCGG
> HL_79299.9 HL_4PMI_006 C   53 G   58
CUUCGG
> HL_79299.9 HL_6QN3_001 C    9 G   14
CUUCGG
> HL_79299.9 HL_4LFB_009 C  342 G  347
CUACGG
> HL_79299.9 HL_2HW8_001 C   15 G   20
CUUCGG
> HL_79299.9 HL_6SY6_001 C   19 G   24
CUUCGG
> HL_79299.9 HL_1UN6_003 C   15 G   64
CUACGG
> HL_79299.9 HL_6QN3_003 C    9 G   14
CUUCGG
> HL_79299.9 HL_4LFB_031 C 1449 G 1454
CUACGG
> HL_79299.9 HL_4V88_196 C  414 G  419
CCAAGG
> HL_79299.9 HL_5J7L_030 C 1449 G 1454
CUUCGG
> HL_79299.9 HL_4AY2_001 C    8 G   13
CUUCGG
> HL_79299.9 HL_6CZR_080 C  338 G  343
CUACGG
> HL_79299.9 HL_3U4M_001 C 2143 G 2148
CUCCGG
> HL_79299.9 HL_7A0S_042 C 1708 G 1713
CUUCGG
> HL_79299.9 HL_1KUQ_001 C    8 G   13
CUUCGG
> HL_79299.9 HL_1I6U_001 C   16 G   21
CUUCGG
> HL_79299.9 HL_5J7L_009 C  342 G  347
CUACGG
> HL_79299.9 HL_4WF9_040 C 1735 G 1740
CUUCGG
> HL_79299.9 HL_5TBW_043 C 1923 G 1928
CUUCGG
> HL_79299.9 HL_1NBS_006 C  152 G  157
CUUCGG
> HL_79299.9 HL_5ML7_002 C 2187 G 2192
CGCUAG
> HL_79299.9 HL_5J7L_171 C 1533 G 1538
CUACGG
> HL_79299.9 HL_6DLR_002 A   61 U   66
AUUCGU
> HL_79299.9 HL_3IGI_008 G  338 C  343
GUUCGC
> HL_79299.9 HL_6CZR_082 C  415 G  420
CUUCGG
> HL_79299.9 HL_5J7L_005 C  207 G  212
CUUCGG
> HL_79299.9 HL_3V7E_002 C   65 G   70
CUUCGG
> HL_79299.9 HL_4U7U_001 C   51 G   56
CGCCAG
> HL_79299.9 HL_2NUE_001 C   21 G   26
CGCAAG
> HL_79299.9 HL_6JQ6_004 C   45 G   50
CUUCGG
> HL_79299.9 HL_6JQ6_002 C   45 G   50
CUUCGG
> HL_79299.9 HL_6CK5_001 A   27 U   32
AUUUGU
> HL_79299.9 HL_1P6V_001 C   26 G   31
CUUCGG
> HL_79299.9 HL_5J7L_200 C 2795 G 2801
CUUUAAG
> HL_79299.9 HL_6DME_002 C   57 G   62
CUUCGG
> HL_79299.9 HL_4Y4O_111 G 271I C 271O
GCUUGUC
> HL_79299.9 HL_2CZJ_007 G   25 C   30
GUUCGC