Alignment of HL_46142.7 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
3

3
7
3
I

8
3

4
9
3
I

10
3

5
11
3
I

12
3

6
13
3
I

14
3

7
15
2
I

16
2

8
17
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_46142.7_Instance_1 HL_46142.7_HL_4FRN_006_U44_A51UUACUUGA
HL_46142.7_Sequence_1 HL_46142.7_HL_4FRN_006_U44_A51UUACUUGAtrue78002.05
HL_46142.7_Instance_2 HL_46142.7_HL_6R47_001_G6_C13GUUCGGGC
HL_46142.7_Sequence_2 HL_46142.7_HL_6R47_001_G6_C13GUUCGGGCtrue86001.37
HL_46142.7_Instance_3 HL_46142.7_HL_5K7D_001_G5_C12GUUAGGGC
HL_46142.7_Sequence_3 HL_46142.7_HL_5K7D_001_G5_C12GUUAGGGCtrue95000.52
HL_46142.7_Instance_4 HL_46142.7_HL_6UFJ_003_G5_C12GUUUGAGC
HL_46142.7_Sequence_4 HL_46142.7_HL_6UFJ_003_G5_C12GUUUGAGCtrue75002.38
HL_46142.7_Instance_5 HL_46142.7_HL_2JLT_002_C5_G12CCUGGGAG
HL_46142.7_Sequence_5 HL_46142.7_HL_2JLT_002_C5_G12CCUGGGAGtrue64003.46
HL_46142.7_Instance_6 HL_46142.7_HL_7A0S_055_C2303_G2310CGCAAAGG
HL_46142.7_Sequence_6 HL_46142.7_HL_7A0S_055_C_2303_G_2310CGCAAAGGtrue92000.76
HL_46142.7_Instance_7 HL_46142.7_HL_4Y4O_159_C2324_G2331CGCAAGGG
HL_46142.7_Sequence_7 HL_46142.7_HL_4Y4O_159_C_2324_G_2331CGCAAGGGtrue100000.00
HL_46142.7_Instance_8 HL_46142.7_HL_5TBW_057_C2693_G2700CAAAAGGG
HL_46142.7_Sequence_8 HL_46142.7_HL_5TBW_057_C_2693_G_2700CAAAAGGGtrue92000.78
HL_46142.7_Instance_9 HL_46142.7_HL_5TBW_060_C2776_G2784CGGAAUUUG
HL_46142.7_Sequence_9 HL_46142.7_HL_5TBW_060_C_2776_G_2784CGGAAUUUGtrue52004.59
HL_46142.7_Instance_10 HL_46142.7_HL_4V9F_014_G416_C424GGCAUCGAC
HL_46142.7_Sequence_10 HL_46142.7_HL_4V9F_014_G416_C424GGCAUCGACtrue39005.81
HL_46142.7_Instance_11 HL_46142.7_HL_3SKI_002_G53_C60GACCCCGC
HL_46142.7_Sequence_11 HL_46142.7_HL_3SKI_002_G53_C60GACCCCGCtrue77002.23
HL_46142.7_Instance_12 HL_46142.7_HL_4WF9_052_U2351_G2358UGUAAAGG
HL_46142.7_Sequence_12 HL_46142.7_HL_4WF9_052_U_2351_G_2358UGUAAAGGtrue83001.59
HL_46142.7_Instance_13 HL_46142.7_HL_3G9C_007_G71_C79GUUCAUCAC
HL_46142.7_Sequence_13 HL_46142.7_HL_3G9C_007_G71_C79GUUCAUCACtrue61003.68
HL_46142.7_Instance_14 HL_46142.7_HL_4V9F_061_G2442_C2450GCUUGAUGC
HL_46142.7_Sequence_14 HL_46142.7_HL_4V9F_061_G_2442_C_2450GCUUGAUGCtrue52004.56
HL_46142.7_Instance_15 HL_46142.7_HL_5J7L_189_U2324_G2331UGCAAUGG
HL_46142.7_Sequence_15 HL_46142.7_HL_5J7L_189_U_2324_G_2331UGCAAUGGtrue91000.87
HL_46142.7_Instance_16 HL_46142.7_HL_3SKL_005_G52_C59GACCCCGC
HL_46142.7_Sequence_16 HL_46142.7_HL_3SKL_005_G52_C59GACCCCGCtrue77002.23
HL_46142.7_Instance_17 HL_46142.7_HL_4V9F_058_U2358_G2365UGCAAGAG
HL_46142.7_Sequence_17 HL_46142.7_HL_4V9F_058_U_2358_G_2365UGCAAGAGtrue83001.58
HL_46142.7_Instance_18 HL_46142.7_HL_6N5P_003_U76_G84UACCUUCUG
HL_46142.7_Sequence_18 HL_46142.7_HL_6N5P_003_U76_G84UACCUUCUGtrue25007.08
HL_46142.7_Instance_19 HL_46142.7_HL_5TBW_009_G303_C312GGUAAAUUCC
HL_46142.7_Sequence_19 HL_46142.7_HL_5TBW_009_G303_C312GGUAAAUUCCtrue27006.96
HL_46142.7_Instance_20 HL_46142.7_HL_4ENC_001_G5_C14GAUGAGGCCC
HL_46142.7_Sequence_20 HL_46142.7_HL_4ENC_001_G5_C14GAUGAGGCCCtrue17007.89

Conserved interactions between motif group positions in HL_46142.7:
1 8 cWW 
2 3 s35 
3 4 s35 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
JAR3D SCFG/MRF model for HL_46142.7:
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 [8] // Initial node U44 - A51 from junction 
BasepairNode | Deletion Probability [0.0000022482900247] | Pair Probability [[0.008459146,0.015372483,0.009888841,0.142484388,0.000000000],[0.063943524,0.011289994,0.187932192,0.011771422,0.000000000],[0.009916647,0.229856576,0.001980943,0.019835530,0.000000000],[0.158930846,0.011619557,0.107462627,0.009255284,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.648355755,0.250996512,0.100355007,0.000280269,0.000012456] | Left Letter Distribution [0.227272727,0.136363636,0.318181818,0.318181818,0.000000000] | 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 [8] // Basepair U44 - A51 cWW 
HairpinNode  | Num Bases [6] | Left Index [2] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node U45:G50
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.204545455,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.159090909,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.340909091,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.295454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U45
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.295454545,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.386363636,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.022727273,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.295454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A46
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.477272727,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.204545455,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.159090909,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.159090909,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C47
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.340909091,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.159090909,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U48
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.159090909,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.340909091,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U49
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.204545455,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.113636364,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.568181818,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.113636364,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G50
Sequences of instances from HL_46142.7:
> HL_46142.7 HL_4FRN_006 U   44 A   51
UUACUUGA
> HL_46142.7 HL_6R47_001 G    6 C   13
GUUCGGGC
> HL_46142.7 HL_5K7D_001 G    5 C   12
GUUAGGGC
> HL_46142.7 HL_6UFJ_003 G    5 C   12
GUUUGAGC
> HL_46142.7 HL_2JLT_002 C    5 G   12
CCUGGGAG
> HL_46142.7 HL_7A0S_055 C 2303 G 2310
CGCAAAGG
> HL_46142.7 HL_4Y4O_159 C 2324 G 2331
CGCAAGGG
> HL_46142.7 HL_5TBW_057 C 2693 G 2700
CAAAAGGG
> HL_46142.7 HL_5TBW_060 C 2776 G 2784
CGGAAUUUG
> HL_46142.7 HL_4V9F_014 G  416 C  424
GGCAUCGAC
> HL_46142.7 HL_3SKI_002 G   53 C   60
GACCCCGC
> HL_46142.7 HL_4WF9_052 U 2351 G 2358
UGUAAAGG
> HL_46142.7 HL_3G9C_007 G   71 C   79
GUUCAUCAC
> HL_46142.7 HL_4V9F_061 G 2442 C 2450
GCUUGAUGC
> HL_46142.7 HL_5J7L_189 U 2324 G 2331
UGCAAUGG
> HL_46142.7 HL_3SKL_005 G   52 C   59
GACCCCGC
> HL_46142.7 HL_4V9F_058 U 2358 G 2365
UGCAAGAG
> HL_46142.7 HL_6N5P_003 U   76 G   84
UACCUUCUG
> HL_46142.7 HL_5TBW_009 G  303 C  312
GGUAAAUUCC
> HL_46142.7 HL_4ENC_001 G    5 C   14
GAUGAGGCCC